############################################################################### # # # Trilinos Release 17.2.1 Release Notes August 28, 2026 # # # ############################################################################### This is a patch release with no new features. Amesos2: - Fix compilation issues in Basker https://github.com/trilinos/Trilinos/pull/15628 Tpetra: - Add a missing header. https://github.com/trilinos/Trilinos/pull/15618 Krino: - Latest snapshot https://github.com/trilinos/Trilinos/pull/15526 Piro: - Fix a compile error https://github.com/trilinos/Trilinos/pull/15637 ############################################################################### # # # Trilinos Release 17.2 Release Notes August 19, 2026 # # # ############################################################################### The test results from Trilinos testing (PRs and nightly builds) are now posted to a public CDash dashboard: https://my.cdash.org/index.php?project=Trilinos Amesos2: - new "partial-factorization" option (to improve performance of computing local Schur complement) with PardisoMKL & MUMPS https://github.com/trilinos/Trilinos/pull/15404 https://github.com/trilinos/Trilinos/pull/15484 Belos: - Solvers now provide more more detailed solve status reporting. The "Unconverged" return type has been split into "MaxItersReached", "MaxRestartsReached". "OrthonormFailure", "NaNDetected", "BreakdownDetected", "LossOfAccuracyDetected", "NonspecificException", "InconsistentState", "Undetermined". https://github.com/trilinos/Trilinos/pull/15231 Galeri: - Added the creation of finite element mass matrices for use in testing. https://github.com/trilinos/Trilinos/pull/15318 Kokkos, KokkosKernels: - Inclusion of version 5.2.1 of Kokkos and Kokkos Kernels https://github.com/trilinos/Trilinos/pull/15453 https://github.com/trilinos/Trilinos/pull/15593 https://github.com/kokkos/kokkos/blob/develop/CHANGELOG.md https://github.com/kokkos/kokkos-kernels/blob/develop/CHANGELOG.md Ifpack2: - Cache local CRS structure in par_ILUT to improve setup related costs https://github.com/trilinos/Trilinos/pull/15439 - Use KSPTRSV as default triangular solver on GPU platforms https://github.com/trilinos/Trilinos/pull/15490 Intrepid2: - Redesigned PointInclusion tools to expose parametric distance and extended CellTools to support beam and shell elements, including mappings from (D+1)-dimensional physical space to D-dimensional reference space. https://github.com/trilinos/Trilinos/pull/15269 - Refactored Intrepid2 operators to improve performance by introducing an orientation operator that stores subcell orientation matrices in compressed-row storage format. https://github.com/trilinos/Trilinos/pull/14450 - Improved the parallel implementation of Basis::getValues. https://github.com/trilinos/Trilinos/pull/15234 Krino: - Snapshot https://github.com/trilinos/Trilinos/pull/15526 Minitensor: - New capability: quaternions and conversions among rotation representations (rotation matrix, unit quaternion, principal rotation vector), using a singularity-free Spurrier extraction, along with a helper that keeps a rotation vector continuous across the 2 pi boundary and the axial vector operator vee(). Also new are exp_sym() and exp_eig_sym(), the eigendecomposition exponential of a symmetric tensor, mirroring the existing log_sym() and log_eig_sym(). https://github.com/trilinos/Trilinos/pull/15532 https://github.com/trilinos/Trilinos/pull/15514 - The general log() and exp() now follow the current published algorithms. For dimensions three and lower, log() uses Gauss-Legendre partial-fraction Pade evaluation inside the Pade trust region and Schur-based inverse scaling and squaring (Al-Mohy and Higham, SIAM J. Sci. Comput. 34(4), 2012) outside it, and exp() uses the parameter selection of Al-Mohy and Higham, SIAM J. Matrix Anal. Appl. 31(3), 2009. Measured against an 80-bit eigendecomposition reference, log() is 1.8 to 4.3 times more accurate and 1.4 to 4.7 times faster away from the identity, with no failures in 17,500 samples. https://github.com/trilinos/Trilinos/pull/15515 - Correctness and robustness fixes. log() no longer aborts in debug builds or writes out of bounds in release builds on ill-conditioned symmetric positive definite tensors, where a catastrophically cancelling determinant produced a non-finite scaling factor: 39 percent of random SPD tensors at condition 1e14 used to fail, none do now. eig_sym() returns a consistent (V, D) pair in two dimensions, the 2x2 singular value decomposition canonicalizes its singular values, operations that require symmetric positive definite input now fail loudly instead of returning garbage, and the 2x2 eigenvalue and square root scaling is safe for Sacado FAD scalars, which repaired downstream code that instantiates log() on a tensor of FAD scalars. https://github.com/trilinos/Trilinos/pull/15513 https://github.com/trilinos/Trilinos/pull/15393 https://github.com/trilinos/Trilinos/pull/15397 https://github.com/trilinos/Trilinos/pull/15398 https://github.com/trilinos/Trilinos/pull/15520 - The headers were reorganized, with no change in functionality. The .i.h and .t.h sub-headers were merged into their parents. The TeuchosCore and KokkosKernels dependencies were dropped. Code that includes MiniTensor.h is unaffected. https://github.com/trilinos/Trilinos/pull/15523 https://github.com/trilinos/Trilinos/pull/15527 https://github.com/trilinos/Trilinos/pull/15529 - The package is now documented. https://trilinos.github.io/docs/minitensor/index.html https://github.com/trilinos/Trilinos/pull/15531 https://github.com/trilinos/Trilinos/pull/15533 - The tests were split by module, property-based tests were added for the matrix decompositions, and every public header is now compiled on its own so that it stays self-contained. https://github.com/trilinos/Trilinos/pull/15395 https://github.com/trilinos/Trilinos/pull/15534 MueLu: - Improve support for Teko-based smoothers via specifying `smoother: type = teko` https://github.com/trilinos/Trilinos/pull/15238 - Add a new stength-of-connection matrix that leverages an approximate inverse of a mass matrix. https://github.com/trilinos/Trilinos/pull/15239 Panzer: - Large update to the documenation https://github.com/trilinos/Trilinos/pull/15503 STK: - Inclusion of version 5.31.3 https://github.com/trilinos/Trilinos/pull/15427 https://github.com/trilinos/Trilinos/pull/15530 https://github.com/trilinos/Trilinos/blob/8aec0c9da36965e5b369dbc77ff97341f90b410b/packages/stk/CHANGELOG.md?plain=1#L3-L41 Tempus: - The tutorial pages and documentation have been updated and extended. https://github.com/trilinos/Trilinos/pull/15365 https://github.com/trilinos/Trilinos/pull/15387 https://github.com/trilinos/Trilinos/pull/15423 Teko: - Port ProbingPreconditionerFactory to Tpetra https://github.com/trilinos/Trilinos/pull/15386 - Port majority of tests/examples to Tpetra Zoltan2: - Provide option to opt-out of potentially expensive symmetrization in metis algorithm https://github.com/trilinos/Trilinos/pull/15496 ############################################################################### # # # Trilinos Release 17.1.2 Release Notes August 13, 2026 # # # ############################################################################### This is a patch release with no new features. Krino: - Remove an unneeded package dependency. https://github.com/trilinos/Trilinos/pull/15360 Tpetra: - Revert a change in setUnion that could result in incorrect results for matrix-matrix multiplication. https://github.com/trilinos/Trilinos/pull/15313 - Bug fix to ETI for FixedHashTable https://github.com/trilinos/Trilinos/pull/15407 Teuchos: - Fix a compilation issue with C++23 https://github.com/trilinos/Trilinos/pull/15304 ############################################################################### # # # Trilinos Release 16.2.2 Release Notes August 13, 2026 # # # ############################################################################### This is a patch release with no new features. Teuchos: - Fix a compilation issue with C++23 https://github.com/trilinos/Trilinos/pull/15304 ############################################################################### # # # Trilinos Release 17.1 Release Notes May 12, 2026 # # # ############################################################################### Compadre: - Inclusion of version 1.7.0 https://github.com/trilinos/Trilinos/pull/15023 Ifpack2: - Added runtime debug control via the IFPACK2_DEBUG environment variable. https://github.com/trilinos/Trilinos/pull/15166 - Fixed missing parILUT max-iteration setup. https://github.com/trilinos/Trilinos/pull/15094 - Add optional row/column 1-norm equilibration of the inner subdomain matrix in additive Schwarz https://github.com/trilinos/Trilinos/pull/15241 Kokkos, KokkosKernels: - Inclusion of version 5.1.1 of Kokkos and Kokkos Kernels https://github.com/trilinos/Trilinos/pull/15035 https://github.com/trilinos/Trilinos/pull/15198 MueLu: - Energy minimization multigrid has been completely refactored. The algorithm now runs on device and uses Belos to solve the optimization problem. https://github.com/trilinos/Trilinos/pull/14989 - An energy minimization preconditioner for Maxwell problems has been added. https://github.com/trilinos/Trilinos/pull/15215 https://github.com/trilinos/Trilinos/pull/15216 https://github.com/trilinos/Trilinos/pull/15218 - Fixed several correctness issues in MultiPhys, Hierarchy setup, and TekoSmoother application. https://github.com/trilinos/Trilinos/pull/15028 https://github.com/trilinos/Trilinos/pull/15082 https://github.com/trilinos/Trilinos/pull/15173 https://github.com/trilinos/Trilinos/pull/15178 Rapid Optimization Library (ROL): - Multi-objective optimization methods, including the sampling of the Pareto frontier using convex combinations of objective functions as well as the normal boundary intersection method. - Interface for robust optimal experimental design (OED) which can account for uncertainty in parameter estimates as well as randomly failing experiments. - Improved OED interface that enables OED for vector valued estimation problems. - Implementation of greedy OED that leverages fast numerical linear algebra and that can be used for solution verification and producing initial guesses for optimization. - New methods for nonsmooth optimization represented as Type-P "proximable" problems, where the objective function is a sum of a smooth nonlinear nonconvex function and a nonsmooth convex function. ShyLU: - Performance improvements in Tacho https://github.com/trilinos/Trilinos/pull/15120 Tpetra: - The computation of global constants in Map construction is now optional. This allows skipping global reductions. https://github.com/trilinos/Trilinos/pull/15093 - Ongoing effort to move more map and import/export computations to device. https://github.com/trilinos/Trilinos/pull/14902 https://github.com/trilinos/Trilinos/pull/14908 - Added matrix-matrix product support for preserving explicit zeros in the sparsity pattern when requested. https://github.com/trilinos/Trilinos/pull/15019 ############################################################################### # # # Trilinos Release 16.2.1 Release Notes May 12, 2026 # # # ############################################################################### This is a patch release with no new features. Kokkos, KokkosKernels: - Inclusion of version 4.7.4 of Kokkos and Kokkos Kernels https://github.com/trilinos/Trilinos/pull/15142 Amesos2, Belos, Panzer, STK, Stokhos, Stratimikos, TrilinosCouplings, Tpetra, Gtest: - Bug fixes. See https://github.com/trilinos/Trilinos/issues/14866 for more details. ############################################################################### # # # Trilinos Release 17.0 Release Notes February 5, 2026 # # # ############################################################################### The following previously deprecated packages have been removed: Amesos AztecOO Epetra EpetraExt Ifpack Intrepid Isorropia ML NewPackage Pliris PyTrilinos ShyLU_DDCore ThyraEpetraAdapters ThyraEpetraExtAdapters Triutils The source code for the archived packages can be found in separate repositories under the Trilinos organization on Github: https://github.com/trilinos Non-deprecated packages that had Epetra capabilities (e.g. Amesos2 or MueLu) have started to remove Epetra support code. Trilinos now requires a C++20 compatible compiler. https://github.com/trilinos/Trilinos/pull/14390 Trilinos now requires CMake 3.27 or newer. Kokkos, KokkosKernels: - Inclusion of version 5.0.2 of Kokkos and Kokkos Kernels https://github.com/trilinos/Trilinos/pull/14840 https://github.com/trilinos/Trilinos/pull/14916 Tpetra, Ifpack2, MueLu, Stokhos: - Previously deprecated code has beeen removed. https://github.com/trilinos/Trilinos/pull/14587 Gtest: - The in-source Gtest package has been removed. Trilinos packages that rely on Gtest instead use the gtest TPL. https://github.com/trilinos/Trilinos/pull/14719 ############################################################################### # # # Trilinos Release 16.2 Release Notes November 24, 2025 # # # ############################################################################### Belos: - Added LSQR example https://github.com/trilinos/Trilinos/pull/14486 Compadre - Update from version 1.5.9 to 1.6.4 https://github.com/sandialabs/compadre/wiki/Changelog Framework: - Shadow warnings have been promoted to errors. - Trilinos now uses pre-commit to run clang-format and cmake-format. https://github.com/trilinos/Trilinos/pull/14478 - Built-in TPL detection improvements to help ensure simpler out-of-the-box configurations on different Linux distributions. - New compiler/MPI support via GitHub Actions CI: gcc@14 gcc@10.4.0+openmpi@4.1.6 cuda@12.4.1+gcc@10.4.0+openmpi@4.1.6 oneapi@2024.2+gcc@11.4 clang@19.1+openmpi@4.1.6 - Removed support for some older compilers: gcc@8.3.0 gcc@10.3.0 clang@11.0.1 oneapi@2024.1 Galeri: - The assembly of example problems was rewritten with Kokkos primitives. https://github.com/trilinos/Trilinos/pull/14120 - Added recirculant example https://github.com/trilinos/Trilinos/pull/14028 Ifpack2: - Improve Chebyshev performance on GPU https://github.com/trilinos/Trilinos/pull/14124 - Added heuristic to Chebyshev to select performant kernel based on architecture https://github.com/trilinos/Trilinos/pull/14154 - Add support for streams in RBILUK https://github.com/trilinos/Trilinos/pull/14127 - Use empirical models for choosing the number of sublines in block tridi (with Schur line splitting). https://github.com/trilinos/Trilinos/pull/14246 MueLu - New parameters for dropping algorithms were introduced that better map to the growing number of available schemes. Old parameters are still valid but will eventually be phased out. https://github.com/trilinos/Trilinos/pull/14113 https://github.com/trilinos/Trilinos/pull/14093 - The MueLu tutorial has been modernized and is now available at https://muelu.github.io/ https://github.com/trilinos/Trilinos/pull/14357 - A new distributed lumping scheme https://github.com/trilinos/Trilinos/pull/14351 - New "combined" max levels option for problems with multiple hierarchies (due to subblocks) https://github.com/trilinos/Trilinos/pull/14387 - New Stratimikos example for demonstrating how to assemble matrix https://github.com/trilinos/Trilinos/pull/14339 - New hands-on material for ATPESC 2025 https://github.com/trilinos/Trilinos/pull/14461 - Clean up of timer usage in MueLu, make timer fencing a configurable option https://github.com/trilinos/Trilinos/pull/14253 - MueLu scaling driver can rebalance initial user matrix github.com/trilinos/Trilinos/pull/14690 github.com/trilinos/Trilinos/pull/14698 NOX - Nox wrappers for Tpetra MultiVector https://github.com/trilinos/Trilinos/pull/14252 Panzer - Caching of connectivity information https://github.com/trilinos/Trilinos/pull/14042 ROL - ROL is now gets snapshotted from https://github.com/sandialabs/rol into Trilinos. ShyLU: - ShyLU-Basker: Threaded sparse-triangular solver https://github.com/trilinos/Trilinos/pull/14065 - Tacho: No-pivoted LDLt factorization https://github.com/trilinos/Trilinos/pull/14537 https://github.com/trilinos/Trilinos/pull/14640 - Tacho: Uniform symbolic factorization interfce to fall-back from Chol to LU or LDLt https://github.com/trilinos/Trilinos/pull/14603 SEACAS - Update to v2025-10-14. See: https://github.com/sandialabs/seacas/releases STK - See: https://github.com/trilinos/Trilinos/blob/master/packages/stk/CHANGELOG.md Teko: - The conversion between Teko blocked operators and Tpetra matrices has been significantly improved. https://github.com/trilinos/Trilinos/pull/14476 Teuchos - MPI communication routines are wrapped in Kokkos Profiling regions. https://github.com/trilinos/Trilinos/pull/14363 - The CommandLineProcessor can now be used to harvest information about the runtime environment by passing --print-system-info https://github.com/trilinos/Trilinos/pull/14494 Tpetra - The new "Ialltofewv" communication option obtains speedups for many-to-few communication. https://github.com/trilinos/Trilinos/pull/14146 - Tpetra can now leverage communication routines from MPI Advance. https://github.com/trilinos/Trilinos/pull/14169 - A reordering of steps during data transfer that should avoid unexpected messages can be used by setting the environment variable TPETRA_GRANULAR_TRANSFERS=ON. https://github.com/trilinos/Trilinos/pull/13947 - The Tpetra assembly examples were updated to better showcase current Kokkos practices. https://github.com/trilinos/Trilinos/pull/14430 - Helper routines for the common use case of generating matrices by applying a filter to the entries of another matrix. https://github.com/trilinos/Trilinos/pull/14583 - Several Epetra matrix transforms have been transitioned to Tpetra - SingletonFiltering: condenses out singleton rows and columns. - SolverMap: checks for missing indices wrt the local rows. - Reindex: reindex based on row map. - Rebalance: rebalance the distribution of linear problem contents (matrix, lhs, and rhs) among MPI nodes. Thyra: - Solver/preconditioner routines can now directly be used with Tpetra objects without having to wrap them to Thyra. https://github.com/trilinos/Trilinos/pull/14459 Zoltan - Additional Hilbert Space filling curves https://github.com/trilinos/Trilinos/pull/13880 Zoltan2 - Reverse Cuthill-McKee can now symmetrize the input matrix. https://github.com/trilinos/Trilinos/pull/14584 ############################################################################### # # # Trilinos Release 16.1 Release Notes March 20, 2025 # # # ############################################################################### A large number of packages have been marked as deprecated in this release. We are planning to remove them in the fall of 2025. The list of packages is - Amesos - AztecOO - Epetra - EpetraExt - Ifpack - Intrepid - Isorropia - ML - NewPackage - Pliris - PyTrilinos - ShyLU_DDCore - ThyraEpetraAdapters - ThyraEpetraExtAdapters - Triutils If you are a user of one of these packages, please transition to the newer software stack. If you need guidance with finding an adequate replacement or are missing a particular feature, please open an issue or a discussion on Github. Belos - Improve caching of state vectors between subsequent solves. https://github.com/trilinos/Trilinos/pull/13751 - Use a pooling strategy for Tpetra MultiVectors. https://github.com/trilinos/Trilinos/pull/13469 Framework - Added option `Trilinos_WARNINGS_MODE` that can control warnings useful for development. There is a list of warnings in `cmake/WarningsErrorsPolicy.cmake` that can be applied as warnings or errors by passing the `WARN` or `ERROR` value for that variable. Turning either of those settings on will also turn on a set of 'promoted' warnings that will always be errors in any mode other than the default. The Pull Request testing will currently use the `WARN` setting for this mode, meaning that any 'upcoming' warnings will show up as warnings, and any 'promoted' warnings will show up as errors. You can also pass additional 'upcoming' warnings via the `Trilinos_ADDITIONAL_WARNINGS` option. Lastly, if either of these modes are enabled, all warnings are disabled for any deprecated packages, in the interest of not spending effort cleaning them. By default, no warnings or errors are added. https://github.com/trilinos/Trilinos/pull/13427 - Set all currently-clean GCC 10 warnings as 'promoted'. - MKL+SYCL support https://github.com/trilinos/Trilinos/pull/13520 Kokkos, Kokkos Kernels - Inclusion of version 4.5.1 of Kokkos and Kokkos Kernels https://github.com/trilinos/Trilinos/pull/13679 MueLu: - Refactor CoalesceDropFactory into smaller composable functors, making it easier to extend. https://github.com/trilinos/Trilinos/pull/13361 - Add a material-aware distance Laplacian aggregation strategy. https://github.com/trilinos/Trilinos/pull/13662 Panzer: - Add capability for transient optimization with ROL and Tempus https://github.com/trilinos/Trilinos/pull/13581 PyTrilinos2: - Thyra and Stratimikos are now exposed. This allows to use solvers from Amesos2, Belos, Ifpack2 and MueLu from Python. https://github.com/trilinos/Trilinos/pull/13690 ShyLU: - New solver features in Tacho https://github.com/trilinos/Trilinos/pull/13585 Stokhos: - Deprecate the PCE scalar type https://github.com/trilinos/Trilinos/pull/13459 ############################################################################### # # # Trilinos Release 16.0 Release Notes July 22, 2024 # # # ############################################################################### A large number of packages have been marked as deprecated in this release. We are planning to remove them in the fall of 2025. The list of packages is - Amesos - AztecOO - Epetra - EpetraExt - Ifpack - Intrepid - Isorropia - ML - NewPackage - Pliris - PyTrilinos - ShyLU_DDCore - ThyraEpetraAdapters - ThyraEpetraExtAdapters - Triutils If you are a user of one of these packages, please transition to the newer software stack. If you need guidance with finding an adequate replacement or are missing a particular feature, please open an issue or a discussion on Github. Amesos2 - Add interface to MKL cluster sparse solver. https://github.com/trilinos/Trilinos/pull/13073 Framework - Marked all deprecated packages as 'Secondary Tested'. - Reset default for `Trilinos_ENABLE_SECONDARY_TESTED_CODE` to `OFF`. This will cause the previously-mentioned deprecated packages to NOT be automatically enabled to help guide users away from them. The old behavior can be restored by setting the variable back to `ON`, but note that the recommended best practice is to explicitly enable packages that the user is depending on (e.g. if you depend on ThyraEpetraAdapters, enable that explicitly instead of Thyra and Epetra and allowing TriBITS to enable the adapters). - Added deprecation warnings to all deprecated packages. The warnings are able to be disabled via the `Trilinos_SHOW_DEPRECATED_WARNINGS` option (this is also available as a per-package option). These warnings are intended to notify users that package capability they are using will be removed in upcoming releases. https://github.com/trilinos/Trilinos/pull/12828 Ifpack2 - RBILUK now supports Kokkos Kernels as a backend https://github.com/trilinos/Trilinos/pull/12911 Kokkos, Kokkos Kernels - Inclusion of version 4.3.1 of Kokkos and Kokkos Kernels https://github.com/trilinos/Trilinos/pull/12995 NOX - Added preconditioner reuse across multiple nonlinear solves. https://github.com/trilinos/Trilinos/pull/12986 Teko - Add Hierarchical Block Gauss-Seidel Capability https://github.com/trilinos/Trilinos/pull/13040 Tpetra - Some Tpetra features can be toggled via environment variables. When an unrecognized variable is found, Tpetra now throws to alert to potentially misspelled variables. https://github.com/trilinos/Trilinos/pull/12944 - Add a test that checks that vendor TPLs for sparse matrix-vector product are called. https://github.com/trilinos/Trilinos/pull/13018 - Add team parallelism to kernels associated with matrix equilibration. https://github.com/trilinos/Trilinos/pull/13017 ############################################################################### # # # Trilinos Release 15.1.0 Release Notes February 26, 2024 # # # ############################################################################### Amesos2 - The interface to SuperLU_DIST now also works for the CUDA-enabled variant of the library. https://github.com/trilinos/Trilinos/pull/12524 Framework - Began using semantic versioning for Trilinos with 15.1.0 release. Ifpack2 - BlockRelaxation can now generate blocks using a Zoltan2. https://github.com/trilinos/Trilinos/pull/12728 Kokkos & Kokkos Kernels - Inclusion of version 4.2.1 of Kokkos and Kokkos Kernels https://github.com/trilinos/Trilinos/pull/12707 MueLu - The reformulated Maxwell solver (RefMaxwell) was generalized to also work for grad-div / Darcy flow problems. https://github.com/trilinos/Trilinos/pull/12142 - In an effort to consolidate the old non-Kokkos code path with the newer Kokkos code path, the following factories were deprecated and should be removed from input decks: NullspaceFactory_kokkos, SaPFactory_kokkos, UncoupledAggregationFactory_kokkos. https://github.com/trilinos/Trilinos/pull/12720 https://github.com/trilinos/Trilinos/pull/12740 Panzer - MiniEM can now also assemble and solve Darcy problems using first or higher order mixed finite elements. https://github.com/trilinos/Trilinos/pull/12142 PyTrilinos2 - New package that auto-generates Python interfaces for Trilinos packages. Currently, most of Tpetra is exposed. We are planning on adding other packages. https://github.com/trilinos/Trilinos/pull/12332 ROL - An auto-generated Python interface was added. A standalone Python package can be downloaded from rol.sandia.gov https://github.com/trilinos/Trilinos/pull/12770 Teko - Block Jacobi and Gauss-Seidel methods allow now to specify preconditioners for the iterative solves of the diagonal blocks. https://github.com/trilinos/Trilinos/pull/12675 Tpetra - Tpetra will now assume by default that the MPI library is GPU aware, unless automatic detection or the user indicates otherwise. https://github.com/trilinos/Trilinos/pull/12517 - Reject unrecognized TPETRA_* environment variable. Misspelled or removed environment variables are no longer silently ignored. https://github.com/trilinos/Trilinos/pull/12722 - In order to allocate in shared host/device space (i.e. CudaUVMSpace, HIPManagedSpace or SYCLSharedUSMSpace) by default, please use the CMake options KokkosKernels_INST_MEMSPACE_CUDAUVMSPACE=ON Tpetra_ALLOCATE_IN_SHARED_SPACE=ON https://github.com/trilinos/Trilinos/pull/12622 ############################################################################### # # # Trilinos Release 15.0 Release Notes November 16, 2023 # # # ############################################################################### CMake - Change the default for `Trilinos_MUST_FIND_ALL_TPL_LIBS` from `OFF` to `ON`. It was turned off by default because it breaks backward compatibility but it also causes problems for new users and new configurations. Users that do not want this new behavior can set `-D Trilinos_MUST_FIND_ALL_TPL_LIBS=OFF`, which is backward compatible. - Change the default for `Trilinos_USE_GNUINSTALLDIRS` from `OFF` to `ON`, in the goal to move Trilinos and TriBITS to modern CMake. TriBITS has had the ability to use that paths selected by the standard CMake module `GNUInstallDirs.cmake` for a long time. But it is turned off in TriBITS by default and was never turned on in Trilinos, both for the sake of backward compatibility. This may break people's existing configurations because it will install libs in `/libs64/` instead of in `/libs/` on many systems (e.g. Linux systems). For example, this will break downstream CMake projects that call `find_package(Trilinos ...)` before defining the compilers (e.g. so they can get the compilers from Trilinos). If the compilers are not defined, `find_package()` will not search `/lib64`. To revert back to using `/lib` but still use `GNUInstallDirs.cmake` for Trilinos, set `-D CMAKE_INSTALL_LIBDIR:STRING=lib` when configuring Trilinos. To avoid the `find_package(Trilinos ...)` problem not searching `/lib64`, consider explicitly specifying the compiler to and having the downstream CMake project define the compilers first with `project( COMPILERS C CXX ...)` before calling `find_package(Trilinos ...)`. (That is, don't try to get the compilers from the installed Trilinos, see https://github.com/trilinos/Trilinos/issues/12306.) NOTE: The setting `-D Trilinos_USE_GNUINSTALLDIRS=OFF` is deprecated and may be removed in the future. (I.e. the usage of `GNUInstallDirs.cmake` may be hard-coded in the future so please try adjusting to the usage of `GNUInstallDirs.cmake` by Trilinos.) See https://github.com/trilinos/Trilinos/issues/12104#issuecomment-1691945033 for additional details and instructions. Amesos2 - Updates to STRUMPACK, SuperLU_DIST, MUMPS and LAPACK adapters Anasazi - Randomized eigensolver - Improved testing with Tpetra Belos - Extend GCRO-DR linear solver to use Kokkos linear algebra for GEMMA - Improved testing with Tpetra Domi - Package has been deprecated and removed from Trilinos FEI - Package has been deprecated and removed from Trilinos Ifpack2 - 4th kind Chebyshev smoother - Algorithmic and performance improvements for BlockTriDiag and BlockJacobi. - Stream based RILU(k) and triangular solves - Optimize Kokkos Kernels MDF ILU(0) solver and expose it in Ifpack2 - Patch solver with data compression Komplex - Package has been deprecated and removed from Trilinos Moertel - Package has been deprecated and removed from Trilinos MueLu - Better ML/MueLu compatibility (parameter translation, aggregation algorithms, ..) - Reitzinger-Schoberl type multigrid for Maxwell problems - BlockCRS support - Improved setup performance on device (TAFC Tpetra changes) - Matrix-free multigrid with user-specified operators - AMG for hierarchical matrices NOX - Refactored internal use of model evaluators - LOCA Householder constraint solver can now be nested within a Tempus transient problem (Tpetra version) Pike - Package has been deprecated and removed from Trilinos Rythmos - Package has been deprecated and removed from Trilinos ShyLU - FastILU algorithmic improvements and testing, new block version - Transpose solve with Basker - Tacho: runs with HIP. - FROSch: fully recursive multi-level implementation - FROSch: monolithic coarse spaces via partition-of-unity approach - FROSch: GPU capabilities Stratimikos - Use of half precision preconditioners (Ifpack2, MueLu, ShyLU/FROSch) Teko - Epetra dependency is now optional TriKota - Package has been deprecated and removed from Trilinos ############################################################################### # # # Trilinos Release 14.2 Release Notes # # # ############################################################################### Kokkos - Subpackages have been removed Kokkos. That means that CMake cache variables like Trilinos_ENABLE_KokkosCore or Trilinos_ENABLE_KokkosAlgorithms no longer exist. Now there is just the top-level package Kokkos enabled with Trilinos_ENABLE_Kokkos. In addition, all downstream Trilinos packages that had dependencies on Kokkos subpackages now just depend on the parent package Kokkos. That means that any optional dependencies on a Kokkos subpackage is now an optional dependency on the parent package Kokkos. For example, the Sacado package had an optional dependency on KokkosCore which could be disabled with -D Sacado_ENABLE_KokkosCore=OFF which now needs to be disabled with -D Sacado_ENABLE_Kokkos=OFF. In addition, the #define macros for optional dependencies on Kokkos subpackages have changed names. For example, the Sacado_config.h file defined the preprocessor macros HAVE_SACADO_KOKKOSCORE and HAVE_SACADO_KOKKOSCONTAINERS but now just defines HAVE_SACADO_KOKKOS. Therefore, downstream C++ code will need to adjust any code that depends on these preprocessor defines. However, other than changes in the names of the the CMake Cache variables `_ENABLE_Kokkos` to `_ENABLE_Kokkos` and the changes in the names of the proprocessor defines ``XXX_KOKKOS`` to ``XXX_KOKKOS``, all other behavior should be identical. ############################################################################### # # # Trilinos Release 14.0 Release Notes # # # ############################################################################### CMake - A switch to modern CMake targets in IMPORTED library targets in installed `Config.cmake` files has been made that **breaks backward compatibility** for some downstream CMake projects by changing how include directories are handled: With the switch to modern CMake IMPORTED targets, now include directories (along with critical compiler options and other modern CMake usage requirements) are propagated through linking to the IMPORTED library targets in downstream customer CMake projects. This makes the usage of the variables `Trilinos_INCLUDE_DIRS` and `Trilinos_TPL_INCLUDE_DIRS` unnecessary in downstream CMake projects. The variable `Trilinos_INCLUDE_DIRS` is still set but the variable `Trilinos_TPL_INCLUDE_DIRS` is empty in this change to modern CMake. To get include directories for Trilinos packages and TPLs, one must link against the Trilinos target `Trilinos::all_libs` or `Trilinos::all_selected_libs` or by linking against the individual package targets `::all_libs` and/or the TPL targets `::all_libs`. To upgrade downstream CMake projects that are showing missing include directories (i.e. header files can't be found on the compile liens) just add `target_link_libraries()` calls with the appropriate `::all_libs` targets for the desired package and/or TPL. (See the section "Using the installed software in downstream CMake projects" in the updated build reference guide.) However, backward compatibility is maintained for most customers which are linking all of their libraries against `${Trilinos_LIBRARIES}`. For these projects, no changes will need to be made. However, this change to modern CMake targets will also cause downstream CMake projects to pull in include directories as `SYSTEM` includes (e.g. using `-isystem` instead of `-I`) from IMPORTED library targets. This changes how these include directories are searched and could break some fragile build environments that have the same header file names in multiple include directories searched by the compiler. Also, this will silence any regular compiler warnings from header files found under these include directories. This constitutes a **break in backward compatibility** that will break some customer CMake project builds that use Trilinos on fragile environments where the search order of the include directories is important. There are several different approaches for addressing this change from `-I` to `-isystem` for the Trilinos include directories described below. **Approach-1:** Update to CMake 3.23 and set the Trilinos configure variable: -D Trilinos_IMPORTED_NO_SYSTEM=ON This will change back the listing of Trilinos include directories in downstream customer CMake projects from `-isystem` and `-I` and will therefore restore about perfect backward compatibility. **Approach-2:** Set the cache variable `CMAKE_NO_SYSTEM_FROM_IMPORTED=TRUE` in a downstream CMake project to set which will restore the include directories for the IMPORTED library targets for the TriBITS project as non-SYSTEM include directories (i.e. `-I`) but it will also cause all include directories for all IMPORTED library targets to be non-SYSTEM (i.e. `-I`) even if they were being handled as SYSTEM include directories before. Therefore, that could still break the downstream project as it might change what header files are found for these other IMPORTED library targets and may expose many new warnings (which may have been silenced by their include directories being pulled in using `-isystem`). **Approach-3:** Clean up the list of include directories that is searched by the compiler so that only the correct header files can be found (regardless of the search order). **Approach-4:** Delete some header files in the set of searched include directories so that only the correct header files can be found (regardless of the search order). **Approach-5:** Use other approaches more specific to the given customer project. For example, if multiple different versions of the googletest (gtest) library header files can be found in the list of include directories, then a customer project can build its own version of googletest and put it's include directories first on the compile line and list them with `-I` to ensure that only that version will be found, no matter how many other versions of gtest are installed on the system. For an example of how this was done for one customer CMake project, see https://github.com/trilinos/Trilinos/issues/8001#issuecomment-1032827124. For more details on this change in the handling of include directories with the switch to modern CMake, see https://github.com/TriBITSPub/TriBITS/issues/443. ############################################################################### # # # Trilinos Release 12.12 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 12.12 general release contains 58 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Domi, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, MueLu, NOX, Optika, OptiPack, Pamgen, Phalanx, Pike, Piro, Pliris, PyTrilinos, ROL, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Tempus*, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. (* denotes package is being released externally as a part of Trilinos for the first time.) Domi - Enhancements - Added more sophisticated processor decomposition algorithm. If the decomposition of the processors along each axis is specified incompletely for two or more axes, Domi now returns a much more logical decomposition - Bug fixes - Fixed memory management error related to Tuple and ArrayView - Update ParameterList documentation so that they display properly in HTML documentation - Fixed bug in MDMap::getAugmentedMDMap() method Ifpack2 - Multithreaded Gauss-Seidel now builds by default (#288) Ifpack2's support for multithreaded Gauss-Seidel uses a new thread-parallel graph coloring algorithm implemented in KokkosKernels. (KokkosKernels currently lives in tpetra/kernels.) Ifpack2 makes this algorithm available in Ifpack2::Relaxation. In the 12.10 release, users had to set CMake configuration options to nondefault values in order to enable this code. Now, this code builds and is available by default. (This fixes GitHub Issue #288.) It is still possible to disable building this code, by setting the following CMake option to OFF: - Ifpack2_ENABLE_Experimental_KokkosKernels_Features Isorropia - Removed experimental Tpetra interface. The macro that would have enabled it was commented out, so it could never have built. See discussion in #1406: https://github.com/trilinos/Trilinos/issues/1406 PyTrilinos - General - PyTrilinos now works with both Python versions 2 and 3 - Internally, PyTrilinos now uses relative imports - Protect against Doxygen version 1.8.13 - Teuchos - Fix ParameterList __cmp__() operator - Improved memory management for wrapped version of sublists - Fixed a memory leak in the definitions for certain directorin typemaps - Epetra - Add AsMap() method to Epetra.BlockMap class - ML - Fixed a dangling reference error in an ML example script. - LOCA - Fixed a memory leak in LOCA example script - Fixed a memory leak in the wrappers for the LOCA::Abstract::Iterator::StepStatus enumeration - Anasazi - Fixed a memory leak that PyTrilinos introduced with the Eigensolution<...>::evecs() and espace() methods Tempus Tempus provides a general infrastructure for the time evolution of solutions to ODEs, PDEs, and DAEs, through a variety of general integration schemes, and can be used from small systems of equations (e.g., single ODEs for the time evolution of plasticity models) to large-scale transient simulations requiring exascale computing (e.g., flow fields around reentry vehicles and magneto-hydrodynamics). - Examples of time-integration methods available are: - Tempus::StepperForwardEuler "Forward Euler" - Tempus::StepperBackwardEuler "Backward Euler" - Tempus::StepperExplicitRK "Explicit Runge-Kutta" - Tempus::StepperDIRK "Diagonally Implicit Runge-Kutta methods" - Newmark-β - Tempus::StepperNewmarkExplicitAForm "Explicit A-form" - Tempus::StepperNewmarkImplicitAForm "Implicit A-form" - Tempus::StepperNewmarkImplicitDForm "Implicit D-form" - Tempus::StepperHHTAlpha "Hilber-Hughes-Taylor (HHT-α)" - Tempus::StepperIMEX_RK "Implicit/Explicit Runge-Kutta (IMEX-RK) methods" - Tempus::StepperIMEX_RK_Partition "Partitioned IMEX-RK methods" ############################################################################### # # # Trilinos Release 12.10 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 12.10 general release contains 58 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Domi, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, MueLu, NOX, Optika, OptiPack, Pamgen, Phalanx, Pike, Piro, Pliris, PyTrilinos, ROL, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. (* denotes package is being released externally as a part of Trilinos for the first time.) Ifpack2 - Experimental multithreaded Gauss-Seidel This uses a new thread-parallel graph coloring algorithm implemented in KokkosKernels. Ifpack2's support for this lives in Ifpack2::Relaxation. Currently, building it is disabled by default (see #288). Enabling it requires enabling the following CMake options that are currently OFF by default: - TpetraKernels_ENABLE_Experimental - Ifpack2_ENABLE_Experimental - Ifpack2_ENABLE_Experimental_KokkosKernels_Features - Ifpack2::Krylov is really SUPER deprecated now It's been deprecated for a LONG time, complete with deprecated warnings. This didn't suffice for warning some users, so I moved the class to the new Ifpack2::DeprecatedAndMayDisappearAtAnyTime namespace. - Encapsulate local sparse triangular solves in a new class, LocalSparseTriangularSolver - Fix various issues Issues fix include (but are not limited to) #672, #570, #567, #558, #551, #544, #409, #234, and #64. Tpetra - Build time and size improvements (fix #700) KokkosKernels now only pre-builds the sparse matrix-vector multiply kernels that Tpetra needs. Also, for integer Scalar types, KokkosKernels no longer optimizes sparse matrix-vector multiply for multiple right-hand sides. It does so only for non-integer (e.g., floating-point) Scalar types. This reduces build time and size. (See Github Issue #700.) Furthermore, KokkosKernels now only pre-builds sparse matrix-vector multiply for the default offset type. - Removed "using Teuchos::*" declarations from Tpetra_ConfigDefs.hpp Tpetra no longer imports Teuchos classes like Comm and RCP (among others) into the Tpetra namespace. This will help us eventually remove all the Teuchos_*.hpp header file includes from Tpetra_ConfigDefs.hpp, thus improving build time. - MultiVector: Add new two-argument randomize(min,max) - MultiVector: Get rid of old-interface DistObject methods Tpetra::MultiVector implements the new DistObject interface. Thus, it no longer needs to provide implementations for the following three old-interface DistObject methods: - createViews - createViewsNonConst - releaseViews - Optimize Map::replaceCommWithSubset for MPI_COMM_SELF (#673) - Fixed many other issues Issues fixed include (but are not limited to) #699, #680, #638, #617, #607, #603, #601, #597, #561, and #46. ############################################################################### # # # Trilinos Release 12.8 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 12.8 general release contains 58 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Domi, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, MueLu, NOX, Optika, OptiPack, Pamgen, Phalanx, Pike, Piro, Pliris, PyTrilinos, ROL, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. (* denotes package is being released externally as a part of Trilinos for the first time.) Domi - Added replicated boundaries - A replicated boundary exists only on a periodic domain, and is simply a convention that the end points are the same points. For example, a left end coordinate that represents 0 degrees and a right end coordinate that represents 360 degrees. Domi now supports either convention, and it affects communication. - Added additional tests for periodic domains - Enhancements - New MDVector constructor that takes a parent MDVector and an array of Slices - MDMap support for axis maps - MDMap getMDComm() method PyTrilinos - General - Improved formatting in example scripts - Domi - Update MDMap constructor for replicated boundaries - Fixed ETI bugs - NOX/LOCA - Fixed memory leak by updating NOX typemaps - Tpetra - Fix difficult-to-wrap Map class by using %inline Tpetra - Stop creating Node instances explicitly! Hi users! Please don't create Node instances explicitly any more. Tpetra::Map creates one for you, if you really need one. You really don't need Node instances: Map's constructors and nonmember "constructors" don't need them any more, nor do Tpetra's Matrix Market readers. Creating Node instances explicitly causes issues with Kokkos initialization. Node will go away eventually, in favor of Kokkos execution spaces and memory spaces. - Lots of bug fixes, especially for CUDA - Computing offsets in CrsGraph and CrsMatrix is now thread parallel CrsGraph's and CrsMatrix's fillComplete method computes row offsets, if they have not yet been computed. This is now thread parallel. It uses Kokkos::parallel_scan. - More BlockCrsMatrix kernels are thread parallel - Interface changes to KokkosSparse::CrsMatrix (the "local" matrix) - The replaceValues and sumIntoValues methods now take "is_sorted" and "force_atomic" arguments. These methods now use binary search (falling back to linear search for short rows) for the sorted case. - Row views in KokkosSparse::CrsMatrix are no longer templated. They now use the ordinal type, rather than the offset type, for indexing. This suffices as long as there are not enough duplicate entries in a row to exceed ordinal_type. This has the beneficial side effect of reducing the number of local sparse matrix-vector multiply kernel instantiations. - Got rid of LittleBlock and LittleVector (for Block* classes) Instead, use the little_block_type, const_little_block_type, little_vec_type, and const_little_vec_type typedefs in BlockCrsMatrix and other related classes. Underlying data layout has NOT changed (yet), but constructors HAVE changed. This is technically a non-backwards-compatible interface change, but all these classes are in an Experimental namespace anyway. - Got rid of KokkosClassic::DefaultArithmetic Stokhos was using this, so we had left it in place in previous releases for backwards compatibility. Now that no other packages depend on it, we have gotten rid of it for good. Its functionality has been replaced by various functions in TpetraKernels. The original idea behind DefaultArithmetic, as suggested in the name, was that users could swap out this "default" implementation of multivector operations with their own implementations. This is generally less useful than swapping out the implementation of sparse matrix kernels (like sparse matrix-vector multiply or sparse triangular solve). As a result, Tpetra never had an implementation (since at least January 2010) of multivector operations other than DefaultArithmetic. ROL - NEW FEATURES - Methods - New phi-divergence capabilities for distributionally-robust optimization. - NonlinearLeastSquaresObjective functionality enables the solution of nonlinear equations through the EqualityConstraint object. - Infrastructure - Composite bound constraint (ROL_BoundConstraint_Partitioned). - Composite equality constraint (ROL_EqualityConstraint_Partitioned) - Merit function for interior point methods. - Adapter for Teuchos::SerialDenseVector. - L1, Lp, Linf norms for interior point methods. - Allow user-defined bracketing objects. - Line searches can take user-defined scalar minimizers. - Ability to supply ScalarMinimizationLineSearch with custom ScalarFunction. - New application development and interface tools for PDE-constrained optimization in PDE-OPT. - New PDE-OPT examples: stochastic Stefan-Boltzmann, stochastic advection-diffusion, etc. - Adaptive sparse grid capabilities with TriKota. Zoltan - Improved robustness of RCB partitioner for problems where many objects have weight = 0 (e.g., PIC codes). Convergence is faster and the stopping criteria are more robust. - Fixed bug that occurred when RETURN_LIST=PARTS and (Num_GID > 1 or Num_LID > 1); GIDs and LIDs are now copied correctly into return lists. - Fixed a bug related to struct padding in the siMPI serial MPI interface. Zoltan2 - Graph/Matrix ordering - Scotch now can be used for graph/matrix ordering. - The ordering interface Zoltan2::OrderingSolution has been updated to allow users to access separator info, if it is available. - Zoltan2::OrderingSolution method getPermutation() is now getPermutationView(). - Partitioning Metrics - Partitioning metrics have been moved out of the PartitioningProblem. They are now accessed through a separate class: Zoltan2::EvaluatePartition. - EvaluatePartition accepts as input a Zoltan2::Adapter and, optionally, a Zoltan2::PartitioningSolution. Thus, it can be used before or after partitioning, and before or after migration. - Imbalance and graph metrics are available. - Task placement - A new PartitionMapping class maps parts to processors. - The MachineRepresentation has been updated, and specializations using Cray RCA and IBM TopoMgr are provided. - Geometric task placement using Multijagged partitioning better handles cases where the machine's network dimension is greater than the dimension of the coordinates. - Multijagged partitioning - Zoltan2's Multijagged partitioner can now partition wrt the longest coordinate dimension, or in specified x-y-z order. - TPLs - Conversions between the index types in TPLs (ParMETIS, Scotch, Zoltan) are handled more robustly through the TPL_Traits class. - Interfaces to ParMETIS' AdaptiveRepart and RefineKway algorithms were added. - Bugs in the Zoltan interface are fixed. ############################################################################### # # # Trilinos Release 12.6 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 12.6 general release contains 58 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Domi, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, MueLu, NOX, Optika, OptiPack, Pamgen, Phalanx, Pike, Piro, Pliris, PyTrilinos, ROL, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. (* denotes package is being released externally as a part of Trilinos for the first time.) Ifpack2 - Fixed Ifpack2's part of Bug 6358 Ifpack2, as well as its tests and examples, no longer require GlobalOrdinal = int to be enabled in Tpetra. - Fixed Bug 6443 One unit test for RILUK had an excessively tight tolerance for Scalar = float. This commit relaxes the tolerance in a principled way. As a result, the test now passes. ROL - Enhancements: - Default template parameters for ROL::TpetraMultiVector. - StdVector, TpetraMultiVector, and PartitionedVector now do dimensional compatibility checks. - More unary and binary elementwise functions added. - New Features: - Methods: - InteriorPointStep class, and classes it uses (e.g. PenalizedObjective, InequalityConstraint, and CompositeConstraint) to solve Interior Point problems with the CompositeStep SQP solver with successive penalty reduction. - Standalone GMRES solver in the Krylov directory. - Mixed quantile risk measure. - New risk measure corresponding to Kullback-Liebler based distributionally robust optimization. - SROM SampleGenerator: The associated samples are determined by solving an optimization problem. Current objective functions correspond to moment matching and the squared L2 error between distribution functions. - The PDE-OPT Application Development Kit (ADK) enables the rapid prototyping of large-scale risk-averse optimization problems with PDE constraints. The PDE-OPT ADK comprises three key modules: -- degree-of-freedom manager, which enables the use of an arbitrary number of simulation, control, and design fields based on finite element discretizations, on 1D, 2D and 3D meshes; -- finite element assembly loops and data structures that enable the development of a variety of multiphysics components, built on Intrepid for local finite element computations and Tpetra for parallel linear algebra data structures; -- interface between the physics module and the SimOpt programming interface. - Infrastructure: - OptimizationProblem class unifies Algorithm::run interface. - StochasticProblem allows for the construction of a general stochastic objective function based on input parameters. - Generalized CVaRVector to RiskVector. This allows for a very general treatment of risk-averse optimization problems. - Risk measure factory. - Default solve implementation for EqualityConstraint_SimOpt. - BoundConstraint capability for Interior Point problems with and without Equality Constraints. Tpetra - Better CUDA testing We added more nightly test builds with CUDA enabled (for running on NVIDIA GPUs). The builds test various combinations of CUDA with different compiler versions and host thread parallelism options (OpenMP, Pthreads, serial). CUDA + GCC 4.7.2 is currently the best-tested option, but we're using these tests to improve support for other options. - CrsMatrix, MultiVector, Vector: Added 'atomic' option to sumInto The sumIntoLocalValues method in Tpetra::CrsMatrix, and the sumIntoLocalValue and sumIntoGlobalValue methods in Tpetra::MultiVector and Tpetra::Vector, now take an optional bool 'atomic' argument. If true, the methods use Kokkos::atomic_add (atomic +=); if false, they use (non-atomic) += as before. This lets different threads call the methods concurrently on the same entry/ies of the matrix, multivector, or vector. To support this, I also modified CrsMatrix::sumIntoGlobalValues so that it does not change Teuchos::RCP reference counts, thus making it thread safe. The default value of 'atomic' depends on the class' execution space. If the execution space is Kokkos::Serial (no threads), atomic is false by default; else, it is true by default. This ensures that existing MPI-only codes do not need to pay the (small integer factor) overhead of atomic updates, while making sumInto always correct by default when using thread parallelism. If you know that different threads will never access the same entries concurrently, you should set atomic=false for best performance. - Block(Multi)Vector: Add "offset view" constructors (Bug 6450) Tpetra::Experimental::{BlockMultiVector, BlockVector} now have two "offset view" constructors. They behave analogously to the offsetView and offsetViewNonConst methods of Tpetra::MultiVector. The constructors view an existing BlockMultiVector with a different mesh Map, and an optional local row offset from which to start the view on each process. The offset is a mesh offset (it gets multiplied by the block size internally in order to find the point offset). The two constructors differ only in that one lets you supply the new point Map, while the other computes it for you. This fixes Bug 6450 (which was a feature request). Zoltan - Minor code cleanup and bug fixes. - New Zoltan_Get_Fn interface returning pointers to callback functions. See zoltan/src/include/zoltan.h for details. - Closest stand-alone Zoltan release is v3.83. http://www.cs.sandia.gov/Zoltan Zoltan2 - New interface to graph partitioning third-party library PuLP (Partitioning using Label Propagation). PuLP is currently single-node, multi-threaded with OpenMP. Work for the next release will include extension to MPI+OpenMP. - Improved handling of TPL data types, especially in the Zoltan interface. - Interface from MatrixAdapter to Zoltan hypergraph algorithms implemented. - Consistent handling of Tpetra explicitly instantiated types; in particular, enabled builds without GlobalOrdinal=int and without Epetra. - PartitioningSolutionQuality class is being refactored and renamed EvaluatePartition; work will continue to next release. ############################################################################### # # # Trilinos Release 12.4 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 12.4 general release contains 58 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Domi, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, MueLu, NOX, Optika, OptiPack, Pamgen, Phalanx, Pike, Piro, Pliris, PyTrilinos, ROL, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. (* denotes package is being released externally as a part of Trilinos for the first time.) Amesos2 - Added MUMPS 5.0 support - KLU2 is enabled by default - Bug fixes - Superlu_dist multiple version support (up to 4.0) Domi - Various bug fixes: - Fixed a bug where a periodic axis under a serial build would not update communication padding. The parallel version uses MPI capabilities to do this, so a serial-only capability had to be added for this corner case. - Fixed a test that was doing a dynamic type comparison to be more robust. - Fixed some minor bugs in the MDVector getTpetraMultiVector() method. - The MDArrayView size() method was made const, as it should be - Created serial tests - Domi does not provide much in the way of unique capabilities if it is compiled in serial. Nevertheless, all tests that run on 1 processor were updated to run under a serial build of Trilinos as well. Ifpack2 - Deprecated Ifpack2::Krylov If you want a Krylov solver, just use Belos. Ifpack2::Factory now throws with an informative exception message if you ask for "KRYLOV". Muelu - MueLu requires certain C++11 features. Minimum compiler versions are gcc 4.7.2 or icc 13. (See https://trilinos.org/about/cxx11.) - Kokkos is a required dependency. - New MatrixAnalysis Factory. - Deprecated Create[TE]petraPreconditioner interfaces taking Tpetra::CrsMatrix types as input argument in favor of interfaces accepting Tpetra::Operator types. - Numerous improvements to MueMex (MueLu's interface to Matlab). - Mumps can now be used as a coarse grid solver through Amesos2. - Unification of MueLu Epetra and Tpetra interfaces through Stratimikos. PyTrilinos - General - Fixed several memory management bugs - Fixed a pervasive bug where C++ exceptions were caught in the wrong order. This fix results in Python errors that have much better messages, making it easier to debug problems that employ cross-language polymorphism. - Epetra - Added new Python-to-C++ converters that convert a wider variety of Python objects to distributed Epetra vectors (Epetra_MultiVector, Epetra_Vector, Epetra_IntVector). This includes any Python object that exports the Distributed Array Protocol, such as Enthought's DistArray. It also includes NumPy arrays when running in a serial environment. - Added __distarray__() method to Epetra vector classes, so that they now export the Distributed Array Protocol. - Memory management issues associated with the Epetra.LinearProblem class and the new Epetra vector converters were fixed. - Tpetra - Fixed wrappers for Tpetra MultiVector and Vector classes. - Added __distarray__() method to Tpetra vector classes, so that they now export the Distributed Array Protocol. - Bug fixes related to latest Tpetra upgrade - LOCA - Introduced a new LOCA test in which the Chan problem is solved using a preconditioner. ROL - Enhancements - Hierarchical XML parameter lists. This makes ROL easier to use and control. Demonstrated in all examples and test. Also created the tierParameterList function to generate a hierarchical list from a flat list, in rol/src/zoo/ROL_ParameterListConverters.hpp, demonstrated in rol/test/parameters. - Algorithm constructor now takes reference-counted pointers to Step and StatusTest. There is another constructor that takes a step name (string) and a parameter list. This makes it easier to initialize a ROL algorithm, based on default choices of steps and status tests. - New elementwise functions in ROL::Vector allow application of general nonlinear unary and binary functions as well as reduce operations. - Modified ROL::BoundConstraint to work with any vector type for which Vector::applyUnary, Vector::applyBinary, and Vector::reduce are implemented. - Modified default behavior of line search so that when the maximum number of function evaluations is reached and sufficient decrease has not been attained, optimization terminates. The previous behavior can be recovered by setting the parameter "Accept Last Alpha" to true in the Step->Line Search sublist. - Added line search parameter "Accept Linesearch Minimizer" to the Step->Line Search sublist. If this parameter is selected to be true, the argmin step length will be used if the maximum number of function evaluations is reached without attaining sufficient decrease. - Renamed CompositeStepSQP to CompositeStep. - New Features - Methods - Bundle Step, for solving nonsmooth problems; see example/minimax/*. - Moreau-Yosida Penalty, for solving general NLPs; see example/burgers-control/example_04. - Augmented Lagrangian, for solving general NLPs; see example/burgers-control/example_04. - Higher Moment Coherent Risk Measure. This method is a new risk measure for stochastic problems, see example/burgers-control/example_06. - Buffered Probability of Exceedance. This method is a new capability to minimize the probability of a stochastic cost function. It is demonstrated in example/burgers-control/example_06. - Infrastructure - In ROL_ScaledStdVector.hpp, added a variant of ROL::StdVector that supports constant (positive) diagonal scalings in the dot product. This variant comprises the pair of classes ROL::PrimalScaledStdVector and ROL::DualScaledStdVector; changed the examples in example/diode-circuit to use variable scalings through these new classes. - Distribution Factory, to enable general sampling for stochastic problems; demonstrated in example/burgers-control/example_05 through _07. - SROMSampler. This method permits the use of optimization-based sampling for stochastic problem. It is demonstrated in test/sol/test_04. - ROL::PartitionedVector, for handling vectors of vectors, e.g., when using slack variables, see /rol/test/vector/test_04.cpp. - Bug Fixes - Removed reset of counters for objective function and gradient evaluations contained in the AlgorithmState in rol/src/step/ROL_TrustRegionStep.hpp. - Corrected reading of the constraint tolerance parameter in ROL::AugmentedLagrangianStep. Tpetra - Changed CMake option for setting default Node type To set the default Node type, use the Tpetra_DefaultNode CMake option. We support the old KokkosClassic_DefaultNode CMake option for backwards compatibility. Tpetra will eventually change from using Node types to using Kokkos::Device types directly. For now, though, if you wish to set the default Node type explicitly, you must use one of the following: - Kokkos::Compat::KokkosCudaWrapperNode (CUDA) - Kokkos::Compat::KokkosOpenMPWrapperNode (OpenMP) - Kokkos::Compat::KokkosSerialWrapperNode (Serial (no threads)) - Kokkos::Compat::KokkosThreadsWrapperNode (Pthreads) Tpetra normally only enables one Node type, so you only need to set the default Node type if you have enabled more than one Node type. - Rules for which Node type gets enabled by default Tpetra only enables one Node type by default, whether or not ETI (explicit template instantiation) is enabled. Here are the rules for which Node type gets enabled by default: 1. If you're building with CUDA, Tpetra uses CUDA by default. 2. Otherwise, if you're building with OpenMP, Tpetra uses OpenMP by default. 3. Otherwise, if Kokkos enables the Serial execution space (if Kokkos_ENABLE_SERIAL is ON), Tpetra uses Serial by default. 4. Otherwise, if Kokkos enables the Threads execution space (if Kokkos_ENABLE_THREADS is ON), Tpetra uses Threads by default. If you wish to enable other Node types, you may set the following CMake options. You do NOT need to set any of these options explicitly if the Node type would be enabled by default anyway. - Tpetra_INST_CUDA (Kokkos_ENABLE_CUDA must be ON, and Trilinos must be built with CUDA; ON by default if building with CUDA) - Tpetra_INST_OPENMP (Kokkos_ENABLE_OPENMP must be ON, and Trilinos must be built with OpenMP support) - Tpetra_INST_PTHREAD (Kokkos_ENABLE_THREADS must be ON) - Tpetra_INST_SERIAL (Kokkos_ENABLE_SERIAL must be ON) While it is legal to enable both the OpenMP and Pthreads back-ends in the same executable, it is a bad idea. Both back-ends spawn their own worker threads, and those threads will fight over cores. - Completely removed the "classic" version of Tpetra You might recall that a while back, we split Tpetra into "classic" (old) and "Kokkos refactor" (new) versions. As of Trilinos 12.0, the classic version was no longer supported, but we kept it in place for a few users. As of this release, we have removed the classic version completely. You no longer need to set Tpetra_ENABLE_Kokkos_Refactor to get the new verson of Tpetra. It is ON (TRUE). If you attempt to set it to OFF (FALSE), Tpetra's CMake raises an error at configure time. Just enable Tpetra -- that's all you need to do! This change affects both the Classic and Core subpackages of Tpetra. All the "classic" Node types are gone now, along with their associated computational kernels. Use the Kernels subpackage of Tpetra for local kernels. (We left KokkosClassic::DefaultArithmetic in place for Stokhos, but ONLY for Stokhos.) The "classic" versions of Tpetra classes are also now gone. We have replaced them completely with their "Kokkos refactor" versions. You might have noticed that Doxygen had a hard time generating documentation for the classes which had "classic" and "refactor" versions. These changes should fix that. Furthermore, it's easier to find header files for classes. In particular, most of the header files in the tpetra/core/src/kokkos_refactor directory now just have trivial definitions and only remain for backwards compatibility. - Improved build times and fewer .cpp files in source directory Tpetra does a better job now of splitting up explicit instantiations into separate .cpp files. In some cases, it uses CMake to generate those .cpp files automatically. This means fewer .cpp files in tpetra/core/src, so it's easier to find what you want. - 128-bit floating-point arithmetic through Scalar = __float128 __float128 is a GCC language extension to C(++) that implements "double-double" 128-bit floating-point arithmetic. It requires linking with libquadmath, which comes with GCC. You must use GCC in order to try this feature. Also, set the following CMake variables: Tpetra_INST_FLOAT128:BOOL=ON CMAKE_CXX_FLAGS:STRING="-std=gnu++11 -fext-numeric-literals" TPL_ENABLE_quadmath:BOOL=ON You may also have to tell CMake where to find the libquadmath library and quadmath.h header file: quadmath_LIBRARY_DIRS:FILEPATH="${QUADMATH_LIB_DIR}" quadmath_INCLUDE_DIRS:FILEPATH="${QUADMATH_INC_DIR}" Here, ${QUADMATH_LIB_DIR} points to the directory containing the libquadmath library (usually your GCC library directory), and ${QUADMATH_INC_DIR} points to the directory containing its header file (quadmath.h). For example, if you use a GCC installed in $HOME/pkg/gcc-5.2.0, you might need to set those variables as follows: QUADMATH_LIB_DIR=$HOME/pkg/gcc-5.2.0/lib QUADMATH_INC_DIR=\ $HOME/pkg/gcc-5.2.0/lib/gcc/x86_64-unknown-linux-gnu/5.2.0/include Trilinos likes to set the "-pedantic" flag, which causes warnings for __float128 literals. The build works regardless, but it would be more pleasing to your eyes if you could figure out how to shut off the warnings. I implemented this because the Kokkos refactor of Tpetra broke QD support (dd_real and qd_real -- "double-double" and "quad-double," 128- resp. 256-bit floating-point arithmetic). Applications were asking for a work-around solution. Zoltan2 - Template argument for arbitrary global identifiers (zgid_t) has been removed for greater efficiency in the code as well as greater conformity with Trilinos. - BasicUserTypes now has only three template parameters; the zgid_t template argument has been removed. - OrderingSolution now has two different template parameters: for - A new test driver capability has been added to Zoltan2 for more robust testing and experimentation. - An interface to the Zoltan partitioners has been added to Zoltan2. Parameter "algorithm" == "zoltan" invokes Zoltan partitioners; parameters needed by Zoltan are provided through a parameter sublist called "zoltan_parameters". Zoltan's geometric and hypergraph methods are available. - A new interface to third-party library ParMA (from Rensselaer Polytechnic Institute) is available. ParMA provides mesh partition improvement to balance both primary and secondary entities. It assumes the number of processors is equal to the number of requested parts, and that the input mesh distribution corresponds to the input part assignments. RPI's SCOREC repository is needed to use ParMA. - A new hypergraph mesh partitioning model is available in Zoltan2 through the MeshAdapter. - Parameters to third-party libraries Scotch and ParMETIS are provided through parameter sublists "scotch_parameters" and "parmetis_parameters", respectively. ############################################################################### # # # Trilinos Release 12.2 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 12.2 general release contains 58 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Domi, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, MueLu, NOX, Optika, OptiPack, Pamgen, Phalanx, Pike, Piro, Pliris, PyTrilinos, ROL*, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. (* denotes package is being released externally as a part of Trilinos for the first time.) Domi - Input arguments that come in the form of const Domi::MDArrayView< int > have been changed to be const-correct, i.e., they are now const Domi::MDArrayView< const int >. This allowed for more logical wrappers in PyTrilinos. - A new Domi::DefaultNode class has been added. If Tpetra is enabled, it uses the Tpetra default node. If Tpetra is not enabled, it uses the serial wrapper node from Teuchos. - Domi's required dependencies have been simplified, to Teuchos, Kokkos, and TeuchosKokkosCompat. Optional dependencies are Epetra, TpetraClassic, and TpetraCore. MueLu - Allow to dynamically switch transfer operators between different multigrid levels. Can be used in context of semi-coarsening. - Enabled semi-coarsening (using Ray's line detection algorithm). - Add support for line smoothing (Ifpack/Ifpack2) [EXPERIMENTAL] - New AMGX Adapter [EXPERIMENTAL] New experimental adapter which allows a user with AMGX installed to utilize this software for the preconditioning and solution of linear systems. If a user provides AMGX configuration options instead of a MueLu input deck, the adapter will be called. Currently supported with Tpetra objects. - Matlab interface for MueLu [EXPERIMENTAL] Setup and solve hierarchies from Matlab and use Matlab functions as MueLu factories. PyTrilinos - General - Updated the Developers Guide - Teuchos - Made Teuchos a required dependency for PyTrilinos. - Domi - Domi wrappers now use new Domi::DefaultNode class - Added HAVE_DOMI as a macro in PyTrilinos_config.h - Fixed docstrings for Domi package - Added a simple Domi example - Fixed Domi.MDVector extensions - Tpetra - Enabled Tpetra wrappers in the release branch - Fixed a dynamic typing problem - Bug fixes in Tpetra.Map - Added HAVE_TPETRA as a macro in PyTrilinos_config.h - Fixed docstrings for Tpetra package - Got wrappers for all requiredTpetra constructors to work - Expanded Tpetra.Vector unit tests - Added unit tests for Tpetra.MultiVector ROL Rapid Optimization Library (ROL) is a C++ package for large-scale optimization. It is used for the solution of optimal design, optimal control and inverse problems in large-scale engineering applications. Other uses include mesh optimization and image processing. ROL aims to combine flexibility, efficiency and robustness. Key features: - Matrix-free application programming interfaces (APIs) --enable direct use of application data structures and memory spaces, linear solvers, nonlinear solvers and preconditioners. - State-of-the-art algorithms for unconstrained optimization, constrained optimization and optimization under uncertainty --enable inexact and adaptive function evaluations and iterative linear system solves. - Special APIs for simulation-based optimization --enable a streamlined embedding into engineering applications, rigorous implementation verification and efficient use. - Modular interfaces throughout the optimization process --enable custom and user-defined algorithms, stopping criteria, hierarchies of algorithms, and selective use of a variety of tools and components. For a detailed description of user interfaces and algorithms included in this release, see the presentation ROL-Trilinos-12.2.pptx (or .pdf) in the doc/presentations directory. Tpetra - Improvements to the "local" part of Tpetra::Map Tpetra::Details::FixedHashTable implements the "local" part of Tpetra::Map, where the "local part" is that which does not use MPI communication. For example, FixedHashTable knows how to convert from global indices to local indices, for all the global indices known by the calling process. FixedHashTable now uses Kokkos for its data structures. Its initialization is completely Kokkos parallel, and its conversions between global and local indices are Kokkos device functions. This achieves an important goal of making the local part of Tpetra::Map functionality available for Kokkos parallel operations. - Many Tpetra classes now split instantiations into multiple files This matters only when explicit template instantiation (ETI) is ON. (This _should_ be ON by default, but is not ON by default yet.) The largest Tpetra classes (e.g., CrsGraph, CrsMatrix, and MultiVector) now split their explicit instantiations into multiple .cpp files. This helps reduce build times and memory usage when ETI is ON, and makes setting ETI ON an even more attractive option for applications. - Fixed Bugs 6335, 6336, 6377, and others - Improved tests to catch errors on processes other than Process 0 - Improved CMake output and internal ETI-related documentation ############################################################################### # # # Trilinos Release 12.0 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 12.0 general release contains 57 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Domi, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, MueLu, NOX, Optika, OptiPack, Pamgen, Phalanx, Pike, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. Domi Domi provides distributed data structures for multi-dimensional data. The inspirational use case is parallel domain decomposition for finite difference applications. To that end, Domi provides the following classes: - MDArray, MDArrayView, MDArrayRCP These classes define multi-dimensional arrays, with arbitrary runtime-defined dimensions, built on top of the Teuchos Array, ArrayView, and ArrayRCP classes, respectively. These are serial in nature and provide the mechanism for data manipulation on each processor of distributed MDVectors. - Slice The Slice class is inspired by the Python slice object, which stores a start, stop, and step index, and can be constructed to utilize a variety of logical default values. Slices can be used on all multi-dimensional objects to return views into subsets of those objects. - MDComm Multi-dimensional communicator. This communicator provides a map between a multi-dimensional array of processors and their ranks, and can be queried for neighbor ranks. MDComms can be sliced, which returns a sub-sommunicator. - MDMap An MDMap describes the decomposition of an MDVector on an MDComm. It stores the start and stop indexes along each dimension, including boundary padding for algorithms that require extra indexes along boundaries, and communication padding used to update values from neighboring processors. MDMaps can be sliced, and the resulting MDMap may reside on a sub-communicator. An MDMap can be converted to an equivalent Epetra or Tpetra Map. - MDVector An MDVector is a multi-dimensional array, distrubuted in a structured manner across multiple processors. This distribution is described by an MDVector's MDMap. The MDVector's data is stored locally on each processor with an MDArrayRCP. An MDVector can update its communication padding from neighboring processors automatically. An MDVector can be sliced, and the resulting MDVector may reside on a sub-communicator. An MDVector can be converted to equivalent Epetra or Tpetra Vectors or MultiVectors. If there are no stride gaps in the data due to slicing, these converted Epetra and Tpetra objects may be views of the original data. MueLU - Hierarchy::Iterate now understands tolerance When MueLu::Hierarchy is being used as a standalone solver, and not as a preconditioner, a user may now create a stopping criteria based on a provided tolerance for the relative residual in addition to the maximum number of iterations - New reuse options option: "tP" This reuse option allows reuse of only tentative prolongators, while rebuilding smoothed prolongator and coarse level operators. - Selected bugfixes: 6301: Operator complexity was computed incorrectly for large size problems Pike PIKE: Physics Integration KErnels Pike is a blackbox multiphysics coupling tool. It provides basic interfaces and implementations for building high level multiphysics coupling strategies. In particular, PIKE provides utilities for Picard-style couplings. For Newton-based couplings, use the NOX and Thyra packages to build the block phsyics systems. In the future, interoperability tools between NOX, PIKE and PIRO will be added. - Initial release! - Supports block Jacobi and block Gauss-Seidel coupling. - Supports global and local convergence criteria. - Supports hierarchical solves. - Supports subcycled transient solves and steady-state. - Support both Parameter and Response interfaces. - Contains a multiphysics distributor to support parallel distribution of applications. - Provides abstract factories for solvers and global status tests - Supports observers for user injection of code. Special observers for logging and debugging are implemeted. - Pure virtual interfaces for applications and data transfers. - Adapter for nesting a solver as a model evaluator for hierarchical solves. **************************************** PyTrilinos - General - Changed to BSD license - Mpi4Py support has been made optional. Previously, if Mpi4Py was found, it was automatically enabled within PyTrilinos. Now that behavior can be turned off. - LOCA - The LOCA module has been refactored and now has been demonstrated to work for the Chan problem. We have two example problems working, one without preconditioning, and one with. - Tpetra - Package is still experimental. The recent refactor has broken MultiVectors and Vectors. - Map support has been improved - Anasazi - Fixed a bug where return eigenvalues are converted to a NumPy array, but the dimension used the wrong type. - Kokkos - Fixed a macro issue - NOX - Started PETSc compatibility. This is still experimental, and includes compatibility with petsc4py. - STK - Removed PyPercept, as it is currently not a part of the new STK. - Domi - Added package Tpetra - Tpetra now requires C++11 This requirement comes in part from Tpetra itself, and in part from the Kokkos package, on which Tpetra depends. - "Kokkos refactor" (new) version of Tpetra is the only version We no longer enable or support the old ("classic") version of Tpetra. The new ("Kokkos refactor") implementation of Tpetra is now the only supported version. Do not use any of the Node types in the KokkosClassic namespace. We do not support any of those Node types anymore. Instead, use any of the following Node types: - Kokkos::Compat::KokkosOpenMPWrapperNode (OpenMP) - Kokkos::Compat::KokkosCudaWrapperNode (NVIDIA CUDA) - Kokkos::Compat::KokkosSerialWrapperNode (no threads) - Kokkos::Compat::KokkosThreadsWrapperNode (Pthreads) Each of these is a typedef for Kokkos::Compat::KokkosDeviceWrapperNode, for the corresponding Kokkos execution space. - Set / rely on the default Node type as much as possible Tpetra classes have a template parameter, "Node", which determines what thread-level parallel programming model Tpetra will use. This corresponds directly to the "execution space" concept in Kokkos. Tpetra classes have a default Node type. Users do NOT need to specify this explicitly. I cannot emphasize this enough: IF YOU ONLY EVER USE THE DEFAULT VALUES OF TEMPLATE PARAMETERS, DO NOT SPECIFY THEM EXPLICITLY. If you need to refer to the default values of template parameters, ask Tpetra classes. For example, 'Tpetra::Map<>::node_type' is the default Node type. Tpetra pays attention to Kokkos' build configuration when determining the default Node type. For example, it will not use a disabled execution space. If you do not like the default Node type, but you only ever use one Node type in your application, you should change the default Node type at Trilinos configure time. You may do this by setting the 'KokkosClassic_DefaultNode' CMake option. Here is a list of reasonable values: "Kokkos::Compat::KokkosSerialWrapperNode": use Kokkos::Serial execution space (execute in a single thread on the CPU) "Kokkos::Compat::KokkosOpenMPWrapperNode": use Kokkos::OpenMP execution space (use OpenMP for thread-level parallelism on the CPU) "Kokkos::Compat::KokkosThreadsWrapperNode": use Kokkos::Threads execution space (use Pthreads (the POSIX Threads library) for thread-level parallelism on the CPU) "Kokkos::Compat::KokkosCudaWrapperNode": use Kokkos::Cuda execution space (use NVIDIA's CUDA programming model for thread-level parallelism on the CPU) You must use the above strings with the 'KokkosClassic_DefaultNode' CMake option. If you choose (unwisely, in many cases) to specify the Node template parameter directly in your code, you may use those names. Alternately, you may let the Kokkos execution space determine the Node type, by using the templated class Kokkos::Compat::KokkosDeviceWrapperNode. This class is templated on the Kokkos execution space. The above four types are typedefs to their corresponding specializations of KokkosDeviceWrapperNode. For example, KokkosSerialWrapperNode is a typedef of KokkosDeviceWrapperNode. This may be useful if your code already makes use of Kokkos execution spaces. - Removed (deprecated classes) Tpetra::VbrMatrix, Tpetra::BlockMap, Tpetra::BlockCrsGraph, and Tpetra::BlockMultiVector. All these classes relate to VBR (variable-block-size block sparse matrix) functionality. We may reimplement that at some point, but for now it's going away. - Removed (deprecated class) Tpetra::HybridPlatform Teuchos - Fixed Teuchos::Ptr::operator=() to catch dangling references (6 April 2015) ############################################################################### # # # Trilinos Release 11.14 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 11.14 general release contains 55 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, MueLu, NOX, Optika, OptiPack, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. Muelu - Support for Amesos2 native serial direct solver "Basker". - ML parameters can be used through MueLu::CreateEpetraPreconditioner and MueLu::CreateTpetraPreconditioner interfaces - Several bug fixes: 6256: ML parameter "coarse: type" does not work in MueLu::MLParameterListInterpreter 6255: Multiple issues in MueLu::MLParameterListInterpreter - Explicit template instantiation (ETI) changes The new version of MueLu uses Tpetra macros for specifying the desired template instantiations values (scalars, local ordinals, global ordinals and note types). As such, Tpetra instantiation configure options provide the necessary MueLu instantiations. For instance, instead of the previous option -D MueLu_INST_DOUBLE_INT_LONGLONGINT=ON a user should write -D Tpetra_INST_INT_LONG_LONG See Tpetra documentation for a full set of options. - New reuse feature [EXPERIMENTAL] MueLu introduced a new experimental reuse feature. A user may specify partial preservation of a multigrid hierarchy through the "reuse: type" option. Few variants have been implemented: - "none" No reuse, the preconditioner is constructed from scratch - "emin" Reuse old prolongator as an initial guess to energy minimization, and reuse the prolongator pattern. - "RP" Reuse smoothed prolongator and restrictor. Smoothers and coarse grid operators are recomputed. - "RAP" Recompute only the finest level smoother. - "full" Reuse full hierarchy, no changes. The current user interface is as follows: // User constructs a hierarchy for the first time Teuchos::RCP > H = MueLu::CreateTpetraPreconditioner(A0, xmlFileName); ... // User reuses existing hierarchy for consequent steps MueLu::ReuseTpetraPreconditioner(A1, *H); - Support for user-provided data [EXPERIMENTAL] New release of MueLu allows user to provide the data for the first few levels of the multigrid Hierarchy, while allowing MueLu to construct remaining levels. At the minimum, user needs to provide the data for fine-level operator A, prolongation operator (P), restriction operator (R) and coarse-level operator (Ac). These operator are required to derive from Xpetra::Operator class. This scenario is driven through a ParameterList interface (see muelu/example/advanced/levelwrap for some use cases). Tpetra - Public release of "Kokkos refactor" version of Tpetra The "Kokkos refactor" version of Tpetra is a new implementation of Tpetra. It is based on the new Kokkos programming model in the KokkosCore subpackage. It coexists with the "classic" version of Tpetra, which has been DEPRECATED and will be removed entirely in the 12.0 major release of Trilinos. Thus, the Kokkos refactor version will become the /only/ version of Tpetra at that time. The Kokkos refactor version of Tpetra maintains mostly backwards compatibility [SEE NOTE BELOW] with the classic version's interface. Its interface will continue to evolve. For this first public release, we have prioritized backwards compatibility over interface innovation. The implementation of the Kokkos refactor version of Tpetra currently lives in tpetra/core/src/kokkos_refactor. It works by partial specialization on the 'Node' template parameter, and by a final 'bool' template parameter (which users must NEVER SPECIFY EXPLICITLY). The "classic" version of Tpetra uses the old ("classic") Node types that live in the KokkosClassic namespace. All of the classic Node types have been DEPRECATED, which is how users can see that classic Tpetra has been deprecated. If you wish to disable the Kokkos refactor version of Tpetra, set the Tpetra_ENABLE_Kokkos_Refactor CMake option to OFF. Please note that this will result in a large number of warnings about deprecated classes. This CMake option will go away in the 12.0 release. - Note on backwards compatibility of Tpetra interface In the new version of Tpetra, MultiVector and Vector implement /view semantics/. That is, the one-argument copy constructor and the assignment operator (operator=) perform shallow copies. (By default, in the classic version of Tpetra, they did deep copies.) For deep copies, use one of the following: - Two-argument "copy constructor" with Teuchos::Copy as the second argument (to create a new MultiVector or Vector which is a deep copy of an existing one) - Tpetra::deep_copy (works like Kokkos::deep_copy) - What if I have trouble building with Scalar=std::complex? The new version of Tpetra should be able to build with Scalar = std::complex or std::complex. If you have trouble building, you may disable explicit template instantiation (ETI) and tests for those Scalar types, using the following CMake options: Tpetra_INST_COMPLEX_FLOAT:BOOL=OFF Tpetra_INST_COMPLEX_DOUBLE:BOOL=OFF - Accessing and changing the default Node type Tpetra classes have a template parameter, "Node", which determines what thread-level parallel programming model Tpetra will use. This corresponds directly to the "execution space" concept in Kokkos. Tpetra classes have a default Node type. Users do NOT need to specify this explicitly. I cannot emphasize this enough: IF YOU ONLY EVER USE THE DEFAULT VALUES OF TEMPLATE PARAMETERS, DO NOT SPECIFY THEM EXPLICITLY. If you need to refer to the default values of template parameters, ask Tpetra classes. For example, 'Tpetra::Map<>::node_type' is the default Node type. Tpetra pays attention to Kokkos' build configuration when determining the default Node type. For example, it will not use a disabled execution space. If you do not like the default Node type, but you only ever use one Node type in your application, you should change the default Node type at Trilinos configure time. You may do this by setting the 'KokkosClassic_DefaultNode' CMake option. Here is a list of reasonable values: "Kokkos::Compat::KokkosSerialWrapperNode": use Kokkos::Serial execution space (execute in a single thread on the CPU) "Kokkos::Compat::KokkosOpenMPWrapperNode": use Kokkos::OpenMP execution space (use OpenMP for thread-level parallelism on the CPU) "Kokkos::Compat::KokkosThreadsWrapperNode": use Kokkos::Threads execution space (use Pthreads (the POSIX Threads library) for thread-level parallelism on the CPU) "Kokkos::Compat::KokkosCudaWrapperNode": use Kokkos::Cuda execution space (use NVIDIA's CUDA programming model for thread-level parallelism on the CPU) You must use the above strings with the 'KokkosClassic_DefaultNode' CMake option. If you choose (unwisely, in many cases) to specify the Node template parameter directly in your code, you may use those names. Alternately, you may let the Kokkos execution space determine the Node type, by using the templated class Kokkos::Compat::KokkosDeviceWrapperNode. This class is templated on the Kokkos execution space. The above four types are typedefs to their corresponding specializations of KokkosDeviceWrapperNode. For example, KokkosSerialWrapperNode is a typedef of KokkosDeviceWrapperNode. This may be useful if your code already makes use of Kokkos execution spaces. - Changes to subpackages Tpetra is now divided into subpackages. What was formerly just "Tpetra" is now "TpetraCore". Other subpackages of Kokkos have moved, some into Teuchos and some into Tpetra. Those subpackages have changed from Experimental (EX) to Primary Tested (PT), so that they build by default if Tpetra is enabled. The most important change is that Tpetra now has a required dependency on the Kokkos programming model. See below. If your application links against Trilinos using either the Makefile.export.* system or the CMake FIND_PACKAGE(Trilinos ...) system, you do not need to worry about this. Just enable Tpetra and let Trilinos' build system handle the rest. - New required dependency on Kokkos Tpetra now has a required dependency on the Kokkos programming model. In particular, TpetraCore (see above) has required dependencies on the KokkosCore, KokkosContainers, and KokkosAlgorithms subpackages of Kokkos. This means that Tpetra is now subject to Kokkos' build requirements. C++11 support is still optional in this release, but future releases will require C++11 support. Please refer to Kokkos' documentation for more details. - Deprecated variable-block-size classes (like VbrMatrix). We have deprecated the following classes in the Tpetra namespace: - BlockCrsGraph - BlockMap - BlockMultiVector (NOT Tpetra::Experimental::BlockMultiVector) - VbrMatrix These classes relate to "variable-block-size" vectors and matrices. Tpetra::BlockMultiVector (NOT the same as Tpetra::Experimental::BlockMultiVector) implements a variable-block-size block analogue of MultiVector. Each row of a MultiVector corresponds to a single degree of freedom; each block row of a BlockMultiVector corresponds to any number of degrees of freedom. "Variable block size" means that different block rows may have different numbers of degrees of freedom. An instance of Tpetra::BlockMap represents the block (row) Map of a BlockMultiVector. Tpetra::VbrMatrix implements a variable-block-size block sparse matrix that corresponds to BlockMultiVector. Each (block) entry of a VbrMatrix is it own dense matrix. These dense matrices are not distributed; they are locally stored and generally "small" (think "fits in cache"). An instance of Tpetra::BlockCrsGraph represents the block graph of a VbrMatrix. Here are the reasons why we are deprecating these classes: - Their interfaces as well as their implementations need a significant redesign for MPI+X, e.g., for efficient use of multiple levels of parallelism. - They are poorly exercised, even in comparison to their Epetra equivalents. - They have poor test coverage, and have outstanding known bugs: see e.g., Bug 6039. - Most users don't need a fully general VBR [1]. - We would prefer to name the VBR classes consistently, both to emphasize the V (variable) part and to distinguish them from the new constant-block-size classes. [1] Many users' block matrices have blocks which are all the same size. They would get best performance by using the new constant-block-size classes that currently live in the Tpetra::Experimental namespace. Others usually only have a small number of different block sizes per matrix (e.g., 3 degrees of freedom per interior mesh point; 2 for boundary mesh points). The latter users could get much better performance by a data structure that represents the sparse matrix as a sum of constant-block-size matrices. Zoltan2 - The PartitioningSolution class's interface has changed. - methods getPartList and getProcList have been renamed to getPartListView and getProcListView to emphasize that a view, not a copy, is being returned. - method getPartListView now returns the part identifiers in the same order that the local data was provided. The user's localData[i] is assigned to getPartListView()[i]. Conversions from global identifiers from PartitioningSolution::getIdList() to local identifiers are no longer needed. - methods getIdList and getLocalNumberOfIds have been removed. - method convertSolutionToImportList has been removed and replaced by the helper function getImportList in Zoltan2_PartitioningHelpers.hpp. - pointAssign and boxAssign methods have been added for some geometric partitioners. Support is provided through MultiJagged (MJ) partitioning. pointAssign returns a part number that contains a given geometric point. boxAssign returns all parts that overlap a given geometric box. - New graph coloring options: - The parameter color_choice can be used to obtain a more balanced coloring. Valid values are FirstFit, Random, RandomFast, and LeastUsed. - New partitioning options: - Scotch interface updated to Scotch v6 or later (Tested against v6.0.3.) - Interface to ParMETIS v4 or later added. (Tested against v4.0.3.) - Miscellaneous: - Parameter "rectilinear_blocks" has been renamed "rectilinear". ############################################################################### # # # Trilinos Release 11.12 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 11.12 general release contains 55 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, MueLu, NOX, Optika, OptiPack, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. Framework Release Notes: - Changed minimum version of CMake from 2.7 to 2.8.11. MueLu Trilinos 11.12 is the initial release of MueLu. MueLu is an extensible multigrid library that is part of the Trilinos project. MueLu works with Epetra (32- and 64-bit versions) and Tpetra matrix types. The library is written in C++ and allows for different ordinal (index) and scalar types. MueLu is designed to be efficient on many different computer architectures, from workstations to supercomputers. While it is MPI based, MueLu is relies on the "MPI+X" principle, where "X" can be threading or CUDA. MueLu's software design allows for the rapid introduction of new multigrid algorithms. MueLu provides a number of different multigrid algorithms: - smoothed aggregation algebraic multigrid (AMG), appropriate for Poisson-like and elasticity problems - Petrov-Galerkin aggregation AMG for convection-diffusion problems - aggregation-based AMG for problems arising from the eddy current formulation of Maxwell's equations A PDF user's guide is located in muelu/doc/UsersGuide. To compile it, simply run "make". PyTrilinos - General * Got rid of NestedEpetra paradigm and now use relative imports to address the problem that NestedEpetra wass supposed to solve. * Changed build system for docstrings. The docstrings are no longer stored in the repository. If the user wants docstrings, then doxygen needs to be installed. Docstrings are built during the configuration phase. * Fixed warnings due to Epetra 32/64 bit handling * Added mpi4py support. Specifically, the Eptra_MpiComm constructors and Teuchos::MpiComm<> constructors can now take MPI sub-communicators, provided by mpi4py.MPI.Comm class. Ignored if mpi4py is not found. * Updated Developers Guide - Teuchos module * Support for the Teuchos::DataAccess enumeration. This enables certain Tpetra and Domi constructors * Add Teuchos::Arrays of int, long, float and double, as valid types for PyTrilinos ParameterLists - DistArray Protocol * Added support for the DistArray Protocol. This is preliminary and unfortunatley, does not provide any functionality with this release. - LOCA module * Re-instated the LOCA wrappers. These are still experimentaland require SWIG 3.0.0 and Python 2.5. * Re-introduction of the LOCA interface required the introduction of relative imports, which require Python 2.5 or higher. - Isorropia module * Refactor of Isorropia directory structure. This should not affect users. Tpetra - Kokkos refactor version of Tpetra The "Kokkos refactor" version of Tpetra is the new version of Tpetra, based on the new Kokkos programming model in the KokkosCore subpackage. It coexists with the "classic" version of Tpetra, which is currently the default version. We plan to deprecate the "classic" version of Tpetra in the 11.14 minor release in January, and to remove it entirely in the 12.0 major release. Thus, the "Kokkos refactor" version of Tpetra will become the /only/ version of Tpetra at that time. The implementation of the Kokkos refactor version of Tpetra currently lives in src/kokkos_refactor. It works by partial specialization on the Node template parameter. If you would like to enable this version of Tpetra, here is a suggested set of CMake options: # Enable OpenMP, and enable Kokkos' OpenMP backend -D Trilinos_ENABLE_OpenMP:BOOL=ON # Set Tpetra's default Node type to use new Kokkos with OpenMP. # You could also use KokkosThreadsWrapperNode or even # KokkosSerialWrapperNode here. -D KokkosClassic_DefaultNode:STRING="Kokkos::Compat::KokkosOpenMPWrapperNode" # Enable the Kokkos refactor version of Tpetra. -D Tpetra_ENABLE_Kokkos_Refactor:BOOL=ON In a debug build, you might like to enable Kokkos' run-time bounds checking. Here's how you do that. These are _optional_ parameters and their default values are both OFF (not enabled). -D Kokkos_ENABLE_BOUNDS_CHECK:BOOL=ON -D Kokkos_ENABLE_DEBUG:BOOL=ON The following options may reduce build times if ETI is enabled: # Disable KokkosClassic::OpenMPNode -D KokkosClassic_ENABLE_OpenMP:BOOL=OFF # Disable KokkosClassic::TPINode -D KokkosClassic_ENABLE_ThreadPool:BOOL=OFF # Shut off Kokkos' Pthreads back-end in favor of OpenMP -D Kokkos_ENABLE_THREADS:BOOL=OFF You must also enable the following subpackages explicitly, since they are not Primary Tested at the moment: - KokkosCore - KokkosCompat - KokkosContainers - KokkosLinAlg - KokkosAlgorithms - KokkosMpiComm If Tpetra_ENABLE_Kokkos_Refactor is ON but any of those subpackages are not enabled, CMake will stop with an error message that tells you what subpackages to enable. If you would like to build with the above subpackages enabled, but would /not/ like to build Tpetra with any of the new Kokkos Nodes, you may try setting the CMake KokkosClassic_ENABLE_KokkosCompat to OFF. This works for me as of 07 Oct 2014, but I do not recommend it, and it is not supported. Fun fact: there are three relevant combinations of (new Kokkos enabled?, Kokkos refactor enabled?), and we test them all! You can use the new Kokkos Node types with "classic" Tpetra, or you can use them with "Kokkos refactor" Tpetra. Most Tpetra tests exercise all enabled Node types, or just use the default Node type. Ifpack2 tests only use the default Node type currently. That's why the above build configuration changes the default Node type. That way, all packages that depend on Tpetra will use the Kokkos refactor version of Tpetra in /their/ tests by default. - Full set of default values of template parameters Usability improvement! Most Tpetra classes now come with a full set of default values of template parameters. In many cases, you need no longer specify _any_ template parameters' values, if you only intend to use their defaults. For example, you may now write the following: // All default template parameters! Tpetra::Map<> map (...); // No "typename" because Map<> is a concrete type. typedef Tpetra::Map<>::local_ordinal_type LO; typedef Tpetra::Map<>::global_ordinal_type GO; for (LO i_lcl = map.getMinLocalIndex (); i_lcl <= map.getMaxLocalIndex (); ++i_lcl) { const GO i_gbl = map.getGlobalElement (i_lcl); // ... } // All default template parameters! // Scalar defaults to double. // LocalOrdinal, GlobalOrdinal, and Node default // to the same values as those of Map<> above. Tpetra::MultiVector<> X (...); Also, if you need to specify (say) GlobalOrdinal explicitly, you don't have to specify Node explicitly. For example: // Don't need to specify Node; it takes its default value. Tpetra::Map map (...); Tpetra::MultiVector X (...); You may specify the default value of Node at Trilinos configure time (that is, when running CMake). The current default is KokkosClassic::SerialNode (no threads; MPI only). This will change, but it will always have a reasonable value for conventional multicore processors. Please, _please_ prefer default values of template parameters! This will make your code shorter, allow more flexibility at configure time, and might even make builds a bit faster. All Tpetra classes come with public typedefs, so you can pick up scalar_type (if applicable), local_ordinal_type, global_ordinal_type, and node_type from Tpetra directly, rather than specifying them explicitly. - Removed the LocalMatOps template parameter CrsGraph, CrsMatrix, VbrMatrix, and other classes used to have a LocalMatOps template parameter. This was the fourth template parameter of CrsGraph and the fifth template parameter of CrsMatrix. It was always optional. Chris Baker intended it as an extension point for users or third-party vendors to insert their own sparse matrix-vector multiply or triangular solve routines. However, no one ever used it for this purpose as far as we know. When it started to hinder the Kokkos refactor effort (see release notes for Trilinos 11.10 below), we removed it. This should speed up compilation times. Lesson: It's always easier to _add_ a template parameter (at the end, if it's optional) than it is to remove one. Getting rid of LocalMatOps does amount to a backwards incompatible interface change. However, we deemed it a harmless change, for the following reasons: 1. LocalMatOps has a reasonable default value. 2. As far as I know, no one other than Chris Baker and myself ever wrote or used alternate implementations of LocalMatOps. 3. Trilinos packages or applications which bothered to specify LocalMatOps never used anything other than the default value. Thus, it never even crossed my mind that applications would bother to specify this thing. Unfortunately, some applications may still LocalMatOps explicitly. This typedef is unnecessary. You do not need to specify this template parameter. The default value was always perfectly fine and has been for years. ############################################################################### # # # Trilinos Release 11.10 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 11.10 general release contains 54 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, NOX, Optika, OptiPack, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. Anasazi - Improved examples and added more explanatory comments. Thanks to Alicia Klinvex (Purdue) for review and suggestions. Ifpack2 - Fixed bug in ReorderFilter (related to Bug 6117). ReorderFilter was computing the number of entries for the wrong row, which caused temporaries (either in Ifpack2::ReorderFilter or in MueLu) to be allocated with the wrong size. This may be related to Bug 6117. - LocalFilter::apply now checks whether X aliases Y. - Performance improvements to apply() of BlockRelaxation, LocalFilter, and Relaxation (10-11 Apr 2014). STK - New STK introduced. A new version of STK has been introduced including a number of performance improvements. The API of STK has changed from the previous version such that it is unlikely that codes that used STK will work without modification. The old STK is still available for use, but will be removed in a future release. The old STK is now in a new namespace "stk_classic" which will also require some changes to continue to use. There is a script that can be used to help. The script can be found in packages/stk/stk_classic/conversion_scripts/stk_to_stk_classic. Use of the script is discussed below. STK and STKClassic share many header names so it is not advisable to enable both in a single build of Trilinos. Linking to both STK and STKClassic at the same time is not supported. - The new STK uses subpackages to better support inter-STK dependencies. - New TPL dependencies. The new STK now depends on Boost 1.54.0 and has been tested with boost 1.55.0. A subset of Boost libraries are required by STK instead of just Boost headers. This requires using the Trilinos TPL named BoostLib, rather than the Boost TPL. In addition the subpackage STKSearchUtil has a required dependency on GLM. Currently only GLM version 0.9.4.3 has been tested. - the old STK is now a subpackage of STK called STKClassic. This version is largely the same as the old STK, however, there are a few important differences. * The namespace has been changed from stk to stk_classic. * The package name STK is no longer used to enable this version. Instead STKClassic should be used. If you only want to use the old STK it is advisable to enable only STKClassic with the varibale Trilinos_ENABLE_STKClassic and not any part of the new STK when configuring Trilinos. This will ensure that there is no opportunity to inadvertantly link against any part of the new STK. - Old STK moved to new namespace stk_classic. The new STK retains the use of the namespace STK. To avoid potential conflicts STKClassic has been moved to the namespace stk_classic. There is a script provided to convert stk namespace to stk_classic. To use the script just cd into a directory containing files you'd like to update and run packages/stk/stk_classic/conversion_script/stk_to_stk_classic (do not copy the script to the directory you want to modify). The script will update any files in the current directory and any subdirectories of the directory you are modifying. * You should not copy the script to the directory you are modifying. * There is a possibility that some instances of the old namespace will be not be fixed correctly and may need some manual attention. However, the script should catch most uses of the stk namespace. * If you had any namespaces like stk they will be updated as well, however it is more likely that not all instances of such namespaces will not be updated properly. - STK Percept and Rebalance have been removed. The Percept and Rebalance capabilities have been moved out of STK. The old versions are still available in STKClassic, but the new version will no longer support those capabilities. There will be a new Trilinos package that will contain the features from Percept and Rebalance in a future Trilinos release. Tpetra - Continued work on the Kokkos refactor version of Tpetra We plan to replace the current "classic" version of Tpetra with a "Kokkos refactor" version, that uses new Kokkos for thread-parallel computational kernels and data structures. The classic version continues to be the default, but the Kokkos refactor version is available via partial specialization on the Node type. You may try out the Kokkos refactor version of Tpetra by doing the following: 1. Enable the KokkosCore, KokkosCompat, KokkosContainers, KokkosLinAlg, and KokkosMpiComm (which does not require MPI) subpackages. 2. Set the CMake option Tpetra_ENABLE_Kokkos_Refactor to ON. 3. Include either Kokkos_DefaultNode.hpp or KokkosCompat_ClassicNodeAPI_Wrapper.hpp, if they are not already included by the relevant Tpetra header files. 4. Use the appropriate Node type in the Kokkos::Compat namespace: KokkosCudaWrapperNode with the Kokkos::Cuda device, KokkosOpenMPWrapperNode with the Kokkos::OpenMP device, KokkosThreadsWrapperNode with the Kokkos::Threads device, or KokkosSerialWrapperNode with the Kokkos::SerialNode. We plan to deprecate the KokkosClassic namespace and its contents in the next minor release (scheduled for October), with the goal of removing it entirely by the next major release. - CrsMatrix: replaceGlobalValues, sumIntoGlobalValues, replaceLocalValues, and sumIntoLocalValues now return error codes, instead of throwing on invalid row or column indices This will facilitate thread parallelism, and porting Tpetra to use new Kokkos. It also partially addresses Bug 4918 (of which Bug 5806 is a duplicate). The error code tells users both whether the row index was valid, and the number of valid column indices. If the return value equals the number of input column indices, the method succeeded. - CrsGraph, CrsMatrix: getLocalRowCopy now does not throw if the input row index is invalid; instead, it sets numEntries=0 and returns. This will facilitate thread parallelism, and porting Tpetra to use new Kokkos. It is also semantically consistent: if the calling process doesn't own that row, then the calling process owns zero entries in that row, so it's correct to set numEntries=0 and return without throwing. - New function: Tpetra::Details::makeOptimizedColMap - MultiVector and Map now have full default template parameters Now, if you write Tpetra::MultiVector<> (empty angle brackets required), that sets Scalar=double. If you write Tpetra::Map<> (again, empty angle brackets required), that sets LocalOrdinal=int. Tpetra includes a unit test for this feature. - New classes in Tpetra::Experimental namespace: BlockCrsMatrix, BlockMultiVector, and BlockVector (constant-size small blocks, with block size determined at run time) - Fixes for Bug 6139 and 6127 - Tpetra::MatrixMarket::{writeMap, writeMapFile} can now handle an overlapping Map. - Import and Export now inherit from a common base class (useful for implementing communication methods) - Refactored and improved examples - CrsMatrix: fillComplete with a const graph now uses the graph's domain and range Maps (thus fixing an unnumbered bug, in which CrsMatrix was instead using the row Map for both) - Map now implements view semantics "View semantics" means that Map's copy constructor and assignment operator (operator=) do a shallow copy, and that empty construction is possible. The new test for isOneToOne (see below) is the first Tpetra test that assumes view semantics of Map. - Map now has an isOneToOne predicate. isOneToOne is a collective which tests whether the Map is one to one (that is, whether every global index is owned by at most one process in the Map's communicator). ############################################################################### # # # Trilinos Release 11.8 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 11.8 general release contains 54 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, NOX, Optika, OptiPack, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. Amesos2 - Amesos2's adapter for Tpetra now caches Import and Export objects, so that it doesn't have to recreate them on every solve. This fixes Bug 6011 and should improve performance of solves. Belos - More Belos solvers now work with complex Scalar type; more now compile for complex Scalar type. This includes GCRODR, LSQR, RCG, and BlockGCRODR. Not all of these solvers are enabled by default; some are still marked "experimental." Galeri - Removed some instances of "using namespace std;" User code that inadvertantly depended on symbols in std being in the global namespace may now have errors. Ifpack - Removed some instances of "using namespace std;" User code that inadvertantly depended on symbols in std being in the global namespace may now have errors. Ifpack2 - RILUK and Krylov may now be used as subdomain solvers in AdditiveSchwarz. - We made many improvements to RILUK and LocalFilter. This will move towards fixes for a number of Ifpack2 bugs, such as 5992 and 5987. Teuchos - New mode for TimeMonitor::summarize (27 Mar 2014) We added a new mode of calculating global statistics to TimeMonitor::summarize. The new mode ignores contributions from processes that either do not have a particular timer, or have a hard zero for a timer. This mode is off by default, meaning that the default summarize behavior is unchanged. This new mode is useful in cases where not all processes have the same timers and/or some timers are zero. This can arise when multiple MPI communicators are in play. A single call to summarize using a global communicator yields reasonable statistics for all timers. The cost is an additional MPI_Allreduce. Consider this example: - proc 0 has timers T1=1.0, T2=0.5 - proc 1 has timers T2=1.0, T3=1.0 - proc 2 has timers T2=2.0, T3=0.5 where MCW is a communicator containing 0,1,2, and MC12 is a communicator containing 1,2. Calling TimeMonitor::summarize(MCW, std::cout, false, true, false, Teuchos::Union) yields - min(T1)=0.0, avg(T1)=0.33, max(T1)=1.0 - min(T2)=0.5, avg(T2)=1.17, max(T2)=2.0 - min(T3)=0.0, avg(T3)=0.5, max(T3)=1.0 Calling TimeMonitor::summarize(MC12, std::cout, false, true, false, Teuchos::Union) yields - min(T1)=0.0, avg(T1)=0.0, max(T1)=0.0 - min(T2)=1.0, avg(T2)=1.5, max(T2)=2.0 - min(T3)=0.5, avg(T3)=0.75, max(T3)=1.0 While each is technically correct for the communicators given, neither by itself gives information that one might want, namely, averages over just the processes that have a timer and mins over the nonzero times. With the new mode, calling TimeMonitor::summarize(MCW, std::cout, false, true, false, Teuchos::Union, "", true) yields - min(T1)=1.0, avg(T1)=1.0, max(T1)=1.0 - min(T2)=0.5, avg(T2)=1.17, max(T2)=2.0 - min(T3)=0.5, avg(T3)=0.75, max(T3)=1.0 - Ptr: Added is_null() method to match RCP (23 Mar 2014) - MpiComm: Improved duplicate(), split(), and createSubcommunicator() (27 Feb 2014). These methods now do MPI_Comm_dup, MPI_Comm_split, resp. MPI_Comm_create, as one would expect. They also do one less MPI_Bcast than before. This is because messages in the new MPI_Comm (which MPI_Comm_dup, MPI_Comm_split, and MPI_Comm_create all create) cannot collide with messages in the old MPI_Comm, so there is no need for a broadcast to agree on a common tag. Tpetra - BACKWARDS IMCOMPATIBLE CHANGE: MultiVector and Vector now implement view semantics. This means that the copy constructor and assignment operator (operator=) of both classes now do shallow copies. This change will support gradual porting to the new ("Kokkos Refactor") version of Tpetra. We have propagated this change to other Trilinos packages that use Tpetra. Please use the new createCopy nonmember function to get a new instance of (Multi)Vector that is a deep copy of an existing (Multi)Vector. Also, please use the new nonmember function deep_copy to do a deep copy between two existing compatible (Multi)Vector instances. - Kokkos Refactor updates. Development continues on the Kokkos Refactor version of Tpetra. This is a partial specialization of some Tpetra classes that uses the new Kokkos programming model. We plan eventually to switch to this version of Tpetra and deprecate the old version. This release adds a Kokkos Refactor version of Map. Its GID->LID and LID->GID conversion methods are now thread-safe and thread-scalable on the host. It also has a "device object" that you can use on CUDA devices. The Kokkos Refactor version of MultiVector now implements "dual view" semantics. This means that the Tpetra interface lets users mark either host or device as modified, and synchronize between host and device on demand, if necessary. - Sparse matrix-matrix multiply performance improvements. This release includes many performance improvements to Tpetra's sparse matrix-matrix multiply routine, and other supporting routines, such as explicit transpose, and {im,ex}portAndFillComplete. Tpetra now has a sparse matrix-matrix multiply variant for implementing Jacobi smoothing of matrices. This is useful for algebraic multigrid. - CrsMatrix: "Preserve Local Graph" defaults true (17 Mar 2014) In CrsMatrix, the undocumented parameter "Preserve Local Graph" now defaults to true. This makes the following scenario work by default: 1. Create a CrsMatrix A that creates and owns its graph (i.e., don't use the constructor that takes an RCP or a local graph) 2. Set an entry in the matrix A, and call fillComplete on it 3. Create a CrsMatrix B using A's graph (obtained via A.getCrsGraph()), so that B has a const (a.k.a. "static") graph 4. Change a value in B (you can't change its structure), and call fillComplete on B Before this commit, the above scenario didn't work by default. This is because A's first fillComplete call would call fillLocalGraphAndMatrix, which by default sets the local graph to null. As a result, from that point, A.getCrsGraph()->getLocalGraph() returns null, which makes B's fillComplete throw an exception. The only way to make this scenario work was to set A's "Preserve Local Graph" parameter to true. (It defaulted to false.) The idea behind this nonintuitive behavior was for the local sparse ops object to own all the data. This might make sense if it is a third-party library that takes CSR's three arrays and copies them into its own storage format. In that case, it might be a good idea to free the original three CSR arrays, in order to avoid duplicate storage. However, resumeFill never had a way to get that data back out of the local sparse ops object. Rather than try to implement that, it's easier just to make "Preserve Local Graph" default to true. The possible data duplication mentioned in the previous paragraph can never happen with the Kokkos Refactor version of CrsMatrix, since it insists on controlling the matrix representation itself. This makes the code shorter and easier to read, and also ensures efficient fill. That will in turn make the option unnecessary. - Many bug fixes. - The most important bug fixed is Bug 6069, an error in Distributor, which would only manifest on MPICH. This bug fix alone is enough reason to upgrade to Trilinos 11.8. PyTrilinos - Various changes to improve the stability and robustness of the build system. Addresses some instability in PyTrilinos introduced with new 64 bit capabilities in Epetra. Some compilation warnings eliminated. SWIG version checks added. Zoltan - Revised Scotch TPL specification in Trilinos' CMake environment to link with all libraries needed by Scotch v6. - Fixed bug in interface to ParMETIS v4 when multiple vertex weights are used. - Fixed bug in interface to Scotch when some processor has no vertices. Zoltan2 - Removed some instances of "using namespace std;" User code that inadvertantly depended on symbols in std being in the global namespace may now have errors. - Simplified input Adapter classes for easier implementation by applications. (This change may break backward compatibility for some users.) - Some parameter names have changed or have been deleted: pqParts --> mj_parts parallel_part_calculation_count --> mj_concurrent_part_count migration_check_option --> mj_migration_option migration_imbalance_cut_off --> mj_minimum_migration_imbalance keep_part_boxes --> mj_keep_part_boxes recursion_depth --> mj_recursion_depth migration_processor_assignment_type deleted. migration_all_to_all_type deleted. migration_doMigration_type deleted. - Added ability to associate coordinates with matrix rows and graph vertices through the MatrixAdapter and GraphAdapter. - Improved the performance and readability of Multijagged Partitioning. - Added weights to graph partitioning via Scotch. - Changed weight specifications in input Adapters; users can no longer provide NULL weight arrays for uniform weights. - Added more robuts testing. - Fixed several bugs. ############################################################################### # # # Trilinos Release 11.6 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 11.6 general release contains 54 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, NOX, Optika, OptiPack, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. Framework Release Notes: - Changed behavior of Trilinos_ENABLE_=ON to enable all subpackages for that package including in propogating forward dependencies. See updated BuildQuickRef.* document. Amesos2 - Added experimental support for Cholmod, a sparse Cholesky solver. Epetra - Removed a few "using std::" statements from Epetra headers. These were for std::{string, istream, ostream, cerr, cout, endl, flush}. User code that inadvertently relied on such names being available in global namespace could see errors. They should explicitly use std::name or place the appropriate "using std::name;" statement in their code. Ifpack2 - AdditiveSchwarz interface changes AdditiveSchwarz implements additive Schwarz domain decomposition. The class also manages and invokes the solver for each subdomain. That solver must implement Ifpack2::Preconditioner. We made two changes to AdditiveSchwarz: 1. Subdomain solver type is now determined entirely at run time 2. Second template parameter (LocalInverseType) is deprecated These changes are related to each other. It used to be that users would specify the type of the subdomain solver as the second template parameter of AdditiveSchwarz, LocalInverseType. The value of LocalInverseType had to be a concrete subclass of Preconditioner. This is no longer the case. Users now may and should omit AdditiveSchwarz's second template parameter. More importantly, they may now specify the subdomain solver's type at run time. They may do so either as a run-time parameter in the input ParameterList of AdditiveSchwarz, or by calling AdditiveSchwarz's setInnerPreconditioner() method. See AdditiveSchwarz's public class documentation for details. AdditiveSchwarz's second template parameter has a default value of Ifpack2::Preconditioner. For backwards compatibility, if users specify a known concrete subclass of Ifpack2::Preconditioner for LocalInverseType, AdditiveSchwarz will implement the previous behavior of creating a subdomain solver of that specific type. In the next major Trilinos release, we plan to remove AdditiveSchwarz's second template parameter entirely. Kokkos - Non-backwards compatible change: In the "Kokkos Classic" subpackage (everything in kokkos/classic), the "Kokkos" namespace has been changed to "KokkosClassic". This will facilitate coexistence of Kokkos Classic with both the new Kokkos programming model and the new Kokkos subpackages that depend on it. Coexistence will be necessary for our planned port of Tpetra to use new Kokkos instead of Kokkos Classic. Kokkos Classic will eventually be deprecated, and Tpetra (and downstream packages) will use new Kokkos instead. NOX - Added a Fixed-point Anderson Acceleration solver. Unit tests exist for Epetra and Thyra adapters. RTOp - Added better runtime support (not dependent on debug-mode builds) for printing the application of RTOps in parallel with the RTOpPack::SPMD_apply_op() functions. This makes parallel debugging much easier (for example, involving Thyra). Thyra - Refactored Thyra support software and Thyra/Epetra adapters to support zero-element processes for vector spaces and maps. Now Thyra::SpmdVectorSpaceBase subclass object can have zero elements on a process and have everything work as it should. The Thyra/Epetra and Thyra/Tpetra adapters should also be able to take Eptra and Tpetra Map objects that have zero elements on a process as well. For most clients and subclasses, these refactorings should maintain 100% perfect backward compatibility except now more use cases are supported than before. See the unit tests and updated class documentation for details. Tpetra - Gradual port to use (new) Kokkos Tpetra will migrate to use the new Kokkos programming model. The tpetra/src/kokkos_refactor directory contains a preview of this migration under development. This will include backwards-incompatible changes. For example, MultiVector and Vector will have view semantics, instead of their current container semantics. This means that their copy constructor and assignment operator (operator=) will make shallow copies, instead of deep copies. This will make Tpetra's semantics more consistent with those of Kokkos. In order to provide deep copies, all Tpetra objects will get the following: - createCopy() method: returns a deep copy of its *this argument - deep_copy() nonmember function: copies the contents of one MultiVector into the contents of another existing MultiVector. This works like deep_copy() for Kokkos::View objects. MultiVector already has both of these functions. Thus, in order to prepare for the backwards incompatible changes to Tpetra, users must find all uses of the copy constructor and assignment operator, and replace them with createCopy() resp. deep_copy(). This will affect at least the following packages which have generic adapters for Tpetra::MultiVector: - Amesos2 (MultiVecAdapter) - Anasazi (MultiVecTraits) - Belos (MultiVecTraits) - Xpetra (Xpetra::TpetraMultiVector) - Accepted non-backwards compatible change to KokkosClassic, in which that subpackage changed its namespace from Kokkos to KokkosClassic. ############################################################################### # # # Trilinos Release 11.4 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 11.4 general release contains 54 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, NOX, Optika, OptiPack, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. Framework Release Notes: - The following packages have been switched to BSD-compatible licenses: Didasko, Ifpack, Ifpack2, Moertel, Stokhos, Stratimikos ForTrilinos - This release includes 11 modules or classes of the Epetra package. - This package is still in its experimental stage and is only supported on AIX. - Sample configure script are provided in Trilinos/sampleScripts/aix-fortrilinos-serial and Trilinos/sampleScripts/aix-fortrilinos-mpif90 for serial and mpi builds respectively. - Because of the object-oriented features used, it requires a XL Fortran compiler v13.1. The source code can be compiled using the xlf compiler option. - Required compiler flags for Fortran include: -qfixed=72 -qxlines: deals with older Fortran source code in other Trilinos packages. These flags are used for mpi builds and must be specified in the configure script. -qxlf2003=polymorphic: allows for the use of polymorphism in the source code. -qxlf2003=autorealloc: allows the compiler to automatically reallocate the left hand side with the shape of the right hand side when using allocatable variables in an assignment. -qfree=f90: informs the compiler that the source code is free form and conforms to Fortran 90. These flags(-qfree=f90 -qxlf2003=polymorphic -qxlf2003=autorealloc) are hardcoded in Trilinos/packages/ForTrilinos/CMakeLists.txt - Required compiler flag for xlc++ include: -qrtti=all: this flag should be included in the configure script. - The project is primarily user-driven; so new interfaces are developed at the request of Trilinos users. Ifpack2 - Relaxation: Use precomputed offsets to extract diagonal As of this release, Tpetra::CrsMatrix has the ability to to precompute offsets of diagonal entries, and use them to accelerate extracting a copy of the diagonal. Relaxation now exploits this feature to speed up compute() (which extracts a copy of the diagonal of the input matrix). The optimization only occurs if the input matrix is a CrsMatrix (not just a RowMatrix) and if it has a const ("static") graph. The latter is necessary so that we know that the structure can't change between calls to compute(). (Otherwise we would have to recompute the offsets each time, which would be no more efficient than what it was doing before.) Kokkos - Non-backwards compatible change: Default Kokkos/Tpetra Node type is now Kokkos::SerialNode User expectation seems to be that the default behavior of Tpetra is MPI-only. These users are therefore experiencing unexpected performance when the default node is threaded, as is currently the case if any of the threading libraries (pthreads, TBB, OpenMP) are enabled. Therefore, after some discussion among Kokkos/Tpetra developers, it was decided to change the default Kokkos node (and therefore, the default node used by Tpetra objects) to Kokkos::SerialNode. This can be overridden at configure time by specifying the following option to CMake when configuring Trilinos: -D KokkosClassic_DefaultNode:STRING="node_type" where node_type is one of the official Kokkos nodes: Kokkos::SerialNode (current default) Kokkos::TBBNode Kokkos::TPINode Kokkos::OpenMPNode Mesquite - Added polygon support to allow reading and writing of vtk files containing polygons and smoothing of meshes containing polygons using the Laplacian smoother. - Rewrote ShapeImprover wrapper determine if mesh to be optimized is tangled or not. If tangled, wrapper now uses a non-barrier metric and if not tangled, a barrier metric is used. - Created a new directory structure underneath meshFiles/3D/vtk and meshFiles/2D/vtk that arranges the mesh files into subdirectories based on element type and whether they are tangled or untangled. - Created new class MeshDomainAssoc to formally associate a Mesh instance with a Domain instance to verify that the mesh and domain are compatible. - Productionized the NonGradient solver. - Added new classes TMetricBarrier and TMetricNonBarrier to TMetric class to provide a clear division between the barrier and non-barrier target metric classes. - Added new classes AWMetricBarrier and AWMetricNonBarrier to AWMetric class for same reason as the TMetric classes. - Added a new error code "BARRIER_VIOLATED" to the MsgError class that is issued when a barrier violation is encountered when using a barrier target metric class. - Added warning when MaxTemplate is used with any solver other than NonGradient. - Made a number of changes to the Quality Summary output to improve readability and provide additional information. PyTrilinos - Updated the NumPy interface to properly deal with deprecated code. If PyTrilinos if compiled an older NumPy, it still works, but if compiled against newer versions of NumPy, the deprecated code is avoided, as are the warnings. Teuchos - Added optional automatic global reductions of pass/fail to Teuchos Unit Test Harness: Prior to this feature addition, only the result on the root process of a parallel unit test would determine pass/fail, even if tests on other proesses failed. This makes it easier to write parallel unit tests and results in more robust test code. For a discussion, see Trilinos issue #5909. An example can be found in teuchos/comm/test/UnitTesting/UnitTestHarness_Parallel_UnitTests.cpp (see the CMakeLists.txt file for how that test is run). NOTE: By default, no global reductions of pass/fail are done as to maintain perfect backward compatibility. - Added new feature to TimeMonitor: You may now enable or disable a timer (instance of Time) by name. Disabled timers ignore start() and stop() calls; calling these methods on a disabled timer does not change its elapsed time or call count. Thus, TimeMonitor's constructor and destructor have no effect on disabled timers. However, the disabled timers still exist, and TimeMonitor's summarize() and report() class methods will print statistics for disabled timers (using their elapsed times and call counts while enabled). Enabling a timer does not reset its elapsed time or call count. This feature is useful if you want to time only certain invocations of a particular function that has an internal timer, without modifying the function's source code. For an example, see packages/teuchos/comm/test/Time/TimeMonitor_UnitTests.cpp, line 175 ("TimeMonitor, enableTimer" unit test). Thyra - Fixed explicit template instantation system in the generation of Thyra_XXX.hpp files to *not* include Thyra_XXX_def.hpp when explicit instantation is turned on. The refactoring of Thyra to use subpackages some time ago broke the generation of Thyra_XXX.hpp files in that they were always including Thyra_XXX_def.hpp files. That was bad because it increased compile time for client code and allowed other includes to get pulled in silently. Now client code that includes Thyra_XXX.hpp when explicit instantiation is turned on will will *not* get the include of Thyra_XXX_def.hpp. This might break some downstream client code that was not properly including the necessary header files and was accidentally getting them from the Thyra_XXX_def.hpp files that were being silently included. However, this technically does not break backward compatibility since client code should have been including the right headers all along. For example, when GCC cleaned up their standard C++ header files this required existing C++ code to add a bunch of missing includes that should have been there the whole time. Tpetra - Performance improvements to fillComplete (CrsGraph and CrsMatrix) - Performance improvements to Map's global-to-local index conversions - MPI performance optimizations Methods that perform communication between (MPI) processes do less communication than before. This should improve performance, especially for large process counts, of the following operations: - Creating a Map - Creating an Import or Export communication plan - Executing an Import or Export (e.g., in a distributed sparse matrix-vector multiply, or in global finite element assembly) - Calling fillComplete() on a CrsGraph or CrsMatrix - Restrict a Map's communicator to processes with nonzero elements, and apply the result to a distributed object Map now has two new methods. The first, removeEmptyProcesses(), returns a new Map with a new communicator, which contains only those processes which have a nonzero number of entries in the original Map. The second method, replaceCommWithSubset(), returns a new Map whose communicator is an arbitrary subset of processes of the original Map's communicator. Distributed objects (subclasses of DistObject) also have a new removeEmptyProcessesInPlace() method, for applying in place the new Map created by calling removeEmptyProcesses() on the original Map over which the object was distributed. These methods are especially useful for algebraic multigrid. At coarser levels of the multigrid hierarchy, it is helpful for performance to "rebalance" the matrices at those levels, so that a subset of processes share the elements. This leaves the remaining processes without any elements. Excluding them from the communicator reduces the cost of all-reduces and other communication operations necessary for creating the coarser levels of the hierarchy. - CrsMatrix: Native SOR and Gauss-Seidel kernels These kernels improve the performance of Ifpack2 and MueLu. Gauss-Seidel is a special case of SOR (Symmetric Over-Relaxation). See the documentation of Ifpack2::Relaxation for details on the algorithm, which is actually a "hybrid" of Jacobi between MPI processes, and SOR (or Gauss-Seidel) within an MPI process. The kernels also include the "symmetric" variant (forward and backward sweeps) of SOR and Gauss-Seidel. - CrsMatrix: Precompute and reuse offsets of diagonal entries The (existing) one-argument verison of CrsMatrix's getLocalDiagCopy() method requires the following operations per row: 1. Convert current local row index to global, using the row Map 2. Convert global index to local column index, using the column Map 3. Search the row for that local column index Precomputing the offsets of diagonal entries and reusing them skips all these steps. CrsMatrix has a new method getLocalDiagOffsets() to precompute the offsets, and a two-argument version of getLocalDiagCopy() that uses the precomputed offsets. The precomputed offsets are not meant to be used in any way other than to be given to the two-argument version of getLocalDiagCopy(). They must be recomputed whenever the structure of the sparse matrix changes (by calling insertGlobalValues() or insertLocalValues()) or is optimized (e.g., by calling fillComplete() for the first time). - CrsGraph,CrsMatrix: Added "No Nonlocal Changes" parameter to fillComplete() The fillComplete() method accepts an optional ParameterList which controls the behavior of fillComplete(), as opposed to behavior of the object in general. "No Nonlocal Changes" is a bool parameter which is false by default. Its value must be the same on all processes in the graph or matrix's communicator. If the parameter is true, the caller asserts that no entries were inserted in nonowned rows. This lets fillComplete() skip the global communication that checks whether any processes inserted any entries in nonowned rows. - Default Kokkos/Tpetra Node type is now Kokkos::SerialNode NOTE: This change breaks backwards compatibility. Users expect that Tpetra by default uses "MPI only" for parallelism, rather than "MPI plus threads." These users were therefore experiencing unexpected performance issues when the default Kokkos Node type is threaded, as was the case if Trilinos' support for any of the threading libraries (Pthreads, TBB, OpenMP) are enabled. Trilinos detects and enables support for Pthreads automatically on many platforms. Therefore, after some discussion among Kokkos and Tpetra developers, we decided to change the default Kokkos Node type (and therefore, the default Node used by Tpetra objects) to Kokkos::SerialNode. This can be overridden at configure time by specifying the following option to CMake when configuring Trilinos: -D KokkosClassic_DefaultNode:STRING="" where any of the official Kokkos Node types, such as the following: - Kokkos::SerialNode (current default) - Kokkos::TBBNode - Kokkos::TPINode - Kokkos::OpenMPNode ############################################################################### # # # Trilinos Release 11.2 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 11.2 general release contains 54 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, NOX, Optika, OptiPack, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra, Zoltan, Zoltan2. AztecOO - Added support for 64-bit global indices. They can be used if 64-bit based Epetra maps are used. Epetra - IndexBase argument for 64-bit maps is now a "long long". No change to 32-bit maps, where it remains an "int". NOX - Added example of user defined preconditioner with a JFNK forward operator to the thyra support. - Removed all usage of EpetraExt::ModelEvaluator in favor of a direct inhertance from the Thyra::ModelEvaluator. The EpetraExt::ModelEvaluator is being deprected. - Added support for the Thyra Group to accept user defined preconditioners and Jacobian operators. - Merged the object code for the library noxthyra into the main nox library to work around a circular dependency for the pseudo-transient solver. - Added a pseudo-transient solver based on Thyra objects. Still under development. PyTrilinos - General - Added STK as an optional dependency of PyTrilinos - Added Pliris as a supported package - Provide better compatibility with external MPI implementations. Specifically, if the user were to "import mpi4py" (for example) prior to importing Teuchos or Epetra, then the Teuchos or Epetra modules will not take responsibility for calling MPI_Finalize(). - Fixed some build errors - Epetra module - Priliminary support for Epetra64. Ultimately, I would like the default behavior to be using 64-bit methods without refering to 64-bit method names. - Added PyTrilnos.Epetra.FECrsMatrix InsertGlobalValues method that had been hidden by a %extend SWIG directive. - EpetraExt module - Gave names to EpetraExt template classes. Using the nameless versions had caused problems with newer versions of SWIG. This should get rid of the need for a patch distributed with Archlinux. - Added the EpetraExt::CrsMatrix_SubCopy class to PyTrilinos.EpetraExt. - NOX module - Improved NOX support, especially NOX.Epetra. This should be largely invisible to the user, but I used to have to always import NOX whether the user wanted it or not, due to nested namespace issues. These issues have been resolved now, and you only import NOX if you specifically request it. - Anasazi module - Added EpetraMultiVecAccessor base class. Anasazi added this base class, and now the PyTrilinos version supports it as well. TriUtils - Added support for 64-bit global indices. They can be used if 64-bit based Epetra maps are used or equivalent TriUtils functions with suffix "64" are called. ############################################################################### # # # Trilinos Release 11.0 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 11.0 general release contains 54 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, NOX, Optika, OptiPack, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, SEACAS, Shards, ShyLU*, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios, Triutils, Xpetra*, Zoltan, Zoltan2*. (* denotes package is being released externally as a part of Trilinos for the first time.) Framework Release Notes: Transitioning due to removal of deprecated code: --------------------------------------------------------------- With the update from Trilinos 10.12 to 11.0, several deprecated classes, function, macros, and files have been removed from the Trilinos 11.0 sources. If a client code was using these deprecated features and upgrades to 11.0, the client code will no longer build. To ease the transition of client code to Trilinos 11.0, the following procedure is recommended: 1) Get the release tarball for Trilinos 10.12. 2) Do a build from scratch of the client application code against Trilinos 10.12 (making sure that deprecated warnings are enabled). Save the full build output to a file to be searched for deprecated warnings. 3) Search the build output of the client code for "deprecated" warnings which give file names and line numbers for deprecated features. For each deprecated warning or feature: 3.a) Look at the Trilinos source code referenced in the "deprecated" warning and see why the feature (or file) was deprecated and what instructions there are for using an alternant implementation. In many cases, the deprecated function or macro will be calling a non-deprecated variation. 3.b) Change the client source code in smaller reasonable sized chucks (looping back to step #3.a multiple times) to removed deprecated usage and re-build and re-test incrementally to ensure the client code continues to build and run correctly. 4) Once all deprecated code has been addressed through various iterations in step #3, go back to step #2 to make sure that no deprecated warnings are found. 5) Rebuild the client code against Trilinos 11.0. For most deprecated features, the above algorithm will cleanly and safely facilitate the upgrade of client code to Trilinos 11.0. If, however, the client code fails to build against Trilinos 11.0 in step #5 after removing all deprecated warnings against 10.12, then a more difficult and risky upgrade process may be necessary. First, consult the release notes and tests and examples for the Trilinos package causing the failures. If that is not helpful, email trilinos-users@software.sandia.gov for advice. To see a discussion of the why and how of the management of deprecated code in Trilinos, see Section 6.5 "Regulated Backward Compatibility: Details" in the TriBITS Lifecycle Model technical report: http://www.ornl.gov/~8vt/TribitsLifecycleModel_v1.0.pdf Sorry for any inconvenience this transition to Trilinos 11.0 may cause due to the removal of deprecated features and code. =============================================================================== Package Release Notes: ------------------------------------------------------------------------------- Amesos2 - Added support for Pardiso-MKL (multithreaded solver) - Several bug fixes Epetra Added support for 64-bit global indices Epetra supports 64-bit global indices beginning with Trilinos Release 11.0 by using the "long long" datatype. Epetra still supports 32-bit global indices and the interface for using them remains the same. - To construct Epetra objects for 64-bit indices, certain input arguments must be "long long" instead of "int". For example, compare 32: Epetra_BlockMap(int NumGlobalElements, int NumMyElements, const int *MyGlobalElements, ...) 64: Epetra_BlockMap(long long NumGlobalElements, int NumMyElements, const long long *MyGlobalElements, ...) - New member functions that return a long long value have a suffix "64". For example, GID64, NumGlobalNonzeros64, MaxAllGID64, etc. These functions work whether the underlying object is 32-bit or 64-bit based. The older non-suffixed functions work for 32-bit objects only. - New classes added for "long long" data: Epetra_LongLongVector, Epetra_LongLongSerialDenseVector, Epetra_LongLongSerialDenseMatrix. - To build Epetra and dependent packages without any 64-bit support turn on the CMake flag Trilinos_NO_64BIT_GLOBAL_INDICES. Default is off. - To enforce that a code is truly compatible with 64-bit Epetra turn on the CMake flag Trilinos_NO_32BIT_GLOBAL_INDICES, and fix any compile-time or run-time errors. Default is off. Epetra 64-bit support FAQ (compile problem) Epetra-dependent code may not compile if it relied on automatic type conversion to "int" from non-int types when constructing Epetra objects or calling certain member functions. This is because now there can be ambiguity due to overloading. Use explicit conversion to either "int" or "long long". Kokkos - Non-backwards compatible change: row pointers for CRS objects are not longer size_t; instead, they are the same Ordinal type as the columns indices - Non-backwards compatible change: construction of Kokkos local graph objects requires specifying number of columns - KokkosArray - Initial release of experimental package for manycore performance-portable kernels using multidimensional array API to transparently swap between "array of structures" and "structure of arrays" as per the manycore device needs. - Proxy-application examples include hybrid parallel (MPI + KokkosArray) nonlinear thermal conduction finite elements and explicit dynamics finite elements. These have been tested with pthreads and Cuda on the Cray XK6. RTOp - Dropped deprecated code in Trilinos 10.12 (see general release notes on dropping deprecated code). ShyLU - Initial public release for ShyLU. ShyLU is a hybrid direct-iterative preconditioner (solver) for general sparse linear systems, based on Schur complement approximation. It uses a hybrid MPI+threads parallel execution model. - Should be used as Ifpack preconditioner (for now). - ShyLU should be considered *EXPERIMENTAL* code. Teuchos - Dropped deprecated code in Trilinos 10.12 (see general release notes on dropping deprecated code). - Teuchos reference BLAS implementations have been corrected to mimic the behavior of their machine-specific counterparts. See bugs 4262 and 5683. This includes fixing the interface to _GER so that the complex instantiation of that routine uses _GERU. Also, _ASUM and _IAMAX were corrected to perform the correct calculations for complex-valued data types. - Fixed SerialDenseSolver class to correctly handle complex-valued data types. See bug 5308. - CommandLineProcessor now properly throws exceptions. See bug 4668 and 5387. By default this tool throws exceptions and must recognize all the options it encounters on the command line. This is enforced through the implementation now. If exception throwing is disabled, then proper error codes will be returned to the user. - Filtering timer labels for global statistics and output The computeGlobalTimerStatistics(), report(), and summarize() class methods of TimeMonitor now support "filtering" timer labels. See Bug 5301: https://software.sandia.gov/bugzilla/show_bug.cgi?id=5301 Both methods take an optional "filter" string. If nonempty, the methods only print timers whose labels begin with that string. This feature could be used to implement "namespaces" for timers. Trilinos packages may take advantage of this feature by prefixing the timer name with the package name. For example: "Teuchos: Timer 1". Users may exploit this feature to reduce the volume of output. The implementation does not compute global statistics for timers that are filtered out, so filtering could also reduce computation and communication. - YAML output option for timing results The report() class method of TimeMonitor now has a YAML output option. See Bug 5302: https://software.sandia.gov/bugzilla/show_bug.cgi?id=5302 YAML (see yaml.org) is a recursive acronym for "YAML Ain't Markup Language." It "is a human-friendly data serialization standard for all programming languages." I've added YAML output on request of Daniel Barnette (SNL), so that timing results can serve as input data for his PylotDB (https://github.com/dwbarne/PYLOTDB) framework for database creation, management, and analysis. YAML is not the default output format of report(). To specify YAML output, give report() a ParameterList with the "Report format" parameter set to "YAML". I have provided two different variants of YAML output: "compact" and "spacious". The default is "spacious". You may set this via the "YAML format" parameter. Thyra - Dropped deprecated code in Trilinos 10.12 (see general release notes on dropping deprecated code). Tpetra - Significant performance improvements to local sparse matrix-vector multiply on CPU nodes. - Removed all deprecated methods. Xpetra - Initial public release of Xpetra. Xpetra is a lightweight wrapper package that provides algorithm developers with a unified interface to the underlying sparse linear algebra library. - Epetra and Tpetra are currently supported. - Xpetra is used by the packages Zoltan2 and MueLu. - Xpetra should be considered *EXPERIMENTAL* code. Zoltan Highlights are listed below; for more details, see Trilinos/packages/zoltan/doc/Zoltan_html/ug_html/ug_release.html . - Zoltan is now released under Trilinos' BSD license. - The following Zoltan features are no longer supported in Trilinos v11: + Zoltan v1 interface (as described in Zoltan include file lbi_const.h) + Partitioning method OCTPART: use partitioning method HSFC instead. - Hierarchical partitioning received several performance, interface and testing improvements. An easier-to-use interface has been added using simple parameters (HIER_ASSIST, PLATFORM_NAME, TOPOLOGY) instead of callback functions; the callback function interface is still supported. - Memory usage in Zoltan Distributed Data Directories is improved, leading to faster execution times for data directories and hierarchical partitioning. - Compilation with gcc 4.7 is now supported. - Zoltan supports PT-Scotch v5.1.12 and ParMETIS v4, as well as some older versions of these TPLs. Zoltan2 - Initial public release of Zoltan2. Zoltan2 is a redesign of the Zoltan combinatorial scientific computing toolkit that uses templating and Trilinos classes for tighter integration with Trilinos. Zoltan2 supports Epetra and Tpetra data structures through the Xpetra interface. ############################################################################### # # # Trilinos Release 10.12 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 10.12 general release contains 51 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, NOX, Optika, OptiPack, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, SEACAS, Shards, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Trios*, Triutils, Zoltan. (* denotes package is being released externally as a part of Trilinos for the first time.) =============================================================================== Package Release Notes: ------------------------------------------------------------------------------- ForTrilinos - This package builds with three compilers: the IBM XL Fortran (xlf) compiler versions 13.1 and higher, the Numerical Algorithms Group Fortran (nagfor) compiler version 5.3 and higher, and the GNU Fortran (gfortran) compiler version 4.7.0 and higher. - The ForTrilinos interfaces have been simplified relative to their C++ counterparts: whereas the lack of array programming support in C++ necessitates passing array size as a separate argument, Fortran arrays carry such information in internal descriptors so there is no need to pass array sizes. - Sample scripts for building ForTrilinos are provided in Trilinos/sampleScripts. - Building with gfortran versions before 4.8 requires setting flags that work around two missing compiler features: support for final subroutines and support for deferred-length character components. A sample script that sets the aforementioned flags is in : Trilinos/sampleScripts/mac-fortrilinos-gcc47-openmpi-debug and Trilinos/sampleScripts/mac-fortrilinos-gcc47-serial for mpi and serial builds respectively. Users who build with gfortran should adopt two practices to prevent memory leaks: 1. Construct ForTrilinos objects using the ForTrilinos constructor subroutines (do not use ForTrilinos constructor functions). 2. Manually destroy all constructed ForTrilinos objects using by invoking the object's "force_finalize" type-bound procedure. - The project is primarily user-driven; new interfaces are developed at the request of Trilinos users. Kokkos - Major (backwards-compatible, internal) refactor of local sparse operators, esp. DefaultSparseOps - Using generic sparse kernels only on host node; CUDA nodes use CUSPARSE. Adaptors for Cusp are work-in-progress. - Added first-touch-allocation support for sparse matrices; should improve performance on NUMA nodes. - Still lots of work in progress on sparse matrix support, expected for Trilinos 11.0 Mesquite - Removed Distance From Target (DFT) based metrics and added Target-Matrix Optimization Paradigm (TMOP) based metrics. - Fix broken patch culling functionality - Update for ITAPS 1.3 release candidate APIs - Added XYPlanarDomain type - Updated Histogram to a more intuitive format. - Added Scaled Histograms feature to QualityAssessor Summary code. - Significant updates to Users Guide. - Fixed QualityMetricTester utility class problem reported by Jason - fixed typo in header include guards reported by Jason Kraftcheck. - Fixed compiler errors using gcc/g++ 4.6 on Linux, Bug #5294 - Fixed the errors in the MPI_DEBUG version of the check-in script on Linux. - Updated constructors in MsqIMeshP.*pp to match those of parent class MsqIMdesh. - Added parallel error handling to parallel Mesquite/VertexMover. - Fixed std::vector not being resized after the number of elements in it was reduced. - Added Windows code to replace tmp_File() function that does not work in Windows 7. - Fixed non-unique cmake global name issue. - Added code for Windows using srand(). Fix for bug #5351. Teuchos - The current behavior of the Teuchos::XMLParameterListReader has been modified to throw an exception (Teuchos::DuplicateParameterSublist) the event that a sublist is duplicated in an XML stream. This change is disabled by default in the XMLParameterListReader class, and is enabled by calling: XMLParameterListReader::setAllowsDuplicateSublists( false ) This is configured, and thereby constitutes a non-backwards compatible change, in the following encapsulating helper methods: Teuchos::updateParametersFromXmlFile(...) Teuchos::updateParametersFromXmlFileAndBroadcast(...) Teuchos::getParametersFromXmlFile(...) Teuchos::updateParametersFromXmlString(...) Teuchos::getParametersFromXmlString(...) This change was requested by Panzer/Drekar developers, to aid in debugging the input of large XML programs specifying a physics application. Tpetra - Major (backwards-compatible, internal) refactor to interaction between Tpetra::CrsGraph/CrsMatrix and their interaction with their LocalSparseOps template parameter. - Removed generic kernels for GPU nodes; GPU sparse kernel support now provided by CUSPARSE library; requires CUDA 4.1 - Additional methods in Reduction/Transformation Interface (RTI) interface, examples in tpetra/examples/MultiPrec - Fixed major bugs in Tpetra Import/Export - Minor bug fixes and documenting tests - Numerous improvements to documentation - Better MatrixMarket support in tpetra/util - Added the ability to construct a Tpetra::Vector/MultiVector using user data (host-based nodes only) - Deprecated: fillComplete(OptimizeStorageOption) on Tpetra::CrsGraph and Tpetra::CrsMatrix, in favor of a ParameterList. Trios - Significant changes to thread support for nessie. - Implemented thread-safe version of nessie client/server... not fully tested. - Removed thread pool and threaded support from server. Assume service developer has their own thread pool. - Valgrind-detected bug fixes for IB port of NNTI. - Modified xfer-service (example) to use multiple servers. - Implemented two different client/partitioning schemes: round robin, block partition. ############################################################################### # # # Trilinos Release 10.10 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 10.10 general release contains 50 packages: Amesos, Amesos2, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, NOX, Optika, OptiPack, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, SEACAS, Shards, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Triutils, Zoltan. Framework Release Notes: - The following packages have been switched to BSD-compatible licenses: FEI, Globipack, Isorropia, Kokkos, LOCA, MOOCHO, NOX, Optika, Optipack, Piro, Tpetra. This brings the total number of packages with BSD-compatible licenses to 30 (out of 50). Please see http://Trilinos.sandia.gov/license.html for more information about the licenses in Trilinos. - Force CMake to use only static third-party libraries Starting with Trilinos 10.8, the option TPL_FIND_SHARED_LIBS can be used to force the TPL system to use only static libraries. By default, shared libraries can be used. To use only static libraries, set the option to "OFF". =============================================================================== Package Release Notes: ------------------------------------------------------------------------------- PyTrilinos - Added support for the use case when Trilinos requests a Teuchos::ArrayView<>. In Python, the user can supply a NumPy array or a Python sequence (input arguments only) and PyTrilinos will convert it to the necessary ArrayView type automatically. This currently only applies to the Teuchos.Comm classes, but the infrastructure is there for future needs. - Changed PyTrilinos string checks to accommodate older Pythons in which strings can only be regular strings and newer Pythons in which strings can be either unicode or regular strings. - Added experimental support for STK package Percept mesh module. Teuchos - Deprecated the non-namespaced family of TEST_FOR_EXCEPTION(...) macros in the file Teuchos_TestForException.hpp: There are now namespaced versions prefixed with TEUCHOS_. ############################################################################### # # # Trilinos Release 10.8 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 10.8 general release contains 50 packages: Amesos, Amesos2*, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Epetra, EpetraExt, FEI, ForTrilinos, Galeri, GlobiPack, Ifpack, Ifpack2, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, NOX, Optika, OptiPack, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, SEACAS*, Shards, STK, Stokhos, Stratimikos, Sundance, Teko, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Triutils, Zoltan. (* denotes package is being released externally as a part of Trilinos for the first time.) Framework Release Notes: - MPI Fortran compiler wrapper search change Starting with Trilinos 10.8, when MPI is enabled and a specific Fortran compiler is not specified at configure time, the first wrapper searched for will be mpif90 instead of mpif77. If a mpif90 wrapper is not found, the search will continue and attempt to find mpif77. Depending on the underlying compilers used and the mpi configuration, a mpif90 wrapper may exist, but not be functional. In those cases, a functional Fortran compiler wrapper should be specified at configure time. - CMake export system changes: The CMake export system used for finding Trilinos in other CMake projects has had some changes to better support CMake projects. First there are now CMake targets for each library that is exported. This will allow easier handling of dependencies for libraries as all of that information is now stored in the CMake Target. The location of the installed *Config.cmake files has changed. They are no longer in the /include directory, but are instead in /lib/cmake//Config.cmake. These paths are more like what CMake expects and should only require minor changes to the search path you give to find_package(...). You should only need to point to the install prefix where Trilinos was installed when using find_package now. More information: Trilinos website: http://trilinos.sandia.gov =============================================================================== Package Release Notes: ------------------------------------------------------------------------------- Amesos2 - Initial Public release of Amesos2. Amesos2 provides a common interface to different direct solver libraries from Trilinos. - Supports SuperLU, SuperLU_MT and SuperLU_Dist direct solvers. - Supports Epetra and Tpetra matrices and mulitvectors. - Supports 64-bit and complex data types. EpetraExt - The EpetraExt interface to Zoltan is deprecated in Trilinos v10.8 and will be removed in Trilinos v11. Users of this interface should switch to the Isorropia package or use Zoltan directly. Isorropia - New class Isorropia::Epetra::Matcher solves the maximum cardinality matching problem for the bipartite graph. This is also known as a maximum transversal, and is typically used to permute a sparse matrix to zero-free diagonal form. The current implementation uses OpenMP and shared memory model. It does not work on distributed matrices. - Isorropia is now supported in PyTrilinos. Kokkos - New multidimensional array sub-package in kokkos/array subdirectory. The MDArrayView, MultiVectorView, and ValueView template classes manage allocated memory on the 'Device' and perform compile-time selection of a device-optimal mapping of array's multi-index space to data members. Includes unit tests, performance tests, and example mini-applications. PyTrilinos - Improved the MPI initialization logic in Teuchos and Epetra modules. Previously, both modules would call MPI_Init() when they were imported into the python interpreter and register MPI_Finalize() with the atexit module (each module did perform checks before executing the calls in case the other module beat it to the punch). Now, each module checks to see if MPI_Init() has already been called, and if so, it does not register MPI_Finalize() with atexit. This way, if the user initializes MPI ahead of importing Teuchos or Epetra (such as with mpi4py, for example), then the user is responsible for finalization, and can assume finer control. - Added the Isorropia package, for partitioning Epetra objects. This includes an IsorropiaVisualizer.py script. - This release contains a large number of internal changes mostly not visible to end users, except for increased stability and bug fixes. One big change is that C++ referenced counted pointers (via the Teuchos::RCP class) are now properly handled. Fixed a couple of bugs in the Amesos, AztecOO and EpetraExt wrappers. Changed the Amesos example scripts to follow PyTrilinos coding standards. Put all C++ code within the PyTrilinos namespace. Changed C++ file names to have PyTrilinos_ prefix. SEACAS - New in Trilinos 10.8 the SEACAS package includes the following libraries and applications: - Libraries: - Exodus: database used to store and retrieve data for finite element analyses - Nemesis: add-on to exodus providing data for parallel finite element analyses - Ioss: C++ front-end to exodus library; provides a higher-level IO support for finite element applications - Aprepro: Can be used to embed aprepro functionality into an application - chaco: graph partitioning library used by nem_slice application - supes: memory management, parsing, and system routines used by seacas fortran applications - suplib: common fortran routines used by the seacas fortran applications - Applications: - algebra: manipulate data in exodus databases using equations and functions. - aprepro: algebraic preprocessor; reads a file containing both general text and algebraic, string, or conditional expressions. It interprets the expressions and outputs them to the output along with the general text. - conjoin: joins two or more Exodus databases into a single database. The input databases should represent the same model geometry with similar variables. - ejoin: used to join two or more Exodus databases into a single Exodus database. The input databases must have disjoint meta and bulk data. - epu: Combines multiple Exodus databases produced by a parallel application into a single Exodus database. Replaces nem_join. - exo2mat: translates exodus data into Matlab mat-file format. Requires matlab libraries. - exodiff: compares results data from 2 exodus databases. - exomatlab: translates exodus global data into a matlab-readable file. - exotxt: convert exodus database to text format - gjoin: join 2 or more exodus databases into a single database. Will combine nodes, blocks, nodesets, sidesets - explore: query an exodus database. - mapvar: transfer solution results from one database to another. - mapvar-kd: same as mapvar with a kd-based internal search; minor other differences. - mat2exo: convert a Matlab mat-file into an exodus database. Requires Matlab libraries. - nem_slice: generate a decomposition of a finite element mesh for use in parallel analyses - nem_spread: use the nem_slice output to spread a finite element mesh into multiple files; one per processor for use in parallel analyses. - txtexo: convert a exotxt-formatted text file into an exodus database. - Scripts: - decomp: drives nem_slice and nem_spread to decompose a mesh for use in parallel analyses. Teuchos - Added automatic stack tracing info for exception messages, segfaults, and aborts. Thanks to the work of Ondrej Certik we now have built-in support for generating stack traces when using g++ when uncaught exceptions are encountered or when a segfault or about occurs. See the Doxygen documentation for more details for how your project can take advantage of this feature. Zoltan - Added new recoloring capability to Zoltan coloring algorithms, providing lower numbers of colors at small additional cost. - Updated Zoltan to allow use of third-party libraries ParMETIS versions 3.1 and 4.0 and Scotch versions up to 5.1.12. - Updated Zoltan's hierarchical partitioning for greater efficiency. - Fixed bug in autotools installation of Zoltan; file Zoltan_config.h is now installed in the specified include directory. - Fixed Fortran90 interface issues that caused compilation and run-time problems with gcc 4.5 and later when compiler optimization was enabled. - Added support for 64-bit builds of Zoltan, enabling operation on more than 2B objects. See details for building in the Zoltan User's Guide. ############################################################################### # # # Trilinos Release 10.6 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 10.6 general release contains 48 packages: Amesos, Anasazi, AztecOO, Belos, CTrilinos, Didasko, Epetra, EpetraExt, FEI, ForTrilinos^, Galeri, GlobiPack, Ifpack, Ifpack2**, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Mesquite, ML, Moertel, MOOCHO, NOX, Optika, OptiPack, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, Shards, STK, Stokhos, Stratimikos, Sundance, Teko*, Teuchos, ThreadPool, Thyra, Tpetra, TriKota, TrilinosCouplings, Triutils, Zoltan. (* denotes package is being released externally as a part of Trilinos for the first time.) (** Ifpack2 was previously released under the name "Tifpack".) (^ ForTrilinos was added to the external release for Trilinos 10.4.1.) Framework Release Notes: - New to Trilinos 10.6 is a small functional example to be used as a template for applications that use CMake and want to build against an installed version of Trilinos. The application automatically pulls required information from Trilinos including compilers, include paths, and library names (in the correct order). The example can be found in demos/buildAgainstTrilinos. More information: Trilinos website: http://trilinos.sandia.gov =============================================================================== Package Release Notes: ------------------------------------------------------------------------------- Anasazi - Better support for Tpetra in Anasazi. ------------------------------------------------------------------------------- Belos - Minor changes in Belos/Tpetra adaptors. ------------------------------------------------------------------------------- ForTrilinos - This release includes 11 modules or classes of the Epetra package. - This package is still in its experimental stage and is only supported on AIX. - Sample configure script are provided in Trilinos/sampleScripts/aix-fortrilinos-serial and Trilinos/sampleScripts/aix-fortrilinos-mpif90 for serial and mpi builds respectively. - Because of the object-oriented features used, it requires a XL Fortran compiler v13.1. The source code can be compiled using the xlf compiler option. - Required compiler flags for Fortran include: -qfixed=72 -qxlines: deals with older Fortran source code in other Trilinos packages. These flags are used for mpi builds and must be specified in the configure script. -qxlf2003=polymorphic: allows for the use of polymorphism in the source code. -qxlf2003=autorealloc: allows the compiler to automatically reallocate the left hand side with the shape of the right hand side when using allocatable variables in an assignment. -qfree=f90: informs the compiler that the source code is free form and conforms to Fortran 90. These flags(-qfree=f90 -qxlf2003=polymorphic -qxlf2003=autorealloc) are hardcoded in Trilinos/packages/ForTrilinos/CMakeLists.txt - Required compiler flag for xlc++ include: -qrtti=all: this flag should be included in the configure script. - The project is primarily user-driven; so new interfaces are developed at the request of Trilinos users. ------------------------------------------------------------------------------- Kokkos Significant internal/external changes to both the Kokkos Node API and the Kokkos Linear Algebra library. Most of these changes are centered around CrsGraph and CrsMatrix and their kernels. Some exciting developments regarding sparse mat-vec on multi-core/GPUs did not make it in this release; look for more development in 10.6.1. - Lots of additional documentation, testing and examples in Kokkos. - Improved debugging in Kokkos Node API - Added isHostNode static bool to all Kokkos nodes (false for ThrustGPUNode) - Imported select Teuchos memory management classes/methods into the Kokkos namespace. - Minor bug fixes, warnings addressed. Changes breaking backwards compatibility: - Kokkos CRS classes (i.e., CrsGraph and CrsMatrix) are now templated on the sparse kernel operator, allowing specialization of the class data according to the implementation of the kernel. - Kokkos CRS classes now contain host-allocated memory, instead of node-allocated memory. This means that use of these buffers by the node will, in general, require a copy. ------------------------------------------------------------------------------- Meros - Meros has been removed from the release. Teko provides replacement Functionality. ------------------------------------------------------------------------------- ML User-Level functionality changes - Modifications to ML to allow user to specify the use of CRS storage. Certain methods in Ifpack are much more efficient if the matrix is in Epetra_CRS_Matrix mode. This new switch tells ML to store things as CSR instead of MSR (it's still the default). - Modifying MLMEX so the solve mode can (optionally) return iteration counts. Only works in ML_Epetra mode, not MLAPI. - Adding ML support for Ifpack-SuperLU(ILUTP) smoother. - Adding a face-based least-squares finite element (LSFEM) preconditioner to ML. See TrilinosCouplings for an example. - Adding MLMEX matlab interface to the cmake build system. Internal changes, output changes and bugfixes - Fixed a bug in ML_Project_Coordinates so that it works where dim != numPDEs. For using auxillary aggregation for problems like linear elasticity. - Fixing a memory leak in ML_Init_Aux. - Adding additional output to ML. This focuses on the IFPACK/SORa smoother as well as improved RefMaxwell output. - Modifications to RefMaxwell to allow direct use of Ifpack (rather than via MLP). - Removing ML's dependence on ZoltanTpl. - Changed the output of the IFPACK-ILU smoother so that it is more informative. ------------------------------------------------------------------------------- Teko Teko is a library for implementation of blocked and segregated preconditioners in the context of iterative solvers for linear systems. This includes a high level interface for manipulating block operators and creating inverse operators using solver and preconditioning capabilities in Trilinos. In addition, utilities are provided that decompose large Epetra_CrsMatrix objects into physically meaningful sub blocks. A brief over view of the capabilities built in Teko is - Generic preconditioners operations: Additive, multiplicative, Neumann series, block Gauss-Seidel, block Jacobi, and 2x2 block LU factorization - Manipulation of abstract linear operators: implicit/explicit operator addition and multiplication, constructing an approximate inverse operator using Trilinos preconditioner and solver technology - Deconstruction of Epetra_CrsMatrix into is physical components - Parameter list driven interface for constructing preconditioners NOTE: A word of caution. The interfaces in Teko are still maturing and may change substantially in the future. ------------------------------------------------------------------------------- Tpetra Significant internal changes in Tpetra for this release, mostly centered around the CrsMatrix class. Lots of new features centering around multi-core/GPUs did not make it in this release; look for more development in 10.6.1. - Lots of additional documentation, testing and examples in Tpetra. - Imported select Teuchos memory management classes/methods into the Tpetra namespace. - Updates to the Anasazi/Tpetra adaptors for efficiency, node-awareness and debugging. - Minor bug fixes, warnings addressed. Changes breaking backwards compatibility: - Tpetra CRS objects (i.e., CrsGraph and CrsMatrix) are required to be "fill-active" in order to be modified. Furthermore, they are required to be "fill-complete" in order to call multiply/solve. The transition between these states is mediated by the methods fillComplete() and resumeFill(). This will only effect users that modify a matrix after calling fillComplete(). Newly deprecated functionality: - CrsGraph/CrsMatrix persisting views of graph and matrix data are now deprecated. New, non-persisting versions of these are provided. ############################################################################### # # # Trilinos Release 10.4 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 10.4 general release contains 47 packages: Amesos, Anasazi, AztecOO, Belos, CTrilinos*, Didasko, Epetra, EpetraExt, FEI, Galeri, GlobiPack*, Ifpack, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Meros, Mesquite, ML, Moertel, MOOCHO, NOX, Optika, OptiPack*, Pamgen, Phalanx, Piro, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, Shards, STK, Stokhos, Stratimikos, Sundance, Teuchos, ThreadPool, Thyra, Tifpack, Tpetra, TriKota, TrilinosCouplings, Triutils, Zoltan. (* denotes packages that are being released externally as a part of Trilinos for the first time.) Framework Release Notes: - Reduction of user CMake cache variables with CMake GUI 2.8.2 and newer Release 2.8.2 of the CMake QT-based GUI now has separate check boxes for "Grouped" and "Advanced" CMake cache variables. This, together with changes in the Trilinos CMake files to only set defaults for cache variables for Trilinos packages that are actually enabled, has made the manipulation of CMake variables much more manageable for Trilinos users. - Export Makefile support added Similar to the find Trilinos capability for cmake-aware projects an export Makefile capability is being officially released. Each package will have a Makefile.export. created for it that can be included in the Makefiles for a project to give it access to information about what was built, which compilers were used etc. Please see commonTools/importing/README.Export_Makefile for more information and instructions on how to use it. - Find Trilinos files moved The installed files for finding Trilinos in a cmake-aware project have moved to the include directory instead of being at the top level. It was felt that installing into the top level could be confusing when the install path was a system path. More information: Trilinos website: http://trilinos.sandia.gov =============================================================================== Package Release Notes: ------------------------------------------------------------------------------- Anasazi - Brought Anasazi/Tpetra adaptors back online (experimental) ------------------------------------------------------------------------------- Belos - Replaced non-const MultiVecTraits::CloneView(MV) with explicit MultiVecTraits::CloneViewNonConst(MV). This is a non-backwards-compatible change to Belos::MultiVecTraits, requiring changes through Belos solver, solver managers, and orthomanagers. The result is that it is much harder to accidentally create a non-const view when a const view is sufficient. To do so requires CloneViewNonConst() be called explicitly, all such calls being manually invoked during this refactorization. - Efficiency improvements for Belos/Tpetra adaptors (experimental) ------------------------------------------------------------------------------- Kokkos Sparse ops: - Combined DefaultSparseSolve and DefaultSparseMultiply into DefaultSparseOps - Added new traits class, DefaultKernels, to specify default sparse and default block sparse objects - Added new classes supporting Tpetra::VbrMatrix MultiVector ops: - Some methods were missing "inline" specifier. This could (should?) improve performance for TPINode. CUDANodeMemoryModel: - Support for tracing/profiling data movement between host and GPU ------------------------------------------------------------------------------- phdMesh - phdMesh has been removed from the release. STK provides replacement functionality. ------------------------------------------------------------------------------- PyTrilinos - The logic for determining the prefix for the install directory for PyTrilinos has been improved. Highest precedence is given to the configure variable PyTrilinos_INSTALL_PREFIX. If this is not set by the user, then next highest precedence is given to CMAKE_INSTALL_PREFIX. If this has not been set by the user, then the prefix of the python interpreter that PyTrilinos is being compiled against is used. ------------------------------------------------------------------------------- Sundance - To compile Sundance explicit instantiation is now required. To enable explicit instantiation you will need to set Trilinos_ENABLE_EXPLICIT_INSTANTIATION to ON when configuring. ------------------------------------------------------------------------------- Teuchos Known breaks in backward compatibility: - Changed direct constructors for ArrayRCP to take (lowerOffset, size) instead of (lowerOffset, upperOffset) to be consistent with the nonmember constructors like arcp(...) and ArrayView. This was done to make these constructors consistent with the non-member constructors. As long clients were using the nonmember constructors this will not break backward compatibility. However, if clients are using the direct constructors, upperOffset becomes size which means that the size will actually become one less with the upperOffset becoming one less. This will therefore not result in memory access errors but will result in exceptions being thrown when accessing the real last element. Given the confusion that having different arguments caused (that I got caught with too) and the inherent safety in the change, I think this break with strict backward compatibility is well worth the (minor) problems it might cause to users. - Removed define of TEUCHOS_PRIVIATE_DELETE_NOT_SUPPORTED for _AIX. The macro TEUCHOS_PRIVIATE_DELETE_NOT_SUPPORTED was designed to be used only internally within Teuchos (and perhaps other parts of Trilinos) but at some point all use of this macro was removed (apparently in all of Trilinos). If client code used this macro for their own purposes, then this change will break client code when _AIX is defined. However, it seems unlikely that there will be such client code around. ------------------------------------------------------------------------------- Tpetra - Kokkos and Tpetra are in the middle of a medium refactor in order to better support GPU and multicore nodes. Therefore, there has been some potential regression in performance for GPU nodes; and some known issues regarding multi-core CPU performance (especially on NUMA platforms) have not been addressed. The rest of this refactor is likely to happen in the development branch, and will not be released until 10.6 (estimated for September 2010). Users that require access to this code should contact a Trilinos developer regarding access to the development branch repository. Improvements to doxygen documentation. - Added ifdefs to support profiling/tracing of host-to-device memory transfers These are enable via cmake options -D Kokkos_CUDA_NODE_MEMORY_PROFILING:BOOL=ON -D Kokkos_CUDA_NODE_MEMORY_TRACE:BOOL=ON VBR capability (experimental) - Added variable-block row matrix (VbrMatrix) and underlying support classes (BlockMap, BlockMultiVector) - Added power method example of VBR classes CrsMatrix: - Now implements DisbObject, allowing import/export capability with CrsMatrix objects (experimental) - Combined LocalMatVec and LocalMatSolve objects into a single template parameter (non BC). This required changes to CrsMatrixMultplyOp and CrsMatrixSolveOp operators as well (non BC). - Access default for this type via Kokkos::DefaultKernels - Removed cached views of object data. this should have no effect on CPU-based nodes, but will result in slower performance for GPU-based nodes. This regression is a result of the release happening mid-refactor. It will not be addressed in the 10.4.x sequence. - Bug fixes regarding complex cases involving user-specified column maps and graphs. DistObject interface: - Added createViews(), releaseViews() methods to allow host-based objects to temporarily cache views of host data during import/export procedure Map: - Added new non-member constructors: createContigMap(), createWeightedContigMap(), createUniformContigMap() - Fixed some bugs regarding use of unsigned Ordinal types - Fixed MPI-stalling bug in getRemoteIndexList() MultiVector: - Added view methods offsetView() and offsetViewNonConst() to create a MultiVector view of a subset of rows - Added non-member constructor Tpetra::createMultiVector(map,numVecs) Vector: - Added non-member constructor Tpetra::createVector(map) Tpetra I/O: - Added Galeri-type methods for generating pedagogical matrices (currently, only 3D Laplacian) External adaptors (experiemental) - Efficiency improvements for Belos/Tpetra adaptors - Brought Anasazi/Tpetra adaptors back online ############################################################################### # # # Trilinos Release 10.2 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The Trilinos 10.2 general release contains 45 packages: Amesos, Anasazi, AztecOO, Belos, Didasko, Epetra, EpetraExt, FEI, Galeri, Ifpack, Intrepid, Isorropia, Kokkos, Komplex, LOCA, Meros, Mesquite*, ML, Moertel, MOOCHO, NOX, Optika*, Pamgen, Phalanx, PhdMesh, Piro*, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, Shards, STK*, Stokhos^, Stratimikos, Sundace, Teuchos, ThreadPool, Thyra, Tifpack*, Tpetra, TriKota*, TrilinosCouplings, Triutils, and Zoltan. (* denotes packages that are being released externally as a part of Trilinos for the first time.) (^ Stokhos was not included in the initial 10.0 release, but was released externally starting in Trilinos 10.0.3.) The limited release contains an additional 2 packages, CTrilinos and ForTrilinos, that are scheduled for external release in the near future. Framework Release Notes: - Find Trilinos capability for CMake-aware client codes CMake-aware client codes can now use the Find Trilinos capability to find Trilinos and its libraries in a more natural way. The Find Trilinos capability has two variants, one for a build tree (the actual directory where Trilinos was built) and one for an installation tree. It works by enabling the CMake function "FIND_PACKAGE(Trilinos PATHS )" to find a copy of Trilinos. Many useful variables are available that can be used in your CMake files. For example, the fully constructed link line for linking against Trilinos libraries is available, as well as the path(s) to Trilinos header files, and the set of compilers and compiler flags used to build Trilinos. This capability can also be used to find individual Trilinos packages. For more information on how to use this capability and what variables are available, please see the documentation in Trilinos/cmake/README.Find_Trilinos or at http://trilinos.sandia.gov/Finding_Trilinos.txt. - Trilinos_ENABLE_ALL_OPTIONAL_PACKAGES is ON by default The default for Trilinos_ENABLE_ALL_OPTIONAL_PACKAGES was changed from OFF to ON. Optional package features will now be available by default, however it will take more time to compile and link Trilinos in most cases. If optional features are not of interest, the variable can be set to OFF manually. More information: Trilinos website: http://trilinos.sandia.gov =============================================================================== Package Release Notes: ------------------------------------------------------------------------------- Epetra Epetra provides initial support for OpenMP. The Epetra_CrsMatrix class supports OpenMP parallel sparse matrix-vector multiply and sparse matrix-multivector multiply (the Multiply() and Apply() methods). The Epetra_MultiVector and Epetra_Vector classes support OpenMP parallelism for all computational functions. The Epetra_CrsMatrix, Epetra_MultiVector, Epetra_Vector and Epetra_CrsGraph classes supports parallel data placement (when not constrained by user-provided data) to improve non-uniform memory access. ------------------------------------------------------------------------------- Mesquite* MESQUITE is a linkable software library that applies a variety of node-movement algorithms to improve the quality and/or adapt a given mesh. Mesquite is designed to address the following commonly encountered mesh optimization problems: * Untangle meshes, * Provide local size control, * Improve angles, orthogonality, and skew, * Increase minimum edge-lengths for increased time-steps, * Improve mesh smoothness, * Perform anisotropic smoothing, * Improve surface meshes, adapt to surface curvature, * Improve hybrid meshes (including pyramids & wedges), * Smooth meshes with hanging nodes, * Maintain quality of moving and/or deforming meshes, * Perform ALE rezoning, * Improve mesh quality on and near boundaries, * Improve transitions across internal boundaries, * Align meshes with vector fields, and * R-adapt meshes to solutions using error estimates. Mesquite improves surface or volume meshes which are structured, unstructured, hybrid, or non-comformal. A variety of element types are permitted. Mesquite is designed to be as efficient as possible so that large meshes can be improved. ------------------------------------------------------------------------------- Optika* The Optika package provides trilinos users with easy access to GUI input methods for their programs. Optika gives developers the tools they need to quickly obtain information from their users, while still implementing a robust GUI. The general work flow of a program utilizing the Optika package goes something like this: 1. Determine what inputs are needed from the user 2. Create a list specifying these inputs 3. Execute the GUI with the getInput() function to obtain the inputs specified in step 2 4. Proceed with the rest of the program with the given user inputs An alternate work flow is also available. In this work flow, the developer specifies a custom function along with the inputs. When the GUI is executed, it stays active for the entire duration of the program. Every time the user clicks a button, the custom function is called with the current input values. If you think Optika might be useful for your application, we encourage you to take a look at some of the examples included with the Optika package. ------------------------------------------------------------------------------- Piro* Piro is a new package in Trilinos 10.2 that is striving to be the single unifying layer above all nonlinear solver, time integration, optimization, and UQ packages. Piro wraps the typical usage of NOX, LOCA, and Rythmos solvers, for applications that present themselves using the EpetraExt::ModelEvaluator abstraction. These solvers all inherit from the same base class, which can in turn be fed into the analysis packages. Piro wraps the black-box mode usage of optimization and UQ analysis libraries, including Moocho and Dakota, under a single call that takes a Thyra::ModelEvaluator and a parameter list. ------------------------------------------------------------------------------- PyTrilinos PyTrilinos.NOX notes: Updated the wrappers so that the Jacobian can be specified using the NOX.Epetra.Interface.Jacobian base class. To get this to work required that the directorin %typemaps for Epetra_Operator used by NOX.Epetra.Interface.Jacobian be updated to downcast the Epetra_Operator argument to our best guess at the derived class. Such a downcast had already been written for the EpetraExt ModelEvaluator, so code was moved around to make it more generally accessible. This uncovered a memory management bug that took some time to track down, but the result now is much more stable memory management all-around. The new capability is demonstrated in serial in example script exNOX_2DSim. ------------------------------------------------------------------------------- STK* STK (Sierra Toolkit) contains capabilities intended to support massively parallel multi-physics computations on dynamically changing unstructured meshes. The primary capability in the STK package is the mesh database which supports creation and manipulation of mesh entities (nodes, elements etc) and computational field data defined on the mesh. STK also contains sub-libraries that support geometric proximity searches, assembly into linear-systems, etc. ------------------------------------------------------------------------------- Teuchos (*) Default debug enable of RCP node tracing: Setting Teuchos_ENABLE_DEBUG=ON now sets Teuchos_ENABLE_DEBUG_RCP_NODE_TRACING=ON by default. This is a more strict type of checking that will catch more errors. (*) Known breaks in backward compatibility: - The type Teuchos_Ordinal has been changed from int to ptrdiff_t by default. On 64 bit machines, this will be 'long int' instead of 'int'. This can be changed back to int by configuring with -DTeuchos_ORDINAL_TYPE:STRING=int. - The size_type typedef in Teuchos::Array has been changed from size_t to Teuchos_Ordinal which is now ptrdiff_t, a signed integer which is *not* int on a 64 bit platform. See the argument for this in Bugzilla bug 4253. - The size_type typedef in Teuchos::ArrayView and Teuchos::ArrayRCP has also been changed to Teuchos_Ordinal to be consistent with Teuchos::Array. - The size_type typedef in Teuchos::Range1D has been changed to Teuchos_Ordinal. - Removed Teuchos_exit.h with the TEUCHOS_EXIT(...) macros. These were a bad idea and where never used in Trilinos. Hopefully no external Trilinos user made use of these either. - Non-member functions related to RCPNode tracing have been collected into a new static class Teuchos::RCPNodeTracer. Given that no user code should ever be calling these functions in production code this should not affect most users. ------------------------------------------------------------------------------- Thyra (*) Added deprecated warnings. When using GCC, the g++ compiler will now emit warning messages when client code uses deprecated types and functions. The developer of the client code should change over to use non-deprecated code because the deprecated code will be removed when Trilinos 11.0 is put out. (*) Deprecated the use of all raw C++ pointers. All use of raw C++ pointers is now deprecated in all functions and classes. For the most part, if a raw pointer was being used in function foo( ..., T*, ... ) the new function prototype is foo( ..., const Ptr&, ... ). A good way to convert from a raw C++ reference T& to an Ptr object is to use Teuchos::outArg(...) or Teuchos::inOutArg(...) depending on the nature of the argument. To convert from a RCP to a Ptr use the function RCP::ptr(). (*) Refactored the Thyra::LinearOp[WithSolve]Base interfaces: - LinearOpBase: Removed double templating. Now requires overriding opSupportedImpl(...) and applyImpl(...). This is a break in strict backward compatibility but making these functions pure virtual was needed to make sure the interface is implemented correctly. Interface should be 100% backward compatible for external clients through deprecated functions. - LinearOpWithSolve: Removed double templating. Now requires overriding solveImpl(...). Interface should be 100% backward compatible for external clients through deprecated functions. Also, the new solve[Impl](...) function only takes a single SolveCriteria object and only returns a single SolveStatus object to simplify usage. - Removed SingleScalarXXX node classes. There is not need for these anymore now that double templating is gone. - Removed SingleRhsXXX node subclasses. These classes just make the inheritance hierarchy deeper without providing a lot of value. - ExampleTridiag[Serial,Spmd]LinearOp subdclasses refactored to directly inherit from LinearOpDefaultBase and use the Detached[Spmd]VectorView classes to get vector data. (*) Explicit template instantiation: Thyra now fully supports explicit template instantiation. This results in code that builds much faster and can avoid internal compiler error on some platforms. ------------------------------------------------------------------------------- Tifpack* Tifpack contains preconditioners that operate on the templated linear-algebra objects provided by the Tpetra package. Tifpack preconditioners support using the same integer and floating-point types that are provided by Tpetra, including extended-precision types from the QD library. Tifpack is intended to replace the capabilities in the existing Trilinos Ifpack package, but only a few preconditioners are supported for this initial release. Preconditioners provided at this time are Relaxation (Jacobi, Gauss-Seidel, Symmetric Gauss-Seidel), Chebyshev, ILUT and RILUK. ------------------------------------------------------------------------------- Tpetra/Kokkos - Experimental support for CPU multi-threading on *nix via ThreadPool (Pthreads) and cross-platform via Intel TBB. - Experimental support for NVIDIA GPUs via CUDA/Thrust. - Support for explicit instantiation of Tpetra classes for scalars float, double, complex and complex. - Numerous bug fixes and performance improvements. - Minor interface changes to improve accessibility and extend functionality. ------------------------------------------------------------------------------- TriKota* TriKota is a new package in Trilinos 10.2. TriKota is a convenience package that builds the Dakota framework underneath Trilinos as if it were another Trilinos package. Dakota contains a wide array of algorithms for optimization and UQ. TriKota provides adaptors between the Trilinos (ModelEvaluator) interface to the Dakota interface, and wraps the typical library-mode usage of Dakota in a convenience class and some simple example problems. Information on the capabilities of the Dakota framework can seen at: http://www.cs.sandia.gov/dakota/index.html. ------------------------------------------------------------------------------- Zoltan v3.3 - Added a local ordering method based on Hilbert Space-Filling Curves for ordering data within a processor to improve cache performance. - Simplified Zoltan_Order interface. - Added an example that uses Zoltan's migration functions. - Added the capability to test a new mesh partitioning model in zdrive using hypergraph partitioning. - Applied several code and documentation bug fixes. ------------------------------------------------------------------------------- ############################################################################### # # # Trilinos Release 10.0 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. Packages: The version 10.0 general release contains 38 packages: Amesos, Anasazi, AztecOO, Belos, Didasko, Epetra, EpetraExt, FEI, Galeri, Ifpack, Intrepid*, Isorropia, Kokkos, Komplex, LOCA, Meros, ML, Moertel, MOOCHO, NOX, Pamgen, Phalanx, PhdMesh, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, Shards*, Stratimikos, Sundace, Teuchos, ThreadPool, Thyra, Tpetra*, TrilinosCouplings, Triutils, and Zoltan. (* denotes packages that are being released externally as a part of Trilinos for the first time.) The limited release contains an additional 8 packages that may be available in special situations by request. These are: CTrilinos, ITAPS, ForTrilinos, Globipack, Optika, Optipack, Stokhos, and TriKota. CMake Build System: Trilinos has switched to a CMake build system from an Autotools build system for the 10.0 release. Instructions for building with cmake are available from the Trilinos homepage: http://trilinos.sandia.gov. General information about CMake, as well as installation binaries and CMake source code are available from the CMake homepage: http://www.cmake.org. Windows Support: Beginning with the 10.0 release, many Trilinos packages now support the Windows platform. Support for additional packages is planned for the near future. Windows binary installers will also be available for Trilinos 10.0. A list of packages that do not support the Windows platform is included below in the "Known issues" section. More information: Trilinos website: http://trilinos.sandia.gov =============================================================================== Package Release Notes: ------------------------------------------------------------------------------- Amesos Amesos includes the KLU and Paraklete solvers. Paraklete works only in 32-bit mode at this time. Third-party direct solvers accessible via the CMake build system include: (*) MUMPS (*) UMFPACK (*) Scalapack (*) SuperLU (*) SuperLUDist (requires ParMETIS to be enabled as well) ------------------------------------------------------------------------------- Didasko Examples have been added for the Tpetra package, as well as for the Hypre and Euclid interfaces that were added to Ifpack and EpetraExt. ------------------------------------------------------------------------------- EpetraExt EpetraExt now supports the use of the scalable solver package Hypre from Lawrence Livermore National Laboratory as a preconditioner with Trilinos solvers. This support includes use of the native Hypre data structures, without copying, allowing current Hypre users to seamlessly integrate Trilinos and Hypre capabilities. ------------------------------------------------------------------------------- Ifpack New interfaces to third party parallel ILU/ILUT solvers in the form of Hypre/Euclid and HIPS have been added to IFPACK. The former provides parallel classical ILU and the latter provides a parallel multilevel ILUT capability. Unlike IFPACK's existing ILU/ILUT capability, these packages preserve off-core entries in the matrix. This makes them especially useful for multicore architectures. ------------------------------------------------------------------------------- Isorropia - New support for geometric partitioning (RCB, RIB, HSFC) via Epetra_MultiVector. - Improved support for parallel Jacobian matrix coloring. - Isorropia now uses its own parameters, separate from Zoltan parameters. Please see the package release notes for details. ------------------------------------------------------------------------------- MOOCHO (*) MS Windows support with MS Visual C++: Several tests fail in strange ways and therefore MOOCHO must be considered not to work for this platform for this release. ------------------------------------------------------------------------------- Stokhos (internal release only) Stokhos is a Trilinos package for applying intrusive stochastic Galerkin uncertainty quantification methods to nonlinear dynamical systems, primarily stochastic partial differential equations. Stokhos supports generating stochastic residual coefficients using automatic differentiation with Sacado and forming and solving stochastic Galerkin linear systems and nonlinear systems using Epetra and the EpetraExt::ModelEvaluator. Stokhos can make use of the Fortran UQ Toolkit of Debusschere et al for generating residual coefficients using Taylor series and time integration methods, and can leverage Dakota for sparse-grid quadrature. Stokhos is primarily developed and maintained by Eric Phipps with significant contributions by Bert Debusschere, Omar Knio, Chris Miller, and Habib Najm. ------------------------------------------------------------------------------- Stratimikos (*) Support for newer Belos solvers has not been added yet. ------------------------------------------------------------------------------- Teuchos (*) Breaks in backward compatibility: - The raw pointer T* argument in Teuchos::set_extra_data(...) has been changed to Teuchos::Ptr&. This requires that you replace: Teuchos::set_extra_data(data, dataName, &rcpObj); with: Teuchos::set_extra_data(data, dataName, Teuchos::outArg(rcpObj)); ------------------------------------------------------------------------------- Thyra (*) MS Windows support with MS Visual C++: - Thyra complex support and float support are disabled by default. The complex-related code just did not work correctly and there was not time to track down the problem. - Several of the tests showed excessive diffs for this platform so their tolerance was loosened. (*) Partial refactoring of code to use safe memory management classes ------------------------------------------------------------------------------- Zoltan Features: * New interface to Scotch and PT-Scotch parallel graph partitioning algorithms. * Simplified interface to graph ordering and coloring algorithms. * Automated symmetrization of graphs for graph partitioning, coloring and ordering. (See parameters GRAPH_SYMMETRIZE and GRAPH_SYM_WEIGHT in the Scotch and ParMETIS graph packages.) * Improved function Zoltan_LB_Eval returns more information about a decomposition to users. * Improved examples showing Zoltan usage in C and C++ are included in zoltan/example. * Improved support for builds under autotools, including builds of Zoltan's F90 interface. * New support for CMake builds and testing through Trilinos; builds of Zoltan's F90 interface are included. * Improved integration into Isorropia partitioners for Trilinos' Epetra classes. Backward compatibility: * Interfaces to Zoltan_Color, Zoltan_Order and Zoltan_LB_Eval have changed. * The Zoltan native build environment, while still distributed, will no longer be supported. Users should use the autotools or CMake systems. Builds of the Zoltan F90 interface are supported in both autotools and CMake. ------------------------------------------------------------------------------- Known issues in Release 10.0: * Several packages do not yet support the Windows platform. Packages that do not yet support the Windows platform will not be enabled with the Trilinos_ENABLE_ALL_PACKAGES, Trilinos_ENABLE_ALL_OPTIONAL_PACKAGES, Trilinos_ENABLE_ALL_FORWARD_DEP_PACKAGES, OR Trilinos_ENABLE_SECONDARY_STABLE_CODE options. Non-supported packages among external release packages currently include: Anasazi, FEI, MOOCHO, Pamgen, Phalanx, Phdmesh, PyTrilinos, Sundance, and Tpetra. * Building with MPI on Windows is not thoroughly tested. There are some issues that need to be resolved. Improved Windows MPI support will be added to an upcoming minor release. * g95 0.91 on OSX is known to produce a configure failure. Consider using gfortran, or disabling Fortran support with Trilinos_ENABLE_Fortran=OFF. Most, not all, Trilinos packages can be built with Fortran support disabled. ------------------------------------------------------------------------------- ############################################################################### # # # Trilinos Release 9.0 Release Notes # # # ############################################################################### Overview: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. All packages are self-contained, with the Trilinos top layer providing a common look-and-feel and infrastructure. Packages: The version 9.0 general release contains 37 packages: Amesos, Anasazi, Aztecoo, Belos, Didasko, Epetra, Epetraext, Fei*, Galeri, Ifpack, Isorropia, Kokkos, Komplex, Loca, Meros, ML, Moertel, Moocho, New_Package, NOX, Pamgen*, Phalanx*, PhdMesh*, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, Stratimikos, Sundance*, Teuchos, ThreadPool*, Thyra, Trilinoscouplings, Triutils, WebTrilinos, and Zoltan* (* denotes packages that are being released as a part of Trilinos for the first time.) The limited release contains an additional 4 packages that are available in special situations by request. These are: Claps, Intrepid, RBGen, and Tpetra. More information: Trilinos website: http://trilinos.sandia.gov =============================================================================== Package Release Notes: ------------------------------------------------------------------------------- Amesos (*) Amesos now includes Paraklete version 0.3. (*) Amesos 2.4 in Trilinos 9.0 is compatible with Tim Davis' SuiteSparse version 3.0.0 (not the latest version). (*) Known bug: Paraklete does not currently work on 64-bit machines. ------------------------------------------------------------------------------- Anasazi (*) The Anasazi package released in Trilinos 9.0 includes a new type of eigensolver. (*) The IRTR solvers are implicit versions of the Riemannian Trust-Region eigensolvers (Absil, Baker, Gallivan 2007). (*) Two implementations are provided, which balance computation/memory trade-offs via the ability to disable caching of operator applications. ------------------------------------------------------------------------------- Epetra Epetra support for PETSc matrices: The Epetra_PETScAIJMatrix class is a lightweight wrapper class for encapsulating PETSc serial and parallel AIJ matrices. Its intended audience is PETSc users who would like to build and apply Trilinos preconditioners and solvers. This class derives from the Epetra_RowMatrix class. ------------------------------------------------------------------------------- Isorropia Isorropia has expanded its scope from partitioning and load-balancing to include other algorithms for combinatorial scientific computing. The primary focus is still on partitioning and load-balancing of matrices and vectors. Version 3.0 includes a significant code refactoring compared to earlier versions to improve efficiency and robustness. (*) Isorropia now depends on Zoltan, which is available as a package in Trilinos 9.0. (Zoltan is automatically enabled by Isorropia.) (*) The default partitioning method for sparse matrices is Zoltan's hypergraph partitioner, which is significantly better than the internal method. (*) New features: Graph/matrix coloring and graph/matrix ordering (nested dissection). (*) Redesign of the class structure to support new features. An Isorropia::Operator is the parent class of Partitioner, Colorer, and Orderer. (*) Significant improvement in the efficiency (run time and memory usage) of redistributing Epetra matrices due to improved memory allocation. (*) New redistribute_reverse() method in the Redistributor to support moving vectors back and forth between two distributions. (*) When redistributing Epetra matrices, improved default choices for the maps. The call to FillComplete() is now optional, allowing the application to supply its own range and domain maps. (*) Several minor changes in interface to enforce more consistent naming schemes, but version 3.0 is fully backwards compatible. ------------------------------------------------------------------------------- Komplex The Komplex package includes a new class that provide equivalent real formulation capabilities to Epetra users called Komplex_LinearProblem.This is the newest capability and should be used if at all possible. Komplex_LinearProblem constructs an Epetra_LinearProblem from existing matrix and coefficient data. A real matrix of twice the dimension of the original complex-valued problem is explicitly constructed as an Epetra_CrsMatrix. Given this matrix and the user-supplied RHS (and possibly an initial guess), the Komplex_LinearProblem object is ready for use with any Trilinos solver and preconditioner. ------------------------------------------------------------------------------- ML (*) New support for PETSc smoothers in the case when the fine grid matrix is really a PETSc data structure. This is meant to be used in conjunction with the Epetra_PETScAIJMatrix class. (*) New use of MPI subcommunicators for direct solves with KLU on the coarsest level. This will mainly impact large scale simulations (>1K processors). (*) New restart capability to ensure behavior can be reproduced exactly from solve to solve. (*) New interfaces to Zoltan's hypergraph repartitioning algorithms. ------------------------------------------------------------------------------- MOOCHO Mostly minor changes which include: (*) Added response-only DiagonalQuadraticResponseOnlyOpt exampled based on an EpetraExt::ModelEvaluator. This is to show users how to run MOOCHO on an unconstrained problem in parallel. (*) Cleaned out some junk ------------------------------------------------------------------------------- Phalanx Phalanx is a local field evaluation kernel specifically designed for general partial differential equation solvers. The main goal of Phalanx is to decompose a complex problem into a number of simpler problems with managed dependencies to support rapid development and extensibility of the PDE code. Through the use of template metaprogramming concepts, Phalanx supports arbitrary user defined data types and evaluation types. This allows for unprecedented flexibility for direct integration with user applications and provides extensive support for embedded technology such as automatic differentiation for sensitivity analysis and uncertainty quantification. ------------------------------------------------------------------------------- RTOp Major refactoring of all code. (*) All interfaces in rtop/src/interfaces are now "memory safe" using Teuchos memory management classes (*) Support code in rtop/src/support has been significantly changed to remove duplication and bloat, provide for memory safely, and make it infinitely easier to create simple RTOp subclasses. (*) All of the concrete RTOp classes in rtop/src/ops_lib have been updated. (*) All of the simpler RTOps now use a simple set of macros and provide good examples for users on how to create their own RTOp classes. This includes very detailed unit tests for all of the code. (*) Old MPI junk that was not needed anymore was removed. (*) Removed SUNDIAL RTOp subclasses since these are not being used and there was no unit tests for them. With few exceptions, all changes should be backward compatible for clients of the RTOpPack::RTOpT abstract interface (search for "deprecated" comments). ------------------------------------------------------------------------------- Stratimikos Mostly minor changes which include: (*) Changed the name of Thyra::DefaultRealLinearSolverBuilder to Stratimikos::DefaultLinearSolverBuilder. (*) Added some better unit tests, especially for adjoint solves. ------------------------------------------------------------------------------- Teuchos The Teuchos package released in Trilinos 9.0 has some additional tools to assist users and developers with memory management and unit testing: (*) Memory Management Classes: The suite of debug-checking memory management classes has been extended to include the Ptr, ArrayView, and Tuple classes. Together with the existing classes RCP, ArrayRCP, and Array, these form a complete memory management system to replace all raw pointers to single objects and contiguous arrays of value-type objects in all application-level code. For a few details on how these should be used, see: http://www.cs.sandia.gov/~rabartl/ThyraCodingGuideLines.pdf (*) xUnit-like Unit Testing Infrastructure: Full featured support for native unit testing has been developed. See examples in teuchos/test/UnitTest. ------------------------------------------------------------------------------- Thyra (*) Added new templated Thyra::DefaultSerialDenseLinearOp[WithSolve]Factory subclasses to allow use of LAPACK for solving linear systems using Thyra::MultiVector objects as input. This was mostly just to allow for better, more independent unit tests. (*) Some refactorings to replace raw C++ pointers with safe Teuchos memory management classes (but a lot of work still needs to be done here) (*) Removed the SUNDIALS RTOp wrappers since they no longer exist in RTOp (*) Changed from Thyra::ETransp to Thyra::EOpTransp to avoid doxygen conflicts with Teuchos::ETransp. A backward-compatible typedef to Thyra::ETransp still exists to not break existing external code. With few exceptions, all changes should be backward compatible (search for "deprecated" comments). ------------------------------------------------------------------------------- Zoltan The Zoltan Toolkit provides critical data-management services to a wide range of parallel applications. Zoltan includes many utilities needed by unstructured and/or adaptive parallel applications. These utilities include (*) a suite of dynamic load-balancing and parallel partitioning tools (including geometric, hypergraph-based and graph-based algorithms) that distribute data over sets of processors for balanced computation with low interprocessor communication costs, (*) data migration tools that simplify movement of data to new parts, (*) parallel graph/matrix ordering algorithms for fill-reducing matrix ordering, including interfaces to PT-Scotch (LaBRI/INRIA-Bordeaux) and ParMETIS (U. Minnesota), (*) parallel graph coloring including distance-1 and distance-2 coloring, (*) distributed data directories that efficiently locate off-processor data, and (*) an unstructured communication package that greatly simplifies interprocessor communication. Zoltan's native interface is object-oriented and easy-to-use; it enables Zoltan to be used by a wide range of different applications. Zoltan is designed to be flexible and extensible, so different algorithms can be used, compared and added easily. Zoltan has been used in particle simulations, finite element methods with adaptive mesh refinement, linear solvers and preconditioners, circuit simulations, crash simulations and contact detection, and biological cell simulations. The Zoltan toolkit was first released in 2001; this release is Zoltan v3.1. New features in Zoltan v3.1 include (*) Graph/Matrix ordering interface to PT-Scotch, a high-quality graph ordering and partitioning library from LaBRI/INRIA-Bordeaux; (*) New matrix ordering interface that returns ordering information such as permutations and separators to the application; (*) New hypergraph partitioning options for inexpensively refining partitions; (*) Robustness improvements to Zoltan's parallel hypergraph partitioner and repartitioner; (*) New Autotools build environment; (*) Serial, non-MPI builds enabled through the Autotools build environment; and (*) Tight integration with the Trilinos project, including Trilinos package Isorropia, a matrix-based interface to Zoltan. Many applications use both Zoltan and Trilinos. Zoltan's inclusion in Trilinos simplifies the configuration and build process for those applications. It also enables tighter coupling between Trilinos packages that use Zoltan, such as the Isorropia package of Epetra-based interfaces to Zoltan's partitioning, ordering and coloring capabilities. Zoltan can still be built as a stand-alone toolkit separate from Trilinos, as backward compatibility with previous Zoltan releases has been maintained. Please visit the Zoltan Home Page (http://www.cs.sandia.gov/Zoltan) for more information on Zoltan. ------------------------------------------------------------------------------- ############################################################################### # # # Trilinos Release 8.0 Release Notes # # # ############################################################################### Overview: Trilinos is a collection of compatible software packages that support parallel linear algebra computations, solution of linear, non-linear and eigen systems of equations and related capabilities. The majority of packages are written in C++ using object-oriented techniques. All packages are self-contained, with the Trilinos top layer providing a common look-and-feel and infrastructure. Packages: The version 8.0 general release contains 30 packages: Amesos, Anasazi, AztecOO, Belos, Didasko, Epetra, EpetraExt, Galeri, IFPACK, Isorropia, Kokkos, Komplex, LOCA, Meros, ML, Moertel, MOOCHO, New_Package, NOX, Pliris, PyTrilinos, RTOp, Rythmos, Sacado, Stratimikos, Teuchos, Thyra, Triutils, TrilinosCouplings, and WebTrilinos. The limited release contains an additional 2 packages that are available in special situations by request. These are: Claps and Tpetra. In addition to many new features across most packages, Trilinos Release 8.0 contains 3 packages that are being released for the first time: - Belos (Next-generation iterative solvers) - Sacado (Automatic differentiation) - TrilinosCouplings (Select trilinos package interfaces) Package-specific features for these new packages, as well as many of the other packages are listed below. More information: Trilinos website: http://trilinos.sandia.gov =============================================================================== New Make Targets Trilinos now supports a large set of make targets. Prior to Trilinos 8.0, "make" built libraries, tests, and examples. Starting with Trilinos 8.0, "make" builds only libraries. Tests can be compiled using "make tests", and examples using "make examples". To build libraries, tests, and examples, the "make everything" make target can be used. Below is a listing of new and modified make targets that will be most useful to users: make - Builds just the libraries make install - Installs just the libraries make examples - Makes just the examples (assumes libraries are built) make install-examples - Install the examples (assumes libraries are installed) make tests - Makes just the tests (assumes libraries are built) make everything - Builds libraries, tests, and examples make install-everything - Installs libraries and examples =============================================================================== Shared Libraries - There is now rudimentary, experimental support for shared libraries under Linux and Mac OS X. Shared versions of Trilinos libraries are now required for the PyTrilinos package, so this is where the shared libraries are built. However, it is not necessary to enable the PyTrilinos package to build the shared libraries. Also, shared libraries are built for ALL enabled packages, not just those with python interfaces. To enable shared libraries without enabling PyTrilinos, use the configuration option --enable-shared Note that the build system for building shared libraries employs python, so this must be installed. However, the other PyTrilinos prerequisites -- swig and numpy -- are not required for building shared libraries. The resulting shared libraries are stored in your build directory in the sub-directory packages/PyTrilinos/shared and are installed in the same directory in which the static libraries are installed. Note that these shared libraries are considered EXPERIMENTAL. Only those shared libraries that are linked to PyTrilinos extension modules get tested. The other shared libraries might possibly have unresolved symbols. Please report any problems. - To get shared libraries to work, it may be necessary to manually add position-independent code options to the compiler flag variables. This is not necessary on Mac OS X or some flavors of Linux, because position-independent code is the default. However, on those Linux versions for which this is not the default, and on 64-bit systems, you will need to add these compiler options. For example, if the proper option for your compiler for position-independent code is "-fPIC", then your configuration invocation should include FFLAGS=-fPIC CFLAGS=-fPIC CXXFLAGS=-fPIC There is a standing feature request that this be done automatically, but it has not been implemented yet. =============================================================================== Package Release Notes: ------------------------------------------------------------------------------- Amesos - KLU and BTF have been upgraded to version 1.0. ------------------------------------------------------------------------------- Belos The Trilinos 8.0 release will contain the first public release of the Belos iterative linear solver package. Belos provides next-generation iterative linear solvers and a powerful linear solver developer framework. This framework includes - Abstract interfaces to linear algebra allowing the user to leverage any existing investment in their description of matrices and vectors. Linear algebra adapters are included for Epetra and Thyra. - Abstract interfaces to orthogonalization; implementations of iterated classical Gram-Schmidt (ICGS), classical Gram-Schmidt with a DGKS correction step, and iterated modified Gram-Schmidt (IMGS) are included. - Abstract interfaces to iteration kernels; implementations of conjugate gradient (CG), block CG, block GMRES, pseudo-block GMRES, block flexible GMRES, and GCRO-DR iterations are included. - Powerful solver managers are provided for solving a linear system using CG or block CG, GMRES or block GMRES with restarting, pseudo-block GMRES for performing single-vector GMRES simultaneously on multiple right-hand sides, and a single-vector recycled Krylov method (GCRO-DR). - Basic linear problem class is provided for the user to define a unpreconditioned or preconditioned (left, right, two-sided) linear system for Belos to solve. - Many examples for solving unpreconditioned, preconditioned linear systems with one or multiple right-hand sides using all the Belos solver managers. ------------------------------------------------------------------------------- Epetra - Epetra contains a new class called Epetra_VbrRowMatrix that completely supports the use of an existing Epetra_VbrMatrix object via the Epetra_RowMatrix interface. This new class addresses the fact that it is impossible to fully support Epetra_RowMatrix directly with Epetra_VbrMatrix (having Epetra_VbrMatrix inherit from Epetra_RowMatrix), so this new class should be used. ------------------------------------------------------------------------------- Moocho - Miscellaneous improvements for Thyra support. ------------------------------------------------------------------------------- Pliris - A problem with a large number of multiple Right Hand Sides has been addressed and a fix implemented. ------------------------------------------------------------------------------- PyTrilinos - PyTrilinos is now a single, self-contained package again. For the most part, this affects developers more than users, with one exception. The PyTrilinos package is enabled with the configuration option --enable-pytrilinos rather than the previous option, --enable-python, which had the effect of enabling python support within each package that provided wrappers. Individual PyTrilinos package wrappers can be enabled or disabled with --enable-pytrilinos-package --disable-pytrilinos-package where "package" refers to a specific Trilinos package. ------------------------------------------------------------------------------- Sacado Sacado is a set of automatic differentiation tools for C++ applications. It provides templated classes for forward, reverse and Taylor mode automatic differentiation. Sacado contains several basic AD classes: * Forward mode AD with the number of derivative components chosen at run-time: Sacado::Fad::DFad (most flexible) * Forward mode AD with the number of derivative components chosen at compile-time: Sacado::Fad::SFad (most efficient) * Forward mode AD with the maximum number of derivative components chosen at compile-time but actual number used chosen at run-time: Sacado::Fad::SLFad (sits between Sacado::Fad::DFad and Sacado::Fad::SFad in flexibility and efficiency) * Reverse mode: Sacado::Rad::ADvar * High-order univariate Taylor polynomials: Sacado::Tay::Taylor ------------------------------------------------------------------------------- Stratimikos - New Belos wrappers (Belos released for first time in Trilinos 8.0) ------------------------------------------------------------------------------- Teuchos - Name change from Teuchos::RefCountPtr to Teuchos::RCP The name of the class Teuchos::RefCountPtr has been changed to Teuchos::RCP and the file Teuchos_RefCountPtr.hpp is not Teuchos_RCP.hpp. You can update all of you C++ code automatically and safely using the script: Trilinos/packages/teuchos/refactoring/change-RefCountPtr-to-RCP-20070619.sh Please see the header of this script for instructions. If you choose not to refactor your code (e.g. by running the above script on it) then you can take your chances and just include the backward compatibility file Teuchos_RefCountPtr.hpp. However, this is *not* recommended because this file uses a terrible macro that is dangerous to have. - Improved parameter validation support ------------------------------------------------------------------------------- Thyra - Improved support for implicit linear operators with object labels and other improvements - Various miscellaneous improvements and additions ------------------------------------------------------------------------------- TrilinosCouplings TrilinosCouplings is a new package that was created as a place to put select interfaces between Trilinos packages. The code for the Trilinos 8.0 release was all taken from existing packages. Currently there is code for interfaces between Ifpack and ML, and ML and NOX. ------------------------------------------------------------------------------- The following packages did not report any significant feature updates for Trilinos 8.0: Anasazi, Aztecoo, Didasko, EpetraExt, Galeri, Ifpack, Isorropia, Kokkos, Komplex, LOCA, Meros, ML, Moertel, New_Package, NOX, RTOp, Rythmos, TriUtils, WebTrilinos =============================================================================== Known Issues - Sacado does not build on the Sun platform with no known workaround. See bugzilla bug 3586 for more information. - The test for TrilinosCouplings is currently not functioning. Changes need to be made to the configuration for the package to fix this issue. We plan to address this in one of the first release updates. On many machines this test will fail in mpi, in other cases, the test will simply output a message and exit. - We are aware of a number of other minor, platform-specific test failures: Linux (mpi): Anasazi BlockDavidson_test.exe (12 processors) PyTrilinos exMLAPI_Simple.p PyTrilinos exMLAPI_Smoother.py PyTrilinos testML_Preconditioner.py TrilinosCouplings ml_nox_1Delasticity_example.exe Linux (serial): Belos gcrodr_hb.exe PyTrilinos exAztecOO_RowMatrix.py PyTrilinos exNOX_1Dfem.py Rythmos basicExample_amesos.exe Mac (mpi): Meros testEpetraThyra.exe ML ml_user_smoothing.exe Mac (serial): Meros testEpetraThyra.exe ############################################################################### # # # Trilinos Release 7.0 Release Notes # # # ############################################################################### Overview: Trilinos is a collection of compatible software packages that support parallel linear algebra computations, solution of linear, non-linear and eigen systems of equations and related capabilities. The majority of packages are written in C++ using object-oriented techniques. All packages are self-contained, with the Trilinos top layer providing a common look-and-feel and infrastructure. Packages: The version 7.0 general release contains 27 packages: Amesos, Anasazi, AztecOO, Didasko, Epetra, EpetraExt, Galeri, IFPACK, Isorropia, Kokkos, Komplex, LOCA, Meros, Moertel, MOOCHO, ML, New_Package, NOX, Pliris, PyTrilinos, RTOp, Rythmos, Stratimikos, Teuchos, Thyra, Triutils, and WebTrilinos. The limited release contains an additional 5 packages that are available in special situations by request. These are: Belos, Capo, Claps, Jpetra, and Tpetra. In addition to many new features across most packages, Trilinos Release 7.0 contains nine packages that are being released for the first time: - Galeri (distributed linear system generation) - Isorropia (repartitioning and rebalancing) - Meros (segregated preconditioning) - Moertel (Mortar methods) - MOOCHO (Multifunctional Object-Oriented arCHitecture for Optimization) - RTOp (reduction/transformation operators) - Rythmos (transient integrator for ordinary differential equations and differential-algebraic equations) - Stratimikos (unified set of Thyra-based wrappers to linear solver and preconditioner capabilities) - WebTrilinos (web-based interface to some Trilinos packages - must be set up on a user's server/machine) Package-specific features for these new packages, as well as many of the other packages are listed below. More information: Trilinos website: http://software.sandia.gov/trilinos =============================================================================== External Package Capability The "external" Trilinos package makes it easy add additional packages that are external to Trilinos to the Trilinos build process. Users who develop additional capabilities on top of and outside of Trilinos may find this tool useful for simplifying their Trilinos interface. Packages that utilize this tool can easily be added to a user's existing set of Trilinos packages. Instructions for using the external package capability can be found in the Trilinos tarball in packages/external/README or on the web at http://software.sandia.gov/trilinos/external.html. =============================================================================== Amesos - Cleaned the MUMPS interface. Improved memory management by using smart pointers. Dropped the not-so-well-tested single-precision MUMPS. Improved passing of CNTL and ICNTL through the parameter list. - Increases the performances of the UMFPACK interface by a factor of at least 2. This means that the time requires by the Amesos wrappers is reduced by 2 -- the time required by UMFPACK still is unaffected. - Added to (almost) all classes profiling to evaluate how much time is spent in the amesos wrappers (that is, without considering any of the time spent in the called solver). This time is printed on screen when PrintTiming() is called. Amesos/Thyra adapters: What’s New: - Timing and output tracing: The Teuchos::TimeMonitor class has been incorporated to time the various factorization and solve operations and produce profiler-like output. In addition, the Teuchos::VerboseObject interface is now supported which allows some informational outputting to be sent to a configurable output stream. Known issues: - Incomplete parameter validation and inconsistent use of parameter lists: Currently, parameters not specified in the input parameter list are not appended with the default values and all parameters and sublists are not fully validated. This is an issue that needs to be resolved in the core Amesos source code. ------------------------------------------------------------------------------- Anasazi In Trilinos Release 7.0, the Anasazi eigensolver framework has been considerably refactored to provide simpler user interfaces as well as powerful eigensolver developer interfaces. - This release provides simpler user interfaces, called solver managers, for three eigensolvers: block Davidson, block Krylov-Schur, and locally-optimal block preconditioned conjugate gradient (LOBPCG). - Powerful lower-level interfaces are provided for each eigensolver, enabling the expert user to specialize their own solver manager. - Status test mechanisms have been incorporated into the Anasazi framework to give the user and solver manager the flexibility to direct the behavior of the eigensolver. - The Anasazi::OrthoManager provides the eigensolver with an abstract interface to orthogonalization and orthonormalization. This enables the user to specialize their own orthogonalization/orthonormalization if those already provided in Anasazi (CGS w/ iterative refinement or SVQB) are not sufficient. - Interfaces to linear algebra are provided through the templated traits classes: Anasazi::MultiVecTraits and Anasazi::OperatorTraits. These classes have template specializations for Epetra and Thyra. Testing functionality is also provided for user-written template specializations via the Anasazi::TestMultiVecTraits() and Anasazi::TestOperatorTraits() functions. - All Trilinos web documentation and Didasko tutorial have been updated to reflect the changes in the Anasazi framework. ------------------------------------------------------------------------------- AztecOO 3.5 - Additional scaling capabilities. - Improved I/O control. - Numerous small "hardening" changes. AztecOO/Thyra Adapters: What’s New: - Timing and output tracing: The Teuchos::TimeMonitor class has been incorporated to time the various setup and solve operations and produce profiler-like output. In addition, the Teuchos::VerboseObject interface is now supported which allows some informational outputting to be sent to a configurable output. - Acceptance of external preconditioner factory object: The AztecOO/Thyra adapters now except an external preconditioner factory object to create preconditioners. This allows Ifpack, ML, and Meros preconditioners to all be used in a seamless way. Any other compatible preconditioner can also be supported as well. - General Thyra operator support: Any general Thyra linear operator can now be supported including implementations based on product vector spaces. To be effective, an appropriate preconditioner factory must also be set to create a preconditioner. This is used in Meros to allow AztecOO to be used with the segregated block preconditioners. ------------------------------------------------------------------------------- Didasko - No significant changes. ------------------------------------------------------------------------------- Epetra 3.5 - New Epetra_BasicRowMatrix class: Facilitates easy development of user-defined adapters for the Epetra_RowMatrix interface. Greatly reduces the number of methods that must be be implemented. - New Epetra_JadMatrix class (which supercedes Epetra_JadOperator). This classes accepts an existing Epetra_RowMatrix object and creates an Epetra_JadMatrix object. The Epetra_JadMatrix object uses the so-called jagged diagonal data structure to store the sparsematrix coefficients in a format especially suitable for vector processors. Once constructed, the JadMatrix object can be used with any Trilinos package that requires an Epetra_RowMatrix or Epetra_Operator object. This implementation also contains special Cray compiler directives (_Pragma "ivdep") to force optimal vectorization. - New Epetra_InvOperator class. A simple class that interprets an existing Epetra_Operator as an inverse operator. - New method for Epetra Map and BlockMap objects to cheaply test if a map has 1-to-1 (uniquely-owned) global IDs: This method facilitates easy testing for whether or not a particular map can be used as an input argument to functions that require the map to have uniquely-owned global IDs. - New function called Create_OneToOne_Map in Epetra_Util namespace that creates an Epetra_Map with unique global IDs from an existing Epetra_Map that may or may not have unique global IDs. - New function called Create_OneToOne_BlockMap in Epetra_Util namespace that creates an Epetra_BlockMap with unique global IDs from an existing Epetra_BlockMap that may or may not have unique global IDs. - New function called Create_Root_Map in Epetra_Util namespace that creates an Epetra_Map from an existing Epetra_Map such that all global IDs are collected to the specified root processor and all other processors own no global IDs. - New method to compute the Frobenius norm of an Epetra_CrsMatrix or Epetra_VbrMatrix object. - Debugging code in Epetra_CrsMatrix to support detailed printing of intermediate matrix-vector multiplication information. This code is compiled if EPETRA_CRS_MATRIX_TRACE_DUMP_MULTIPLY is defined at compile time. Epetra/Thyra adapters: What’s New: - Refactored for new SPMD classes: The “fake” Epetra/Thyra adapters have been updated for the new Thyra SPMD support software. The names of the conversion functions in Thyra_EpetraThyraWrappers.hpp have also be simplified. ------------------------------------------------------------------------------- EpetraExt 3.5 - New class EpetraExt_ProductOperator: Supports implicit composition of multiple Epetra_Operator objects to act as a single operator. - New class EpetraExt_BlockCrsMatrix: Supports aggregation of multiple Epetra_CrsMatrix as sub-matrix objects to act as a single matrix. - New class EpetraExt_MultiMpiComm: Supports two-level communication where each processor is part of the global communicator and a sum-domain communicator. - EpetraExt_MatrixMatrix performance improvements: Substantial improvements to sparse matrix time sparse matrix multiplication for most cases. - InOut facilities: Substantial improvement to input and output functions that read and write matrix and vector objects to and from files. Added simplified interfaces that allow distributed matrix construction without requiring the user to define Epetra_Maps. Added support to write the implied matrix coefficients of an Epetra_Operator. Added support for HDF5 and XML formatted files. - ModelEvaluator: New capabilities to support generic solution interfaces for linear and non-linear systems via Thyra. EpetraExt/Thyra adapters: What’s New: - Thyra::EpetraModelEvaluator: This class wraps an EpetraExt::ModelEvaluator object (which deals only in Epetra-based objects) and provides an implementation of the Thyra::ModelEvaluator interface strictly in terms of abstract Thyra objects. Any linear solver and preconditioner can be supported by configuring a EpetraExt::ModelEvaluator object with a compatible linear solver factory object. ------------------------------------------------------------------------------- Galeri (new) Understanding, validating, using and developing algorithms and software tools for distributed linear algebra solvers, like Krylov accelerators and preconditioners, requires input data. This data should have three critical properties: 1. reflect real-life applications to a sufficient extent so that we can use them to predict performance; 2. be sufficiently simple to be amenable to mathematical analysis; 3. it is possible to write generators that easily provide instances of these problems. The goal of the Galeri package is exactly to produce these input data for linear solvers. As regards real-life applications, we have here selected PDE-type problems. Although Galeri can generate some non-PDE linear systems, surely there is a strong focus on PDE applications. Among them, the Laplace problem is probably the most widely studied application, and a broad range of results are available. For most solvers and preconditioners, often there is a sharp convergence bound that can be used to validate a particular class, or to get a sense of the performances of a new method. A Trilinos package that uses Galeri is the MatrixPortal module of WebTrilinos. Galeri's Matrix generation capabilities can help to make examples shorter and easier to read, since they can produce challenging linear systems in a few code lines. Therefore, the attention of the example's reader is not distracted by complicated instructions aiming to build this or that linear system. Since most linear algebra packages of Trilinos use Galeri, users will quickly become familiar with it. Galeri is used in the examples of the Amesos, IFPACK, and ML packages. For more details, please check the Galeri web page (http://software.sandia.gov/trilinos/packages/galeri). ------------------------------------------------------------------------------- Ifpack 3.1 - New class Ifpack_Chebyshev: Chebyshev polynomial preconditioner. - New class Ifpack_DiagPreconditioner: Simplifies construction and use of diagonal preconditioners. - New functionality to test if Teuchos ParameterList values are valid for Ifpack preconditioner. - Changed the hash table class for ICT and ILUT. The latter is then much faster than the previous version. The new class has a better memory usage and it is simpler to modify and extend. - Fixed a few memory leaks in the ILU factorization class. - Added Chebyshev preconditioner with point diagonal scaling. - Added support for UseTranspose(true) in Ifpack_AdditiveSchwarz, Ifpack_ILUT and Ifpack_Amesos. Ifpack/Thyra adapters: Thyra preconditioner factory adapters for Ifpack are new for this release. Known issues: - Incomplete parameter validation and inconsistent use of parameter lists: Currently, parameters not specified in the input parameter list are not appended with the default values and all parameters and sublists are not fully validated. This is an issue that needs to be resolved in the core Ifpack source code. ------------------------------------------------------------------------------- Isorropia 1.0 (new) - initial release, version 1.0 - Isorropia is a Trilinos interface to Zoltan repartitioning/balancing capabilities - requires Zoltan version 2 - several example programs illustrate usage - doxygen documentation on Trilinos website ------------------------------------------------------------------------------- Kokkos 1.1 - New experimental interface to OSKI optimized kernels. ------------------------------------------------------------------------------- Komplex 1.1 - No significant changes. ------------------------------------------------------------------------------- LOCA - Many of the internals of LOCA have been rewritten to more fully support multi-parameter continuation, constraint tracking, higher-order predictors and advanced bifurcation algorithms. The old framework has been completely removed, and therefore all users must upgrade their interface to the new framework. For a brief description of the new framework, see the New LOCA Framework page. In addition, some of the parameter list entries that control LOCA have changed. See the LOCA Parameter Reference Page for a description of the new parameter list structure. - A minimally augmented turning point formulation has been added to LOCA. This method appears to be significantly faster and more robust than the turning point methods based on the Moore-Spence formulation. - A modified pitchfork bordering method has been added to LOCA, which is similar to the modified turning point method already available. This method avoids the singular matrix solves in the original pitchfork bordering method. - Parallel and serial Hopf support has been added to LOCA. ------------------------------------------------------------------------------- Meros 1.0 (new) Meros is a segregated preconditioning package. It provides scalable block preconditioning for problems that couple simultaneous solution variables such as Navier-Strokes problems. The source documentation can be found on the Meros web page: http://software.sandia.gov/Trilinos/packages/meros/ For more information, see Trilinos/packages/meros/README-MEROS ------------------------------------------------------------------------------- ML ML/Thyra Adapters: Thyra preconditioner factory adapters for ML are new for this release. Known issues: - Incomplete parameter validation, inconsistent use of parameter lists, non-XML compatible parameters: Currently, parameters not specified in the input parameter list are not appended with the default values and all parameters and sublists are not fully validated. In addition, many of the ML parameters can not be read in from an XML file. For example, the parameters that control AztecOO from ML can not be directly read in from an XML file. These are issues that need to be resolved in the core ML source code. ------------------------------------------------------------------------------- Moertel (new) - Supplies capabilities for nonconforming mesh tying and contact formulations in 2 and 3 dimensions using Mortar methods. - Uses dual and standard Mortar methods to construct Lagrange multiplier constraints for nonconforming interfaces. - Serves as a programming language for other types of mesh tying approaches. ------------------------------------------------------------------------------- MOOCHO (new) MOOCHO is collection of software for the solution of large-scale simulation-constrained optimization problems using primarily reduced-space successive quadratic programming algorithms. Known issues: - Incomplete support for all Thyra::ModelEvaluator options: All of the bells and whistles for the different possible modes for simulation-constrained optimization through the Thyra::ModelEvaluator classes are not yet in place. Right now, the code handles the cases of exact direct sensitivities, finite difference direct sensitivities and adjoint sensitivities with some caveats. For example, even through the direct sensitivity method only requires the application of the operator DgDx (ModelEvaluator notation) onto vectors, the current implementation requires that a vector for transpose(DgDx ) be explicitly returned. In the next release of Trilinos, all modes should be fully supported without imposing undue requirements on the application. - Outdated linear algebra and model interfaces: MOOCHO currently uses its own linear algebra layer called AbstractLinAlgPack that actually predates (and helped to inspire) Thyra. In the next release, it is highly possible that MOOCHO will be refactored to use a linear algebra layer based directly on Thyra and perhaps the new Thyra handle layer which will help to help other Trilinos developers to be able to understand and develop algorithms in MOOCHO. This refactoring is also likely to radically change the NLP interfaces to move to a single ModelEvaluator-like interface that will allow for faster prototyping of new optimization algorithms. ------------------------------------------------------------------------------- New_Package - No significant changes. ------------------------------------------------------------------------------- NOX - NOX is now using reference counted smart pointers (RCPs) for memory management. Passing an RCP wrapped object through a method call implies a persisting relationship. We are using the Teuchos::RefCountPtr object for the RCP. - The NOX::Parameter::List has been removed. We are now using the Teuchos::ParameterList object. This has the same functionality with minor changes to the syntax of method calls. - NOX now has a non-optional dependency on the Teuchos package (also part of Trilinos). While it can be built stand-alone, we recommend building NOX as part of Trilinos with the teuchos library enabled to simplify dependencies. - NOX and LOCA now generate Makefiles that users can include in their own makefiles to get all dependencies correct. For example if NOX is built with Epetra support enabled, nox depends on epetra, aztecoo and ifpack headers and libraries. To keep the user from having to learn about those packages so they can link nox into their codes, just include the NOX file Makefile.export.nox file to get variables that have all sub package dependencies correct. In the installation directory, look at the files include/Makefiles.export.nox and include/Makefiles.export.nox.macros. The important flags in Makefile.export.nox are NOX_INCLUDES, NOX_LIBS, LOCA_INCLUDES, and LOCA_LIBS flags. The Makefile.export.nmox.macros file contains the compiler flags that were used to build the NOX and LOCA packages. It is very important to use consistent flags when linking your application against Trilinos. - Multivector support is no longer a configure option, but is automatically built as part of the library. - The epetra interfaces (NOX::Epetra::Interface namespace) have been changed. They now take an Epetra_Operator as an argument when evaluating the Jacobian and preconditioner objects. While this is redundant for our base epetra group (since it shares the same operator between groups), this allows users to override the eptra group and use separate operators for each group if desired. - There are 2 options for creating an Ifpack preconditioners. The original code where the "Preconditioner" option in the "Linear Solver" sublist was set to "Ifpack" and the new ifpack code "New Ifpack". The original option explicitly constructs an ifpack ilu object that has since been deprecated and will most likely be removed in the next release (Trilinos 8.0). The option "New Ifpack" uses the new ifpack factory object. You can now create a parameter list that directly uses the ifpack factory arguments and can create any ifpack preconditioner (not limited to ILU). We recommend switching to the "New Ifpack" preconditionerr interface asap. - In the epetra support, the preconditioner options "AztecOO", "New Ifpack", and "ML" allow users to recompute the preconditioner using the same graph so that preconditioner memory is not allocated and destroyed each linear solve. The new "Linear Solver" sublist key is "Preconditioner Reuse Policy" with the possible values "Rebuild", "Reuse", and "Recompute". If you choose "Rebuild", this is what nox has done in previous releases - destroy, reallocate and recompute the preconditioner for each linear solve. "Reuse" will use the same preconditioner for every linear solve. "Recompute" will recompute the preconditioner, but will try to efficiently reuse any objects that don't need to be destroyed. How efficient the "Recompute" option is depends on the type of preconditioner. For example if we are using ILU in Ifpack, the graph that is allocated does not need to be destroyed and recomputed even though the computation will recompute the factorization when the matrix changes. These changes support native Aztec, Ifpack and ML preconditioners. ------------------------------------------------------------------------------- Pliris 1.1 - Added a new method - Solve. This allows a user to split the factor and solve for a dense matrix. This is useful when the right hand side is changing in the numerical simulation. - A test case has been added to test this functionality. ------------------------------------------------------------------------------- PyTrilinos 3.0 PyTrilinos 3.0 is a significant structural change from version 2.0, although most of these changes will be invisible to the typical user. "PyTrilinos" used to refer to both a python package (here using the python definition of package, meaning "a module of modules") and to a small Trilinos package (here using the Trilinos definition of package, meaning a set of one or more related compiled libraries) of utility classes that helped to enable the python modules. The classes that used to comprise the PyTrilinos library have either been eliminated or moved to other Trilinos packages. The PyTrilinos Trilinos package now serves to enable certain cleanup functions. The most important of these is to fix a problem seen with MPI builds, where bad_cast exceptions can be raised because the python extension modules are linked to static libraries. If you are building Trilinos on Linux or Mac OS X and have enabled both python and MPI, the PyTrilinos package will go back and create dynamic versions of various Trilinos libraries (e.g., libepetra.so). These get stored in your build directory under packages/PyTrilinos/src PyTrilinos then goes back again and re-links the python extension modules (e.g. _Epetra.so) to these new dynamic libraries. This has eliminated several (but not all) problems seen when running PyTrilinos scripts in parallel. Note that if you wish to run python test scripts *prior* to installing Trilinos, you need to tell your shell how to find the dynamic libraries. You do this by setting an environment variable, either LD_LIBRARY_PATH, or DYLD_LIBRARY_PATH for Linux and Mac OS X respectively, to include the directory that contains the dynamic libraries. When you invoke mpirun, you must export this environment variable. For example, mpirun -x LD_LIBRARY_PATH -np 4 testVector.py -t When you run "make install", the dynamic libraries will get installed as well. Depending on where you specify installation, this may eliminate the need to specify and export these environment variables. -------------------- Several other changes have been made since PyTrilinos 2.0/Trilinos 6.0: * As the first part of these release notes indicate, MPI is explicitly supported. This support was considered "experimental" in PyTrilinos 2.0. * The build process has been significantly improved. PyTrilinos now uses the export Makefiles that are supported by many Trilinos packages, and this has greatly helped in using accurate lists of include paths, library paths and libraries. Furthermore, the PyTrilinos build system now parses Makefiles directly to obtain the values of user-configured variables, eliminating another source of build error. * NumPy support. PyTrilinos has been upgraded from compatibility with the now-obsolete Numeric module to its successor, NumPy. As of this writing, NumPy is in beta testing for release 1.0. PyTrilinos is compatible with NumPy 0.9.6 and 0.9.8, and has been tested against NumPy 1.0b, versions 2 and 4. * Much focus has been placed on improving the Epetra module. Previously, many Epetra class methods were wrapped, but if they had pointers in the argument list representing C arrays, these methods could not actually be used in python. A large percentage of these methods have been updated. Any python sequence can be used in place of input array arguments, and NumPy arrays are returned for output arrays. * More Epetra array-like classes now doubly-inherit from NumPy arrays. These classes are: + Epetra.IntSerialDenseMatrix + Epetra.IntSerialDenseVector + Epetra.IntVector + Epetra.MultiVector + Epetra.SerialDenseMatrix + Epetra.SerialDenseVector + Epetra.Vector When you instantiate one of these classes, the resulting object can also be treated as and will be recognized as a NumPy array. This creates a high-degree of compatibility with other python packages, such as SciPy, matplotlib, etc. * Exception handling added. Not all cases are yet handled, but many of the common ones are, and an infrastructure is in place for PyTrilinos developers to convert C++ exceptions into python exceptions. * The Teuchos module has been added and ParameterLists are explicitly handled now, but python dictionaries can be used in their place. Also, nested dictionaries are now recognized as sub-lists, greatly increasing the usefulness of this feature. * The Galeri module has been added. * For Trilinos release 7.0, the NOX module has been disabled. We have been unable to keep up with the significant changes made in the NOX package, but we are working on it. Hopefully, this module will be re-enabled in a minor future update, 7.0.x. * Documentation has been expanded. The documentation section of the PyTrilinos web site now covers prerequisites, build notes and has an individual page for each module covering differences between the C++ and python interfaces. ------------------------------------------------------------------------------- RTOp (new) RTOp (reduction/transformation operators) provides the basic mechanism for implementing vector operations in a flexible and efficient manner. This software was basically refactored out of Thyra from the last release of Trilinos 6.0 since MOOCHO, and in the future Tpetra, directly depends on RTOp but not Thyra. Contained in RTOp is: a) a small number of interoperability interfaces b) support software including code for the parallel SPMD mode based on only Teuchos::Comm (and not MPI directly) c) a library of pre-implemented RTOp subclasses for everything from simple AXPYs and norms, to more specialized vector operations. ------------------------------------------------------------------------------- Rythmos 1.0 (new) Rythmos is a transient integrator for ordinary differential equations and differential-algebraic equations with support for explicit, implicit, one-step and multi-step algorithms. The fundamental design of Rythmos is aimed at supporting operator-split algorithms, multi-physics applications, block linear algebra, and adjoint integration. New Features: - Everything is new. This is the first release for Rythmos. - Implicit Backward Differentiation Formula Stepper: This stepper provides a re-implementation of the implicit algorithms in the LLNL Sundials code CVODE. This is an implicit BDF integrator for ODEs which uses variable step-sizes and variable-orders first through fifth. - Explicit Runge-Kutta Stepper: This stepper provides a four stage fourth order explicit RK steper with fixed step-sizes provided by the application. Full variable step-size support and application provided Butcher tableaus will be supported in the next release. - Forward Euler Stepper: This stepper provides the explicit forward Euler algorithm with fixed step-sizes provided by the application. Full variable step-size support will be in the next release. - Backward Euler Stepper: This stepper provides the implicit backward Euler algorithm with fixed step-sizes provided by the application. This class supports ODEs and DAEs. Full variable step-size support will be in the next release. Known Issues: - Currently Rythmos does not have an interface to NOX. This will be provided through an EpetraExt::ModelEvaluator interface in NOX in the next release. Therefore the nonlinear solving capabilities in Rythmos are limited to a simple undampened Newton iteration in Thyra::TimeStepNewtonNonlinearSolver. - The InterpolationBuffer base class is just starting to be developed and has not been compiled or tested in any way yet. It is provided as an example of what the interface could look like and where the integrator class will be derived from. - An integrator class does not yet exist. It will depend on the InterpolationBuffer class and both of these will be completed in the next release. Therefore users should use the Stepper class directly to step differential equations forward in time. When this class is implemented it will enable solving operator-split and multi-physics problems. - The Explicit Taylor Polynomial Stepper is in active development and under current research. It is provided only as an example interface. This stepper may be completed in the next release. ------------------------------------------------------------------------------- Stratimikos (new) Stratimikos is a set of wrappers of common linear solver functionality through Thyra. In this initial release, Stratimikos provides the “Façade” class Thyra::DefaultRealLinearSolverBuilder that provides a single parameter list (i.e. Teuchos::ParameterList) driven interface to much of the linear solver and preconditioner capability contained in Trilinos. For example, the class Thyra::DefaultRealLinearSolverBuilder is the recommended way to access the linear solver adapters in Amesos/Thyra, AztecOO/Thyra, and Belos/Thyra (not in Trilinos 7.0) as well as the preconditioner adapters in Ifpack/Thyra and ML/Thyra. With a single parameter list that can be read from an XML file, the user can select for a wide variety of different linear solver and preconditioner combinations. Known issues: - Incomplete parameter validation and inconsistent use of parameter lists: While many of the parameter lists and sublists accepted by the Stratimikos façade class Thyra::DefaultRealLinearSolverBuilder are fully validated and will write default parameter values when missing in the input parameter list such as for AztecOO/Thyra, other sublists for other solvers are not. This is not specifically a Stratimikos issue but instead is an issue for the core code in Ifpack, ML, and Amesos. ------------------------------------------------------------------------------- Teuchos In Trilinos Release 7.0, the Teuchos tools package has some additional functionality available to Trilinos developers and users: - This release provides a simple XML parser that is compiled by default when eXpat is not available, enabling the perpetual use of Teuchos' XML utilities like XML-ParameterList reading and writing in any code. Also, the Teuchos' XML utilities are now built by default. - Complex scalar-type support is built by default for scalar-type templated utilities like the ScalarTraits, BLAS, LAPACK, and SerialDenseMatrix. - A reference-counted class similar to RefCountPtr designed to manage an array of objects is available, called ArrayRefCountPtr. ------------------------------------------------------------------------------- Thyra What's New: - Implicit Linear Operators: Thyra now includes support software that implements implicit zero, identity, diagonal, added, multiplied, scaled/adjoint, and blocked linear operators that complement the existing product vector space and (multi)vector subclasses. These implicit operators allow you to create arbitrarily complex, nested, linear operators that are useful in a variety of contexts (e.g. Schur complement solvers, block preconditioners, time/space discretizations etc.). Look for these in the “ANA Operator/Vector Support” collection and click on “ANA Development Support” link. - Removal of explicit MPI support/dependence: The separate serial and MPI support software collections for vector spaces, vectors, multi-vectors and linear operators have been merged into a single set of SPMD support software that is only dependent on the small new Teuchos::Comm interface. This got rid of a lot of duplicate code and will allow for other more specialized implementations of communication. - Java-like handle classes supporting Matlab-like operator overloading: Thyra now includes a set of Java-like handle classes for wrapping vector spaces, vectors and linear operators and allowing you to write expressions like y=x+alpha*z and y=beta*A*x + B*y that don’t result in any unnecessary temporary copies unless required.. The linear operator handle class also provides full support for the implicit linear operator subclasses described above. Look for these in the “ANA Operator/Vector Support” collection and click on “ANA Development Support” link. - Zero-based indexing: All of Thyra has been changed from largely 1-based indexing to completely zero-based indexing. This especially impacted the multi-vector column access and subview functions. Therefore, any current users are cautioned to carefully review their codes to see what impact this will have. Note that most single-vector ANAs will not be affected by this change at all since there is not such indexing used in these types of algorithms. - Compile-time enabled runtime checks: Almost all runtime tests in Thyra-related software must be explicitly enabled by adding –enable-teuchos-debug to the configure line. This replaces having to manually define a _DEBUG macro as was required in the last release of Trilinos. We highly recommend that this flag be turned on by all users and developers while developing with Thyra-related software. Once a program is working and you want to run timed studies, then you should remove –enable-teuchos-debug, and turn up the compiler optimization flags. - Expanded linear solver and preconditioner factory interfaces: The Thyra linear solver interfaces in Trilinos 6.0 have been refined to now include the concept of a preconditioner factory. Adapters are found in Amesos, AztecOO, Ifpack and ML. - Nonlinear model evaluator: The Thyra::ModelEvaluator interface now supports functionality for simulation-constrained optimization (i.e. as used by MOOCHO). Known issues: - Long compilation times: Compilation times for the examples and tests can be very excessive on older machines or when using some compilers. The reason for this is that Thyra is entirely templated code currently and uses implicit template instantiation. Therefore, when every *.cpp test/example file is compiled, the compiler has to parse and analyze every header and create instantiations over and over again. In the future, the option of performing explicit template instantiation will be available and this will greatly speed up the build process but will also inhibit some of the flexibility of supporting different Scalar types and might complicate the build process. In the mean time for this release, to speed up the builds for Trilinos, users might consider adding –disable-thyra-tests and –disable-thyra-examples to the configure line. - Wrong behavior of explicit element access functions: The behavior of the Thyra::[Multi]VectorBase::acquireDetachedView(…) functions is not consistent with the nature of abstract numerical algorithms (ANA) in single program multiple data (SPMD) mode. The current behavior facilitates the interoperability of abstract vectors in an SPMD configuration without requiring lots of dynamic casts but is the wrong behavior from the ANA perspective. This will be corrected in the next version of the release and specialized interfaces will be developed for (multi)vector-(multi)vector interoperability and the behavior of the functions Thyra::[Multi]VectorBase::acquireDetachedView(…) will be the same in every process of an SPMD, or any other type, of runtime configuration. Therefore, users are warned to isolate any code that depends on the current behavior of the Thyra::[Multi]VectorBase::acquireDetachedView(…) functions since this behavior will change on the next release. Note that most user code will never use these functions so this future refactoring this should cause serious problems for users. - Unnecessary temporary creation in handle layer code: The performance of handle-based code can be less efficient that nonhandle-based code in some cases, such as the creation of extra temporary vectors. This may be fixable in later releases through more careful consideration operator evaluation logic. In the mean time, studying the current implementation and some experimentation may help. - Does not compile on IBM xlC compiler: Thyra and all Thyra-related software can not be compiled on the IBM AIX C++ compiler (i.e. xlC). The problem is that this C++ compiler gets tripped up with calling one version of an overloaded virtual function and declares the call to be ambiguous (which about 6 other distinct compilers consider the call to be non-ambiguous). Specifically, it declares that a call to the acquireDetachedView(…) function to be ambiguous. The next release of Thyra might remove the overloaded functions and replace them with distinct names. - ConstHandle classes will be removed: The handle layer (e.g. Thyra::[Const]Vector, Thyra::[Const]LinearOperator etc.) is likely to change after the initial release of Trilinos 7.0. The change will involve getting rid of the ConstHandle classes and going to a runtime protection of const involving just a single Handle class (e.g. Thyra::Vector and Thyra::LinearOperator). Any code that uses the two-class handle system [Const]Handle should have no little problem being updated after the refactoring. In fact, typedefs could allow all user code to be recompiled without change in most cases (but an actual code change would be a better long term solution). ------------------------------------------------------------------------------- TriUtils - No significant changes. ------------------------------------------------------------------------------- WebTrilinos (new) WebTrilinos is a scientific portal, a web-based environment to use several Trilinos packages through the web. If you are teaching sparse linear algebra, you can use WebTrilinos to present code snippets and simple scripts, and let the students execute them from their browsers. If you want to test linear algebra solvers, you can use the MatrixPortal module, and you just have to select problems and options, then plot the results in nice graphs. From the user's perspective, the only component required to use WebTrilinos is any browser and an internet connection. Then, (simple) C++ and Python programs can be written on a web form, executed on a server, and the output is sent back to the user's browser. Code snippets for most of Trilinos and PyTrilinos packages are already available in convenient repositories. WebTrilinos also contains a problem solving environment (PSE) for the analysis of linear algebra solvers, like direct solvers, Krylov solvers, and preconditioners. This environment is called MatrixPortal. To be installed, WebTrilinos requires the following: 1. a web server, like Apache; 2. PHP installed on the web server; 3. an installed version of Trilinos, with the following packages: Teuchos, Epetra, EpetraExt, AztecOO, IFPACK, Amesos, ML, Galeri, PyTrilinos (and, of course, WebTrilinos itself); 4. the PyChart package; 5. the convert *nix tool to convert image files. WebTrilinos comes with a set of easy-to-use tools that suggest the configuration options. For more details, please check the WebTrilinos web page (http://software.sandia.gov/trilinos/packages/webtrilinos). ############################################################################### # # # Trilinos Release 6.0 Release Notes # # # ############################################################################### Overview: Trilinos is a collection of compatible software packages that support parallel linear algebra computations, solution of linear, non-linear and eigen systems of equations and related capabilities. The majority of packages are written in C++ using object-oriented techniques. All packages are self-contained, with the Trilinos top layer providing a common look-and-feel and infrastructure. Packages: The version 6.0 general release contains 18 packages: Amesos, Anasazi, AztecOO, Didasko, Epetra, EpetraExt, Ifpack, Kokkos, Komplex, LOCA, ML, New_Package, NOX, Pliris, PyTrilinos, Teuchos, Thyra, and Triutils. The limited release contains an additional 9 packages that are available in special situations by request. These are: Belos, Capo, Claps, Jpetra, Meros, Rythmos, Tpetra, TSF, and TSFExtended. In addition to many new features across most packages, Trilinos Release 6.0 contains one new package, Thyra. This package represents our first general release of an abstract interface to support generic programming. Thyra contains interfaces for basic linear algebra objects, a first linear solver interface, and supporting software. Furthermore, adapters for Amesos, AztecOO, Epetra, Ifpack, ML, NOX and Teuchos provide a broad set of functionality to users of Thyra. Finally, since Thyra is fundamentally an interface, users can write code based on Thyra without committing to any particular concrete linear algebra package, but instead have access to a growing collection of supported concrete libraries. A second major feature is the much improved design and implementation of PyTrilinos. PyTrilinos capabilities are now primarily distributed across Trilinos packages (although critical common functionality is still in the PyTrilinos package), so that Epetra, EpetraExt, Triutils, AztecOO, Amesos, Ifpack, ML, LOCA, NOX and New_Package are accessible to Python applications. PyTrilinos also supports parallel MPI execution without additional Python modules, and parallel performance for large-grain computations matches native Trilinos performance. Finally, Python users are able to define their own matrix modules in Python, satisfying Trilinos abstract interface, that can be used by Trilinos solvers. Other package-specific features are listed below. More information: Trilinos website: http://software.sandia.gov/trilinos =============================================================================== Amesos - Improved memory management and performances - Added Scalapack, TAUCS and PARDISO support. - Python interface for the factory and most classes. - Amesos_Klu: - Improved performance on small matrices - Supports non-standard indexing (i.e. {1,2,5,8,9} - Supports domain and range maps which differ from the matrix row map - Amesos_Superlu and Amesos_Superludist: - Compatible with all Amesos solvers - Memory leaks eliminated - Thyra wrappers for linear solve interface. These adapter subclasses allow any amesos direct solver to be incorporated, in a seamless way, into abstract numerical algorithms written using the Thyra operator/vector abstractions. - Makefile.export support - Eliminated dependence on triutils - Improved robustness through enhanced nightly testing Known bugs: - Amesos_Dscpack has memory leaks, prints to standard out and may crash if SymbolicFactorization() is called multiple times on the same Amesos object. - Amesos packages other than Amesos_Klu do not accept non-standard maps (e.g. one with indices {1,2,5,8,9, ... } ) - Amesos packages other than Amesos_Klu do not accept range and domain maps which differ from the matrix map - Superludist fails on some matrices - Error handling on singular and near singular matrices is inconsistent ------------------------------------------------------------------------------- Anasazi In Trilinos Release 6.0, Anasazi has a new solver, enhanced functionality and much more documentation. - This release of Anasazi provides abstract implementations of three eigensolvers: block Davidson, block Krylov-Schur, and locally-optimal block preconditioned conjugate gradient (LOBPCG). LOBPCG is the newest abstract eigensolver implementation in the Anasazi framework for computing solutions to symmetric eigenvalue problems. - All three eigensolvers in Anasazi use the Anasazi::SortManager to sort for the eigenvalues of interest. This functionality was previously available for only the block Krylov-Schur implementation. - Anasazi solvers now collect timing information that will be outputted if the Anasazi::OutputManager is given the Anasazi::TimingDetails flag. - The Anasazi framework now provides testing functionality for user-written interfaces to Anasazi::MultiVecTraits and Anasazi::OperatorTraits. This functionality gives users a way to perform a sanity check on their interface. - Anasazi has an updated and expanded tutorial in Didasko. ------------------------------------------------------------------------------- AztecOO - Python interface. - Thyra linear solver adapters : Allows an AztecOO solver to be incorporated, in a seamless way, into abstract numerical algorithms written using the Thyra operator/vector abstractions. ------------------------------------------------------------------------------- Didasko - New chapter on Anasazi. ------------------------------------------------------------------------------- Epetra - Python interface for several objects, in serial and MPI: Epetra_Map, Epetra_CrsMatrix, Epetra_LinearProblem, Epetra_Vector, Epetra_MultiVector, Epetra_SerialDenseVector Epetra_SerialDenseMatrix, and more. - Thyra adapters for vector space, linear operator, vector and multivector classes. ------------------------------------------------------------------------------- EpetraExt - Python interface for I/O ------------------------------------------------------------------------------- IFPACK - Python interface for the factory class ------------------------------------------------------------------------------- Kokkos - No notable changes. ------------------------------------------------------------------------------- Komplex - No notable changes. ------------------------------------------------------------------------------- LOCA New features: - A constraint tracking feature has been added to LOCA where the user can specify additional algebraic constraints that must be satisfied along with the residual. Examples include boundary conditions, phase conditions in periodic orbits, etc. The resulting Newton system can be efficiently solved using the QR method discussed below. This capability is only available using the LOCA::NewStepper also discussed below. - A QR method for solving augmented systems of equations in parallel has been added, and is an extension of the Householder method already available to systems with more than one augmented row/column. This method allows bordered systems of equations to be solved in roughly the same time as original system and is well-conditioned even when the original system is nearly singular. This capability is only available using the LOCA::NewStepper discussed below. - Many of the internals of LOCA have been rewritten to more fully support multi-parameter continuation, constraint tracking, higher-order predictors and advanced bifurcation algorithms. This process is mostly, but not fully complete. This functionality is available by choosing the LOCA::NewStepper for continuation instead of the original LOCA::Stepper. However pitchfork and Hopf continuation are currently not available in the new framework. Documentation for this new framework can be found on the New LOCA Framework page. - LOCA's interface to eigensolvers has changed slightly and now uses a strategy interface approach instead of relying on the group to provide computeEigenvalues() and saveEigenvalues() methods. This provides a more natural decoupling of the parallel linear algebra data structures (i.e., the group) from the eigensolver method/package (eigensolver strategy object). The use of strategy interfaces instead of group methods is a major theme in the new LOCA framework, and is discussed more fully on the new framework page. Other notes: - Teuchos::RefCountPtr support has been added to improve software quality. For the most part, ref-count pointers are only used in the new framework. - Many regression tests have been added to improve software quality. - Libtool support has been removed from LOCA due to portability issues. - Python support is temporarily disabled in this release due to a major refactor of the build system for python wrappers in Trilinos. Portability notes: - There currently is a portability issue with LOCA to the Solaris platform using the Sun Forte 7 compilers. LOCA builds on this platform but does not run correctly. It appears the problem is compiler related as the virtual table for some LOCA objects is not setup correctly. All of the LOCA examples and any LOCA tests involving continuation runs fail with a segmentation fault. It is not known whether LOCA runs correctly when built with version 10 of the Sun compilers. See bugzilla bug 1238 for more information on this issue. ------------------------------------------------------------------------------- ML - Improved the organization of the MLAPI source files and examples. Now the compilation of the MLAPI sources is about 20% faster, and the compilation of the MLAPI examples up to 3 times faster. Some never-used examples and classes have been deleted. - Drop the support for command line parameters. A similar capability is supported by the Python interface. - Repartitioning is now fully available through the MultiLevelPreconditioner interface. - Completed the ML wrapper for Python, using SWIG. The ML module still requires a manual configuration of shared libraries, as done (on Linux/GCC at the moment) with script make_shared_linux.sh, located in the PyTrilinos directory. The basic functionalities of the MultiLevelPreconditioner class are available, for both serial and parallel runs. The ML module is compatible with the Epetra and AztecOO modules. - Changed the wrapper names and contents for Epetra matrices. Now the dynamic cast to Epetra_CrsMatrix and/or Epetra_VbrMatrix is done only once in the construction of the preconditioner. This results in an improvement of the performances up to 30% for smore test problems. - Added a simple finite element code, that can be used to test ML and MLAPI preconditioners. The code offers a pure Galerkin and a SUPG discretization for second order PDEs, in 2D and 3D, using triangles, quads, tets, and hexahedra. L2 and H1 norms of the computed solution and error can be computed. Results can be visualized using MEDIT. - In the MLAPI namespace, added class MultiLevelAdaptiveSA, which implements the \alpha SA algorithm (computation of slow converging modes for problems with non-smooth kernels). - Added a class, Ifpack_ML, that wraps an MultiLevelPreconditioner as Ifpack_Preconditioner, so that ML can be used as local solver in a domain decomposition preconditioner. - Extended capabilities to read matrices from file in various formats. - Added support for adaptive smoothed aggregation within MLAPI. A new class, called MultiLevelAdaptiveSA, has been added. - Added a prototype of class for non-symmetric smoothed aggregation. - Added capability to write visualization files in legacy VTK (Visualization toolkit) format. These are readable by paraview, which is freely available from www.paraview.org. Supports 1D/2D/3D point cloud visualization for aggregates, as well as solution visualization. ------------------------------------------------------------------------------- New_Package - PyTrilinos support: Illustrates how a package can provide Python support. Used by several other packages to provide new capabilities for PyTrilinos. ------------------------------------------------------------------------------- NOX - Refactor of configure for nox to align with the rest of Trilinos. We now use the same m4's that other packages use. Also changed the way the examples are configured so they are consistent with the tests. Added implicit compilation of ml and anasazi support. - Addition of the export makefile system to enable easy interfacing to external applications. - NOX now has a required dependency on Teuchos, it must be built as part of Trilinos. ------------------------------------------------------------------------------- Pliris - No notable changes. ------------------------------------------------------------------------------- PyTrilinos In addition to python support present in Trilinos Release 5.0 for Epetra EpetraExt NOX NOX.Epetra python interfaces have been added for the following packages: Amesos AztecOO IFPACK LOCA ML New_Package Triutils Additionally, MPI support has been added. Specifically, the Epetra.MpiComm class has been wrapped. A new class, Epetra.PyComm, has been added, which returns an Epetra.SerialComm for serial builds and an Epetra.MpiComm for MPI builds. For an MPI build, MPI_Init() is automatically called when the Epetra module is imported and MPI_Finalize() is automatically registered with the "atexit" module. Thus python scripts can be written that are identical for serial and MPI runs. Configuration, building and installing -------------------------------------- Python interfaces are enabled at configuration time now using the --with-python[=path] or --enable-python[=path] options, which are equivalent. During "make", python interfaces will be built for every package that both supports python and is enabled. (In Release 5.0, the four supported packages all had to be enabled. The --enable-pytrilinos configuration option, which enabled PyTrilinos in Release 5.0, now only enables a small utility library used by all of the python interfaces. The --enable-pytrilinos option is not strictly needed by end users, as the PyTrilinos package is automatically enabled by either --with-python or --enable-python.) Python 2.3 or higher is highly recommended. Some packages can be built against python 2.2, but there are some packages that require python 2.3. SWIG (Simple Wrapper Interface Generator) version 1.3.23 or higher is required to generate the wrapper code. These wrappers are not pre-built because they can be affected by configuration options. Configure will find swig if it is in your standard path, or you can tell configure where to find it using the --with-swig=PATH option. The Numeric python module is required. Do not configure with C flags -ansi or -pedantic. Python supports arbitrary precision integers and these options will cause the compiler to fail. The "make install" command will install the python interfaces (in addition to the standard package libraries and header files, of course). If configured with --prefix=PATH, the modules will be installed in PATH/lib. Make sure your PYTHONPATH environment variable is set correctly. If --prefix=PATH is not provided, the modules will be installed in the standard location determined by where the python executable is installed. This is often not /usr/local/, which is the default installation location for other Trilinos packages. Depending on how python was installed, this usually requires root access. Testing ------- >From the top build directory, or from a package top build directory, you can invoke "make run-pyexamples" or "make run-pytests" to execute all the scripts in the example or test directories, respectively. This will give concise output regarding failure or success for each script. Detailed results of the tests that have been run can be found in the packages/PACKAGE_NAME/test/runtests-results/ directory of the build directory. Examples -------- An important change was made to the directory structure for Release 6.0. The python wrapper generation code is now contained within each package, under a directory named "python". Within this directory are "src", "test", "example" and possibly other sub-directories. For example, the epetra directory structure now includes packages/epetra/python/ packages/epetra/python/example/ packages/epetra/python/src/ packages/epetra/python/test/ In the python/example sub-directory of each supported package, there will be one or more example python scripts demonstrating how to use the given module interface. The python/test sub-directories are for unit tests. If you are familiar with the python unittest module, these test scripts can provide additional examples of how to use the given module interface. The example and test scripts are copied from the source directory to the build directory when "make" is run. If these scripts are run from the build directory, they are designed to import the local build (uninstalled) versions of the Trilinos python interface modules. If run from a different location (say, the source directory, or if you have copied them to another location), the scripts will still work as long as the python interfaces have been installed in a location where python can find them. Using PyTrilinos ---------------- At this time, PyTrilinos documentation is admittedly incomplete. However, some documentation is available at http://software.sandia.gov/trilinos/packages/pytrilinos/documentation.html where you can find current lists of what packages are supported and which classes and functions within those packages have been wrapped. PyTrilinos modules should be imported from a python script using, for example, the >>> from PyTrilinos import Epetra syntax. Not all classes of all supported packages have been wrapped. One way to see what is available is to use the dir() function on a module: >>> dir(Epetra) For the most part, the python versions of functions, constructors and class methods use the same return values and argument lists as their C++ counterparts. Therefore, the individual package documentation is a good starting place for what is available, and for proper usage. However, it often makes sense to change the python argument lists -- for example, we may allow the use of a python list in place of a pointer to a C array, and we may then eliminate the integer size argument from the argument list, since it can now be obtained implicitly; or an output argument may be moved to a function's return value, often changing the return value to a tuple. Fortunately, all wrapped methods and functions have a documentation string that indicates correct usage. Documentation strings in python can be obtained with the help() function. For example: >>> help(Epetra.CrsMatrix.InsertGlobalValues) Help on method InsertGlobalValues in module Epetra: InsertGlobalValues(*args) unbound Epetra.CrsMatrix method InsertGlobalValues(self, int GlobalRow, int NumEntries, double Values, int Indices) -> int InsertGlobalValues(self, int Row, int Size, SerialDenseVector Values, IntSerialDenseVector Entries) -> int InsertGlobalValues(self, int row, PyObject Values, PyObject Indices) -> int The PyObject type that will often appear in these documentation strings refer to arbitrary python objects, but often are expected to be containers such as lists, tuples or Numeric arrays. In these cases, some experimentation may be in order. For Developers -------------- By convention, the code to build individual python interfaces now resides within each package, in the sub-directory "python". For a template of how to wrap a Trilinos package, see the new-package package, and in particular the packages/new_package/python/Instructions.txt file. The PyTrilinos package itself is now a small library of utility classes and functions, intended to ease repetitive tasks that come up frequently when wrapping Trilinos packages. For more details, contact Bill Spotz, wfspotz@sandia.gov. ------------------------------------------------------------------------------- Teuchos - No notable changes. ------------------------------------------------------------------------------- Thyra (new) - Defines fundamental abstract interfaces for vectors, multi-vectors, vector spaces, and linear operators that form the foundation for all abstract numerical algorithms. - These interfaces will eventually be use to provide uniform interoperability between a number of Trilinos (e.g. Belos, Anasazi, NOX, Rythmos, MOOCHO) and non-Trilinos packages and to encapsulate application/physics codes. - Also included are a small number of extended interoperability interfaces such as: - Interface for linear operators that support a solve operation - Other miscellaneous interoperability interfaces - Also included is adapter support code and very general concrete implementations for: - Support for specialized scalar products for vector spaces - Support serial vector, multi-vector, vector space, and linear operator implementations - Support MPI-based parallel vector, multi-vector, vector space, and linear operator implementations - Also included is utility code for helping to write abstract numerical algorithms: - Unit tests for linear operators - Composite objects: product vectors, implicit operators (diagonal, scaled/transposed, multiplicative etc.) - Explicit access to vector and multi-vector coefficients ------------------------------------------------------------------------------- Triutils - Python interface for the matrix gallery ------------------------------------------------------------------------------- CLAPS (limited release only) - The CLAPS package now contains two domain decomposition preconditioners/solvers. The first, named CLOP, is based on a classic overlapping Schwarz approach with an algebraically constructed coarse space. The second, named CLIP, is an iterative substructuring (Schur complement) approach that can be viewed as a primal counterpart of FETI-DP. ############################################################################### # # # Trilinos Release 5.0 Release Notes # # # ############################################################################### Overview: Trilinos is a collection of compatible software packages that support parallel linear algebra computations, solution of linear, non-linear and eigen systems of equations and related capabilities. The majority of packages are written in C++ using object-oriented techniques. All packages are self-contained, with the Trilinos top layer providing a common look-and-feel and infrastructure. Packages: The version 5.0 general release contains 17 packages: Amesos, Anasazi, AztecOO, Didasko, Epetra, EpetraExt, Ifpack, Kokkos, Komplex, LOCA, ML, New_Package, NOX, Pliris, PyTrilinos, Teuchos, and Triutils. The limited release contains an additional 9 packages that are available in special situations by request. These are: Belos, Claps, Jpetra, Meros, Tpetra, TSF, TSFCore, TSFCoreUtils and TSFExtended. Some of the significant new features: - Four new packages: Anasazi (Eigensolvers), Didasko (Tutorial), Pliris (Distributed dense solvers), PyTrilinos (Python interface to Trilinos libraries). - Trilinos tutorial delivered as part of a new package called Didasko. - Kernel performance in Epetra substantially improved, especially for multiple rights. - Initial kernel support for vector architectures in Epetra. - Significant improvements and enhancements in most existing packages. More information: Trilinos website: http://software.sandia.gov/trilinos =============================================================================== Amesos (version 2.0) - Improved handling of Epetra_RowMatrix operators - Memory leaks have been reduced - Simplified configuration using --with-ldflags=-L/home/kstanley/Trilinos3PL/lib --with-libs=-lsuperludist --with-incdirs=-I/home/kstanley/Trilinos3PL/include - Known bugs: - Amesos_Dscpack has memory leaks, prints to standard out and may crash if SymbolicFactorization() is called multiple times on the same Amesos object. - Amesos packages do not accept non-contiguous maps (e.g. one with indices {1,2,5,8,9, ... } ) - Superludist fails on some matrices - Error handling on singular and near singular matrices is inconsistent ------------------------------------------------------------------------------- Anasazi (new) - Anasazi framework includes abstract description of eigenproblem, eigensolver, sorting, and linear algebra. - Templated implementations of two block eigensolvers ( block Krylov-Schur and block Davidson ) are included in this release. - Anasazi eigensolvers can use Epetra through linear algebra adapters. - A basic implementation of the abstract eigenproblem class is given for solving standard and generalized eigenvalue problems. - A basic implementation of the abstract sorting class is given for the block Krylov-Schur method. The block Davidson computes only the smallest eigenvalues at this time. - Many examples for solving standard and generalized eigenvalues problems using Anasazi are provided in this release. ------------------------------------------------------------------------------- AztecOO - Robust support for multiple simultaneous instances of AztecOO objects. Prior releases had a very fragile memory management approach that require user intervention. - Support (optional dependence on Teuchos) for ParameterList-driven use of AztecOO via Teuchos ParameterList objects. ------------------------------------------------------------------------------- Didasko (new) - Didasko now contains the tutorial PDF file and examples. All the tutorial material is located in the Trilinos/packages/didasko subdirectory. - The doxygen documentation has been improved. - All examples are configured with autotools. Users can enable the compilations of the examples by adding --enable-didasko to their configure line. ------------------------------------------------------------------------------- Epetra - Memory efficiency improvement for MultiVector, CrsGraph and CrsMatrix classes. - MultiVector uses much less O(NumVector) storage in important situations. - CrsGraph and CrsMatrix support a static profile mode that allows one-time allocation of memory. - CrsGraph and CrsMatrix support a more robust OptimizeStorage capability that improves memory use and performance. - Performance improvement for CrsMatrix and VbrMatrix kernels. - CrsMatrix matrix multiplication and triangular solves are 20% to 100% faster that Version 4.0 - VbrMatrix matrix multiplication is also improved for some important classes of problems. - Initial vector architecture support for sparse matrix-vector multiplication. - A new class called JadOperator supports matrix-vector multiplication using the so-called Jagged Diagonal data format. This format is especially effective for vector machines such as the Cray X1 and NEC SX series machines. ------------------------------------------------------------------------------- EpetraExt - Scalable parallel distance-1 and distance-2 graph coloring. - Sparse matrix Add for Epetra CRS matrices. - Global index map "reindexing" tool for Epetra objects. ------------------------------------------------------------------------------- Ifpack - IFPACK 3.0 defines a general interface for preconditioners, through class Ifpack_Preconditioner. - Class Ifpack_AdditiveSchwarz can be used to define general overlapping one-level domain decomposition preconditioners. - IFPACK now offers point and block relaxation schemes, of Jacobi, Gauss-Seidel, and symmetric Gauss-Seidel type. For block schemes, the package supports both dense and sparse blocks. - Two new factorizations, ILUT and ICT, have been introduced. - A new user's guide is available. The doxygen documentation has been improved. ------------------------------------------------------------------------------- Kokkos (version 1.1) - No notable new features. ------------------------------------------------------------------------------- Komplex (version 2.0) - No notable new features. ------------------------------------------------------------------------------- LOCA - The LOCA library can now be built as a shared library using libtool. Known issues with this are: - Extra link libraries passed using the --with-libs configure flag should use the "-Lpath -lname" format instead of "path/libname.a" - Building LOCA as a static library on DEC architectures using template repositories does not work. On these architectures, only build LOCA as a shared library using the --enable-shared and --disable-static configure flags, or turn off template repositories using the "-tweak" C++ compiler flag. Note that if the later method is chosen, a large number of warnings will be issued each time an executable is linked against LOCA. - When building shared libraries on SGI systems in 64 bit, one must supply the "-64" C++ compiler flag to not only the compiler and linker through CXXFLAGS and LDFLAGS, but also to libtool using LIBTOOL_CCLINKER_FLAGS or --with-libtool-cclinker-flags. Also one must turn off template repositories and the template prelinker using the flags "-ptused -no_prelink -no_auto_include". - When building shared libraries on Solaris systems, one should add "-xlic_lib=sunperf" to CFLAGS, "-library=sunperf" to CXXFLAGS and LIBTOOL_CCLINKER_FLAGS, and make sure neither of these flags appear in LDFLAGS. - A basic, but functional python interface to NOX and LOCA now exists. A test exhibiting this functionality can be found in the Trilinos/packages/nox/test/lapack/LOCA_python directory. ------------------------------------------------------------------------------- ML (version 3.1) - ML now supports Zoltan as a coarsening scheme (RCB only). Zoltan can be used to create the aggregates and to redistribute the next-level operator among the specified number of processors (which can be less than the available number of processes, for Maxwell solver only). - a variable-block partitioning scheme (based on METIS) is now available. - ML now supports IFPACK smoothers, like variable block Jacobi, Gauss-Seidel and symmetric Gauss-Seidel preconditioners, and generic additive Schwarz preconditioner. - Updated ML user's guide and Doxygen documentation. - Improved MultiLevelPreconditioner class (now derived from Epetra_Operator and no longer from Epetra_RowMatrix). Updated filtering/GGB algorithm, based on the Anasazi package. - Solving Maxwell equations via MultiLevelPreconditioner is now supported. - Improved organization of the examples, more detailed comments and additional README files. - Wrapping an ML_Operator struct as Epetra_RowMatrix is now supported. - Improved test coverage. ------------------------------------------------------------------------------- New_Package (version 1.1) - New tests are working examples of how to add tests to the Trilinos Test-Harness. ------------------------------------------------------------------------------- NOX - A new Tensor based solver that is independent of the underlying linear solver is now implemented (in the prerelease section). Previously the Tensor method was hardwired to use an iterative solver. - Inexact Trust Region Techniques are fully supported (also in the prerelease section). - Improved support for Epetra objects - The NOX::EpetraNew::Group should be used in place of the NOX::Epetra::Group. In the future we will be phasing out the NOX::Epetra::Group and replace it with NOX::EpetraNew::Group. - A multi-physics technique for code coupling has been demonstrated in the test/epetra/Multiphysics directory. This will be expanded to a generic capability in the next year. ------------------------------------------------------------------------------- Pliris (new) - An Object Oriented interface to a Dense Parallel LU Solver is now in place. - The matrix is described in terms of Epetra Vectors and Multivectors. - Multiple right hand sides can be addressed. - Configure with --enable-pliris - Test code allows performance studies - performance is dependent on highly optimized Level 3 BLAS. ------------------------------------------------------------------------------- PyTrilinos (new) - Requires SWIG version 1.3.23 or higher (http://www.swig.org). - Requires python Numeric (http://www.pfdubois.com/numpy). - Configure with --enable-pytrilinos. - Currently provides access to Epetra, EpetraExt and NOX. From python, use "from PyTrilinos import name", where "name" is the desired module. - Online documentation provides list of which classes have been wrapped. - Wrapped classes support almost all of the class methods. See documentation of wrapped packages for details. ------------------------------------------------------------------------------- Teuchos - Additional BLAS/LAPACK wrappers - Teuchos::ScalarTraits template specializations for the GNU MP and Arprec arbitrary precision libraries - Code enabling the conversion from NOX::Parameter::List to Teuchos::ParameterList, and vice versa. ------------------------------------------------------------------------------- Triutils - No notable new features.