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[ 98%] Built target mdrun-mpi-test Scanning dependencies of target tests [ 98%] Built target tests Scanning dependencies of target run-ctest-nophys [100%] Running all tests except physical validation Test project /home/madhu/gromacs/gromacs-2019.1/build Start 1: TestUtilsUnitTests 1/40 Test #1: TestUtilsUnitTests ............... Passed 0.77 sec Start 2: TestUtilsMpiUnitTests 2/40 Test #2: TestUtilsMpiUnitTests ............ Passed 0.77 sec Start 3: MdlibUnitTest 3/40 Test #3: MdlibUnitTest .................... Passed 0.75 sec Start 4: AppliedForcesUnitTest 4/40 Test #4: AppliedForcesUnitTest ............ Passed 0.74 sec Start 5: ListedForcesTest 5/40 Test #5: ListedForcesTest ................. Passed 0.75 sec Start 6: CommandLineUnitTests 6/40 Test #6: CommandLineUnitTests ............. Passed 0.74 sec Start 7: DomDecTests 7/40 Test #7: DomDecTests ...................... Passed 0.75 sec Start 8: EwaldUnitTests 8/40 Test #8: EwaldUnitTests ................... Passed 1.69 sec Start 9: FFTUnitTests 9/40 Test #9: FFTUnitTests ..................... Passed 0.86 sec Start 10: GpuUtilsUnitTests 10/40 Test #10: GpuUtilsUnitTests ................ Passed 8.73 sec Start 11: HardwareUnitTests 11/40 Test #11: HardwareUnitTests ................ Passed 0.73 sec Start 12: MathUnitTests 12/40 Test #12: MathUnitTests .................... Passed 0.75 sec Start 13: MdrunUtilityUnitTests 13/40 Test #13: MdrunUtilityUnitTests ............ Passed 0.75 sec Start 14: MdrunUtilityMpiUnitTests 14/40 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.79 sec Start 15: OnlineHelpUnitTests 15/40 Test #15: OnlineHelpUnitTests .............. Passed 0.75 sec Start 16: OptionsUnitTests 16/40 Test #16: OptionsUnitTests ................. Passed 0.75 sec Start 17: RandomUnitTests 17/40 Test #17: RandomUnitTests .................. Passed 0.78 sec Start 18: RestraintTests 18/40 Test #18: RestraintTests ................... Passed 0.73 sec Start 19: TableUnitTests 19/40 Test #19: TableUnitTests ................... Passed 0.96 sec Start 20: TaskAssignmentUnitTests 20/40 Test #20: TaskAssignmentUnitTests .......... Passed 0.74 sec Start 21: UtilityUnitTests 21/40 Test #21: UtilityUnitTests ................. Passed 0.76 sec Start 22: UtilityMpiUnitTests 22/40 Test #22: UtilityMpiUnitTests .............. Passed 0.78 sec Start 23: FileIOTests 23/40 Test #23: FileIOTests ...................... Passed 0.75 sec Start 24: PullTest 24/40 Test #24: PullTest ......................... Passed 0.74 sec Start 25: AwhTest 25/40 Test #25: AwhTest .......................... Passed 0.74 sec Start 26: SimdUnitTests 26/40 Test #26: SimdUnitTests .................... Passed 0.80 sec Start 27: CompatibilityHelpersTests 27/40 Test #27: CompatibilityHelpersTests ........ Passed 0.75 sec Start 28: GmxAnaTest 28/40 Test #28: GmxAnaTest ....................... Passed 0.78 sec Start 29: GmxPreprocessTests 29/40 Test #29: GmxPreprocessTests ...............***Timeout 30.06 sec [==========] Running 26 tests from 4 test cases. [----------] Global test environment set-up. [----------] 4 tests from GenconfTest [ RUN ] GenconfTest.nbox_Works [ OK ] GenconfTest.nbox_Works (2 ms) [ RUN ] GenconfTest.nbox_norenumber_Works [ OK ] GenconfTest.nbox_norenumber_Works (1 ms) [ RUN ] GenconfTest.nbox_dist_Works [ OK ] GenconfTest.nbox_dist_Works (1 ms) [ RUN ] GenconfTest.nbox_rot_Works center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 [ OK ] GenconfTest.nbox_rot_Works (1 ms) [----------] 4 tests from GenconfTest (5 ms total) [----------] 5 tests from InsertMoleculesTest [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration Reading solute configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Try 1 success (now 8 atoms)! Added 1 molecules (out of 1 requested) Writing generated configuration to /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro Output configuration contains 8 atoms in 4 residues [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (3 ms) [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Try 1 success (now 2 atoms)! Try 2 success (now 4 atoms)! Try 3 success (now 6 atoms)! Try 4 success (now 8 atoms)! Try 5 success (now 10 atoms)! Added 5 molecules (out of 5 requested) Writing generated configuration to /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro Output configuration contains 10 atoms in 10 residues [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (3 ms) [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox Reading solute configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Try 1 success (now 8 atoms)! Try 2 success (now 10 atoms)! Added 2 molecules (out of 2 requested) Writing generated configuration to /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro Output configuration contains 10 atoms in 4 residues [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (2 ms) [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement Reading solute configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Try 1 success (now 650 atoms)! Try 2 success (now 652 atoms)! Try 3 success (now 654 atoms)! Try 4 success (now 656 atoms)! Added 4 molecules (out of 4 requested) Replaced 8 residues (24 atoms) Writing generated configuration to /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro Output configuration contains 632 atoms in 212 residues [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (12 ms) [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Read 4 positions from file /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat Try 1 success (now 2 atoms)! Try 2 success (now 4 atoms)! Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) Try 13 success (now 6 atoms)! Added 3 molecules (out of 4 requested) Writing generated configuration to /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro Output configuration contains 6 atoms in 3 residues [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (3 ms) [----------] 5 tests from InsertMoleculesTest (23 ms total) [----------] 12 tests from GetIrTest [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp, line 12]: /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Ignoring obsolete mdp entry 'title' Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (3 ms) [ RUN ] GetIrTest.HandlesOnlyCutoffScheme [ OK ] GetIrTest.HandlesOnlyCutoffScheme (4 ms) [ RUN ] GetIrTest.UserErrorsSilentlyTolerated NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp, line 5]: /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. [ OK ] GetIrTest.UserErrorsSilentlyTolerated (3 ms) [ RUN ] GetIrTest.DefineHandlesAssignmentOnRhs NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp, line 2]: /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. [ OK ] GetIrTest.DefineHandlesAssignmentOnRhs (3 ms) [ RUN ] GetIrTest.EmptyInputWorks NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp, line 1]: /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. [ OK ] GetIrTest.EmptyInputWorks (3 ms) [ RUN ] GetIrTest.ProducesOutputFromElectricField NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp, line 2]: /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. [ OK ] GetIrTest.ProducesOutputFromElectricField (2 ms) [ RUN ] GetIrTest.ProducesOutputFromElectricFieldPulsed NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp, line 2]: /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. [ OK ] GetIrTest.ProducesOutputFromElectricFieldPulsed (3 ms) [ RUN ] GetIrTest.ProducesOutputFromElectricFieldOscillating NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp, line 2]: /home/madhu/gromacs/gromacs-2019.1/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. [ OK ] GetIrTest.ProducesOutputFromElectricFieldOscillating (3 ms) [ RUN ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys [WARNING] /home/madhu/gromacs/gromacs-2019.1/src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 3 threads. Start 30: Pdb2gmxTest 30/40 Test #30: Pdb2gmxTest ...................... Passed 10.04 sec Start 31: CorrelationsTest 31/40 Test #31: CorrelationsTest ................. Passed 1.40 sec Start 32: AnalysisDataUnitTests 32/40 Test #32: AnalysisDataUnitTests ............ Passed 0.77 sec Start 33: SelectionUnitTests 33/40 Test #33: SelectionUnitTests ............... Passed 0.90 sec Start 34: TrajectoryAnalysisUnitTests 34/40 Test #34: TrajectoryAnalysisUnitTests ...... Passed 1.15 sec Start 35: EnergyAnalysisUnitTests 35/40 Test #35: EnergyAnalysisUnitTests .......... Passed 0.93 sec Start 36: ToolUnitTests 36/40 Test #36: ToolUnitTests .................... Passed 0.94 sec Start 37: MdrunTests 37/40 Test #37: MdrunTests .......................***Failed 18.69 sec [==========] Running 29 tests from 11 test cases. [----------] Global test environment set-up. [----------] 1 test from GromppTest [ RUN ] GromppTest.EmptyMdpFileWorks NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp, line 1]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to 902009595 Generated 279 of the 1225 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 12.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size NOTE 4 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GromppTest.EmptyMdpFileWorks (31 ms) [----------] 1 test from GromppTest (32 ms total) [----------] 1 test from ImdTest [ RUN ] ImdTest.ImdCanRun NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Setting the LD random seed to -1825540377 Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Group 'SecondWaterMolecule' with 3 atoms can be activated for interactive molecular dynamics (IMD). Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun.tpr, VERSION 2019.1 (single precision) Changing nstlist from 10 to 80, rlist from 1.121 to 1.479 Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). IMD: Enabled. This simulation will accept incoming IMD connections. IMD: You chose a port number < 1. Will automatically assign a free port. IMD: Pulling from IMD remote is enabled (-imdpull). IMD: Turning on IMD - port for incoming requests is 0. IMD: Setting up incoming socket. IMD: Listening for IMD connection on port 39600. IMD: -imdwait not set, starting simulation. starting mdrun 'spc2' 2 steps, 0.0 ps. turning all bonds into constraints... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.134 nm, buffer size 0.134 nm Set rlist, assuming 4x4 atom pair-list, to 1.121 nm, buffer size 0.121 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.399 0.200 199.9 (ns/day) (hour/ns) Performance: 5.195 4.619 [ OK ] ImdTest.ImdCanRun (2553 ms) [----------] 1 test from ImdTest (2553 ms total) [----------] 2 tests from PmeTest [ RUN ] PmeTest.ReproducesEnergies NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Setting the LD random seed to 1397023712 Generated 279 of the 1225 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 12.00 NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size Estimate for the relative computational load of the PME mesh part: 1.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: The CPU has >25% more load than the GPU. This imbalance wastes GPU resources. Core t (s) Wall t (s) (%) Time: 0.368 0.184 199.9 (ns/day) (hour/ns) Performance: 9.843 2.438 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Writing final coordinates. NOTE: The CPU has >25% more load than the GPU. This imbalance wastes GPU resources. Core t (s) Wall t (s) (%) Time: 0.342 0.171 199.9 (ns/day) (hour/ns) Performance: 10.605 2.263 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Writing final coordinates. NOTE: The CPU has >25% more load than the GPU. This imbalance wastes GPU resources. Core t (s) Wall t (s) (%) Time: 0.882 0.441 200.0 (ns/day) (hour/ns) Performance: 4.112 5.836 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (9176 ms) [ RUN ] PmeTest.ScalesTheBox NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to 1865738183 Generated 279 of the 1225 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Searching the wall atom type(s) Number of degrees of freedom in T-Coupling group rest is 13.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: NVE simulation: will use the initial temperature of 966.268 K for determining the Verlet buffer size Estimate for the relative computational load of the PME mesh part: 1.00 NOTE 4 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. There were 4 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc-and-methanol' 0 steps, 0.0 ps. NOTE: The CPU has >25% more load than the GPU. This imbalance wastes GPU resources. Core t (s) Wall t (s) (%) Time: 0.006 0.003 196.5 (ns/day) (hour/ns) Performance: 26.562 0.904 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 This run will generate roughly 0 Mb of data [ OK ] PmeTest.ScalesTheBox (2440 ms) [----------] 2 tests from PmeTest (11617 ms total) [----------] 1 test from CompelTest [ RUN ] CompelTest.SwapCanRun NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Setting the LD random seed to -1416698504 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type 'OCT' Excluding 1 bonded neighbours molecule type 'NA' Excluding 1 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type 'OCT' Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Split0 group 'Ch0' contains 83 atoms. Split1 group 'Ch1' contains 83 atoms. Solvent group 'SOL' contains 11931 atoms. Swap group 'NA+' contains 19 atoms. Swap group 'CL-' contains 19 atoms. Number of degrees of freedom in T-Coupling group System is 27869.00 NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.1 (single precision) Changing nstlist from 10 to 20, rlist from 1.26 to 1.454 Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). SWAP: Determining initial numbers of ions per compartment. SWAP: Setting pointers for checkpoint writing SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules starting mdrun 'Channel_coco in octane membrane' 2 steps, 0.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 21.640755, max 270.792023 (between atoms 1787 and 1788) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 264 265 89.9 0.1530 0.1241 0.1530 265 266 90.2 0.1530 1.0534 0.1530 266 267 120.7 0.1530 9.2113 0.1530 267 268 40.9 0.1530 10.2883 0.1530 268 269 89.9 0.1530 0.1798 0.1530 535 536 44.1 0.1530 0.2023 0.1530 536 537 89.9 0.1530 0.4163 0.1530 537 538 110.6 0.1530 10.7595 0.1530 656 657 123.3 0.1530 16.3547 0.1530 657 658 89.9 0.1530 0.0656 0.1530 691 692 90.0 0.1530 0.1677 0.1530 692 693 90.1 0.1530 1.3017 0.1530 776 777 90.9 0.1530 0.0935 0.1530 777 778 124.9 0.1530 16.1875 0.1530 780 781 123.4 0.1530 11.5459 0.1530 781 782 90.1 0.1530 0.4616 0.1530 808 809 102.6 0.1530 15.9562 0.1530 809 810 90.1 0.1530 0.2045 0.1530 847 848 89.9 0.1530 1.3288 0.1530 848 849 91.0 0.1530 16.4129 0.1530 850 851 90.2 0.1530 0.9654 0.1530 851 852 88.9 0.1530 0.1115 0.1530 887 888 90.3 0.1530 11.7409 0.1530 888 889 123.0 0.1530 11.3442 0.1530 889 890 90.9 0.1530 0.1818 0.1530 890 891 114.1 0.1530 16.3229 0.1530 891 892 85.7 0.1530 16.2535 0.1530 892 893 90.2 0.1530 0.4108 0.1530 1175 1176 74.1 0.1530 16.9742 0.1530 1176 1177 93.1 0.1530 33.1407 0.1530 1177 1178 49.0 0.1530 16.0110 0.1530 1326 1327 89.1 0.1530 0.1527 0.1530 1327 1328 90.5 0.1530 1.3155 0.1530 1328 1329 117.3 0.1530 16.1413 0.1530 1329 1330 37.1 0.1530 15.8578 0.1530 1374 1375 90.1 0.1530 0.4233 0.1530 1375 1376 41.6 0.1530 18.0774 0.1530 1376 1377 52.5 0.1530 18.5883 0.1530 1377 1378 90.0 0.1530 1.6144 0.1530 1381 1382 91.2 0.1530 0.2473 0.1530 1382 1383 123.3 0.1530 10.4250 0.1530 1384 1385 113.7 0.1530 8.3031 0.1530 1385 1386 90.4 0.1530 0.3072 0.1530 1651 1652 88.0 0.1530 11.2286 0.1530 1652 1653 126.6 0.1530 12.7383 0.1530 1654 1655 55.6 0.1530 38.0850 0.1530 1656 1657 110.1 0.1530 14.5564 0.1530 1657 1658 90.4 0.1530 0.1827 0.1530 1659 1660 105.4 0.1530 10.1912 0.1530 1660 1661 131.9 0.1530 10.9618 0.1530 1661 1662 89.7 0.1530 0.3267 0.1530 1662 1663 90.5 0.1530 0.4112 0.1530 1663 1664 127.3 0.1530 17.8572 0.1530 1664 1665 118.5 0.1530 18.2261 0.1530 1669 1670 67.2 0.1530 0.2442 0.1530 1670 1671 89.8 0.1530 0.9062 0.1530 1672 1673 131.3 0.1530 12.7215 0.1530 1673 1674 89.9 0.1530 0.3929 0.1530 1734 1735 92.7 0.1530 0.0620 0.1530 1736 1737 77.8 0.1530 17.1668 0.1530 1737 1738 51.5 0.1530 17.9986 0.1530 1780 1781 84.6 0.1530 17.8432 0.1530 1781 1782 90.9 0.1530 0.0773 0.1530 1788 1789 93.8 0.1530 16.0219 0.1530 1789 1790 90.1 0.1530 0.8050 0.1530 1790 1791 90.9 0.1530 0.0792 0.1530 1855 1856 108.7 0.1530 15.3687 0.1530 1856 1857 89.8 0.1530 1.3519 0.1530 1857 1858 90.0 0.1530 0.2833 0.1530 step 0: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates SWAP: Warning: Inconsistency while assigning 'NA+' molecules to compartments. !inA: 19, !inB: 19, total molecules 19 SWAP: Warning: 19 molecules are in group 'NA+', but altogether 0 have been assigned to the compartments. SWAP: Warning: Inconsistency while assigning 'CL-' molecules to compartments. !inA: 19, !inB: 19, total molecules 19 SWAP: Warning: 19 molecules are in group 'CL-', but altogether 0 have been assigned to the compartments. SWAP: Warning: Inconsistency while assigning 'SOL' molecules to compartments. !inA: 3977, !inB: 3977, total molecules 3977 SWAP: Warning: 3977 molecules are in group 'SOL', but altogether 0 have been assigned to the compartments. ------------------------------------------------------- Program: mdrun-test, version 2019.1 Source file: src/gromacs/swap/swapcoords.cpp (line 1868) Fatal error: Could not get index of SOL atom. Compartment contains 0 SOL molecules before swaps. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- turning all bonds into constraints... turning all bonds into constraints... turning all bonds into constraints... turning all bonds into constraints... turning all bonds into constraints... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 1 Mb of data -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- Start 38: MdrunNonIntegratorTests 38/40 Test #38: MdrunNonIntegratorTests ..........***Failed 43.05 sec [==========] Running 12 tests from 2 test cases. [----------] Global test environment set-up. [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = -1.0231507e+02 Maximum force = 2.9245001e+02 on atom 1 Norm of force = 1.3011585e+02 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 This run will generate roughly 0 Mb of data /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure In item: /spc5/steep/Potential/Time 0.000000 Step 0 in frame 0 Actual: -96.7020263671875 Reference: -9.6231422424316406 Difference: 87.0789 (27750156 single-prec. ULPs, rel. 9.05) Tolerance: 150 ULPs Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 0.000000 Step 0 in frame 0 /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'steep' energy minimization for simulation 'spc5' Reading energy frame 1 time 1.000 /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure In item: /spc5/steep/Potential/Time 1.000000 Step 1 in frame 1 Actual: -100.9490966796875 Reference: -16.824483871459961 Difference: 84.1246 (21187941 single-prec. ULPs, rel. 5) Tolerance: 150 ULPs Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 1.000000 Step 1 in frame 1 /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'steep' energy minimization for simulation 'spc5' Reading energy frame 2 time 4.000 /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure Reference data item /spc5/steep/Potential/Time 4.000000 Step 4 in frame 2 not found Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 4.000000 Step 4 in frame 2 /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'steep' energy minimization for simulation 'spc5' Last energy frame read 2 time 4.000 /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:265: Failure Failed Reference data items not used in test: /spc5/steep/Potential/Time 2.000000 Step 2 in frame 2 /spc5/steep/Potential/Time 3.000000 Step 3 in frame 3 /spc5/steep/Potential/Time 4.000000 Step 4 in frame 4 [ FAILED ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0, where GetParam() = ("spc5", "steep") (2272 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 3.02331e+02 on atom 3 F-Norm = 1.18024e+02 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = -9.9520966e+01 Maximum force = 3.1745987e+02 on atom 1 Norm of force = 1.2459617e+02 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 This run will generate roughly 0 Mb of data /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure In item: /spc5/cg/Potential/Time 0.000000 Step 0 in frame 0 Actual: -96.7020263671875 Reference: -9.6231422424316406 Difference: 87.0789 (27750156 single-prec. ULPs, rel. 9.05) Tolerance: 150 ULPs Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 0.000000 Step 0 in frame 0 /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'cg' energy minimization for simulation 'spc5' Reading energy frame 1 time 0.000 /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure In item: /spc5/cg/Potential/Time 0.000000 Step 0 in frame 1 Actual: -99.570014953613281 Reference: -14.332059860229492 Difference: 85.238 (23188411 single-prec. ULPs, rel. 5.95) Tolerance: 150 ULPs Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 0.000000 Step 0 in frame 1 /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'cg' energy minimization for simulation 'spc5' Reading energy frame 2 time 4.000 /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure In item: /spc5/cg/Potential/Time 4.000000 Step 4 in frame 2 Actual: -99.520965576171875 Reference: -55.862255096435547 Difference: 43.6587 (6789065 single-prec. ULPs, rel. 0.782) Tolerance: 150 ULPs Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 4.000000 Step 4 in frame 2 /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'cg' energy minimization for simulation 'spc5' Last energy frame read 2 time 4.000 [ FAILED ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1, where GetParam() = ("spc5", "cg") (3427 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 22.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = 3.1937726e+02 Maximum force = 9.9988691e+03 on atom 9 Norm of force = 4.6167015e+03 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (3692 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' NOTE 3 [file glycine_vacuo.top, line 12]: For accurate cg with LINCS constraints, lincs-order should be 8 or more. Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 22.00 NOTE 4 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 2.41575e+04 on atom 10 F-Norm = 1.18451e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.5174426e+02 Maximum force = 7.4208799e+03 on atom 9 Norm of force = 3.5692986e+03 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (3569 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = -1.5698431e+02 Maximum force = 4.5708105e+02 on atom 17 Norm of force = 1.8328513e+02 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (3589 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. NOTE 4 [file unknown]: For accurate cg with LINCS constraints, lincs-order should be 8 or more. Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 5 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 1.06798e+03 on atom 28 F-Norm = 4.26915e+02 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = -1.6941229e+02 Maximum force = 2.1844173e+02 on atom 17 Norm of force = 7.9236186e+01 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (3585 ms) [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (20134 ms total) [----------] 6 tests from MinimizersWork/EnergyMinimizationTest [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 writing lowest energy coordinates. Steepest Descents converged to Fmax < 10 in 1 steps Potential Energy = -9.7425717e-01 Maximum force = 4.0132132e+00 on atom 1 Norm of force = 1.6383874e+00 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (3514 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 4.01321e+00 on atom 1 F-Norm = 1.63839e+00 writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps Potential Energy = -9.9064201e-01 Maximum force = 2.5781698e+00 on atom 1 Norm of force = 1.0525334e+00 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (3879 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. WARNING 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Low-Memory BFGS Minimizer: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Using 10 BFGS correction steps. F-max = 4.01321e+00 on atom 1 F-Norm = 1.63839e+00 writing lowest energy coordinates. Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps Potential Energy = -9.9064201e-01 Maximum force = 2.5781698e+00 on atom 1 Norm of force = 1.0525334e+00 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (3534 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = 3.1939676e+02 Maximum force = 9.9704229e+03 on atom 9 Norm of force = 4.6227534e+03 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (3565 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 2.41672e+04 on atom 10 F-Norm = 1.19357e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.5625763e+02 Maximum force = 7.5018252e+03 on atom 9 Norm of force = 3.6139022e+03 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (3643 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. WARNING 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes There was 1 warning Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Low-Memory BFGS Minimizer: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Using 10 BFGS correction steps. F-max = 2.41672e+04 on atom 10 F-Norm = 1.19357e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.8472423e+03 Maximum force = 2.1261639e+04 on atom 9 Norm of force = 1.0198860e+04 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (3454 ms) [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (21589 ms total) [----------] Global test environment tear-down [==========] 12 tests from 2 test cases ran. (41723 ms total) [ PASSED ] 10 tests. [ FAILED ] 2 tests, listed below: [ FAILED ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0, where GetParam() = ("spc5", "steep") [ FAILED ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1, where GetParam() = ("spc5", "cg") 2 FAILED TESTS YOU HAVE 45 DISABLED TESTS Start 39: LegacyGroupSchemeMdrunTests 39/40 Test #39: LegacyGroupSchemeMdrunTests ...... Passed 2.04 sec Start 40: MdrunMpiTests 40/40 Test #40: MdrunMpiTests ....................***Failed 50.19 sec [==========] Running 25 tests from 9 test cases. [----------] Global test environment set-up. [----------] 1 test from DomainDecompositionSpecialCasesTest [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to 142733661 Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 0 steps, 0.0 ps. NOTE: 31 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.003 0.002 193.4 (ns/day) (hour/ns) Performance: 53.879 0.445 This run will generate roughly 0 Mb of data [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (2239 ms) [----------] 1 test from DomainDecompositionSpecialCasesTest (2239 ms total) [----------] 4 tests from MimicTest [ RUN ] MimicTest.OneQuantumMol NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to 1378212582 Generated 10 of the 10 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' Reading frames from gro file 'Generated by gmx solvate', 12 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 NOTE: 23 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.002 0.001 194.2 (ns/day) (hour/ns) Performance: 77.301 0.310 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data [ OK ] MimicTest.OneQuantumMol (3423 ms) [ RUN ] MimicTest.AllQuantumMol NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to 1162713942 Generated 10 of the 10 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' Reading frames from gro file 'Generated by gmx solvate', 12 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 NOTE: 24 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.002 0.001 194.1 (ns/day) (hour/ns) Performance: 78.763 0.305 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data [ OK ] MimicTest.AllQuantumMol (3440 ms) [ RUN ] MimicTest.TwoQuantumMol NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to 1001521967 Generated 10 of the 10 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' Reading frames from gro file 'Generated by gmx solvate', 12 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 NOTE: 27 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.002 0.001 192.4 (ns/day) (hour/ns) Performance: 84.809 0.283 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data [ OK ] MimicTest.TwoQuantumMol (3712 ms) [ RUN ] MimicTest.BondCuts NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to 377266883 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 66.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: NVE simulation: will use the initial temperature of 300.368 K for determining the Verlet buffer size NOTE 4 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/ala.gro' Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 NOTE: 26 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.002 0.001 194.0 (ns/day) (hour/ns) Performance: 75.845 0.316 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file Reading energy frame 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure In item: /Potential/Time 0.000000 Step 0 in frame 0 Actual: 88.503814697265625 Reference: 153.63571166992188 Difference: 65.1319 (6856906 single-prec. ULPs, rel. 0.424) Tolerance: abs. 0.00201, rel. 0.0001 Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 0.000000 Step 0 in frame 0 Last energy frame read 0 time 0.000 [ FAILED ] MimicTest.BondCuts (3613 ms) [----------] 4 tests from MimicTest (14188 ms total) [----------] 1 test from MultiSimTerminationTest [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) [----------] 1 test from MultiSimTerminationTest (0 ms total) [----------] 2 tests from PmeTest [ RUN ] PmeTest.ReproducesEnergies NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Setting the LD random seed to -885366827 Generated 279 of the 1225 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 12.00 NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size Estimate for the relative computational load of the PME mesh part: 1.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: The CPU has >25% more load than the GPU. This imbalance wastes GPU resources. Core t (s) Wall t (s) (%) Time: 0.372 0.186 200.0 (ns/day) (hour/ns) Performance: 9.753 2.461 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Writing final coordinates. NOTE: The CPU has >25% more load than the GPU. This imbalance wastes GPU resources. Core t (s) Wall t (s) (%) Time: 0.349 0.175 200.0 (ns/day) (hour/ns) Performance: 10.383 2.312 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Writing final coordinates. NOTE: The CPU has >25% more load than the GPU. This imbalance wastes GPU resources. Core t (s) Wall t (s) (%) Time: 0.763 0.381 200.0 (ns/day) (hour/ns) Performance: 4.756 5.046 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (8866 ms) [ RUN ] PmeTest.ScalesTheBox NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to 571303761 Generated 279 of the 1225 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Searching the wall atom type(s) Number of degrees of freedom in T-Coupling group rest is 13.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: NVE simulation: will use the initial temperature of 966.268 K for determining the Verlet buffer size Estimate for the relative computational load of the PME mesh part: 1.00 NOTE 4 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. There were 4 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.1 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc-and-methanol' 0 steps, 0.0 ps. NOTE: The CPU has >25% more load than the GPU. This imbalance wastes GPU resources. Core t (s) Wall t (s) (%) Time: 0.008 0.004 197.3 (ns/day) (hour/ns) Performance: 20.569 1.167 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 This run will generate roughly 0 Mb of data [ OK ] PmeTest.ScalesTheBox (2424 ms) [----------] 2 tests from PmeTest (11290 ms total) [----------] 1 test from ReplicaExchangeTerminationTest [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total) [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = -1.0231507e+02 Maximum force = 2.9245001e+02 on atom 1 Norm of force = 1.3011585e+02 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 This run will generate roughly 0 Mb of data /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure In item: /spc5/steep/Potential/Time 0.000000 Step 0 in frame 0 Actual: -96.7020263671875 Reference: -9.6231422424316406 Difference: 87.0789 (27750156 single-prec. ULPs, rel. 9.05) Tolerance: 150 ULPs Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 0.000000 Step 0 in frame 0 /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'steep' energy minimization for simulation 'spc5' Reading energy frame 1 time 1.000 /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure In item: /spc5/steep/Potential/Time 1.000000 Step 1 in frame 1 Actual: -100.94910430908203 Reference: -16.824483871459961 Difference: 84.1246 (21187942 single-prec. ULPs, rel. 5) Tolerance: 150 ULPs Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 1.000000 Step 1 in frame 1 /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'steep' energy minimization for simulation 'spc5' Reading energy frame 2 time 4.000 /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure Reference data item /spc5/steep/Potential/Time 4.000000 Step 4 in frame 2 not found Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 4.000000 Step 4 in frame 2 /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'steep' energy minimization for simulation 'spc5' Last energy frame read 2 time 4.000 /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:265: Failure Failed Reference data items not used in test: /spc5/steep/Potential/Time 2.000000 Step 2 in frame 2 /spc5/steep/Potential/Time 3.000000 Step 3 in frame 3 /spc5/steep/Potential/Time 4.000000 Step 4 in frame 4 [ FAILED ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0, where GetParam() = ("spc5", "steep") (1541 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 3.02331e+02 on atom 3 F-Norm = 1.18024e+02 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = -9.9520966e+01 Maximum force = 3.1745987e+02 on atom 1 Norm of force = 1.2459617e+02 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 This run will generate roughly 0 Mb of data /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure In item: /spc5/cg/Potential/Time 0.000000 Step 0 in frame 0 Actual: -96.7020263671875 Reference: -9.6231422424316406 Difference: 87.0789 (27750156 single-prec. ULPs, rel. 9.05) Tolerance: 150 ULPs Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 0.000000 Step 0 in frame 0 /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'cg' energy minimization for simulation 'spc5' Reading energy frame 1 time 0.000 /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure In item: /spc5/cg/Potential/Time 0.000000 Step 0 in frame 1 Actual: -99.570014953613281 Reference: -14.332059860229492 Difference: 85.238 (23188411 single-prec. ULPs, rel. 5.95) Tolerance: 150 ULPs Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 0.000000 Step 0 in frame 1 /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'cg' energy minimization for simulation 'spc5' Reading energy frame 2 time 4.000 /home/madhu/gromacs/gromacs-2019.1/src/testutils/refdata.cpp:929: Failure In item: /spc5/cg/Potential/Time 4.000000 Step 4 in frame 2 Actual: -99.520965576171875 Reference: -55.862255096435547 Difference: 43.6587 (6789065 single-prec. ULPs, rel. 0.782) Tolerance: 150 ULPs Google Test trace: /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 4.000000 Step 4 in frame 2 /home/madhu/gromacs/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'cg' energy minimization for simulation 'spc5' Last energy frame read 2 time 4.000 [ FAILED ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1, where GetParam() = ("spc5", "cg") (1547 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 22.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = 3.1937726e+02 Maximum force = 9.9988691e+03 on atom 9 Norm of force = 4.6167015e+03 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (1532 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' NOTE 3 [file glycine_vacuo.top, line 12]: For accurate cg with LINCS constraints, lincs-order should be 8 or more. Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 22.00 NOTE 4 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 2.41575e+04 on atom 10 F-Norm = 1.18451e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.5174426e+02 Maximum force = 7.4208799e+03 on atom 9 Norm of force = 3.5692986e+03 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (1587 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = -1.5698431e+02 Maximum force = 4.5708105e+02 on atom 17 Norm of force = 1.8328513e+02 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (1541 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. NOTE 4 [file unknown]: For accurate cg with LINCS constraints, lincs-order should be 8 or more. Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 5 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 1.06798e+03 on atom 28 F-Norm = 4.26915e+02 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = -1.6941229e+02 Maximum force = 2.1844173e+02 on atom 17 Norm of force = 7.9236186e+01 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (1553 ms) [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (9301 ms total) [----------] 6 tests from MinimizersWork/EnergyMinimizationTest [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 writing lowest energy coordinates. Steepest Descents converged to Fmax < 10 in 1 steps Potential Energy = -9.7425717e-01 Maximum force = 4.0132132e+00 on atom 1 Norm of force = 1.6383874e+00 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1532 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 4.01321e+00 on atom 1 F-Norm = 1.63839e+00 writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps Potential Energy = -9.9064201e-01 Maximum force = 2.5781698e+00 on atom 1 Norm of force = 1.0525334e+00 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (1519 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. WARNING 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Low-Memory BFGS Minimizer: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Using 10 BFGS correction steps. F-max = 4.01321e+00 on atom 1 F-Norm = 1.63839e+00 writing lowest energy coordinates. Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps Potential Energy = -9.9064201e-01 Maximum force = 2.5781698e+00 on atom 1 Norm of force = 1.0525334e+00 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (1650 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = 3.1939676e+02 Maximum force = 9.9704229e+03 on atom 9 Norm of force = 4.6227534e+03 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (1602 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 2.41672e+04 on atom 10 F-Norm = 1.19357e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.5625763e+02 Maximum force = 7.5018252e+03 on atom 9 Norm of force = 3.6139022e+03 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (1585 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 NOTE 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. WARNING 1 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes There was 1 warning Reading file /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) Using 1 MPI process Using 2 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Low-Memory BFGS Minimizer: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Using 10 BFGS correction steps. F-max = 2.41672e+04 on atom 10 F-Norm = 1.19357e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.8472423e+03 Maximum force = 2.1261639e+04 on atom 9 Norm of force = 1.0198860e+04 Opened /home/madhu/gromacs/gromacs-2019.1/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1610 ms) [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (9498 ms total) [----------] 2 tests from InNvt/MultiSimTest [ RUN ] InNvt/MultiSimTest.ExitsNormally/0 [ OK ] InNvt/MultiSimTest.ExitsNormally/0 (0 ms) [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 (0 ms) [----------] 2 tests from InNvt/MultiSimTest (0 ms total) [----------] 2 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 (0 ms) [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 (0 ms) [----------] 2 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest (0 ms total) [----------] Global test environment tear-down [==========] 25 tests from 9 test cases ran. (48708 ms total) [ PASSED ] 22 tests. [ FAILED ] 3 tests, listed below: [ FAILED ] MimicTest.BondCuts [ FAILED ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0, where GetParam() = ("spc5", "steep") [ FAILED ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1, where GetParam() = ("spc5", "cg") 3 FAILED TESTS 90% tests passed, 4 tests failed out of 40 Label Time Summary: GTest = 190.53 sec*proc (40 tests) IntegrationTest = 114.75 sec*proc (5 tests) MpiTest = 2.33 sec*proc (3 tests) SlowTest = 10.04 sec*proc (1 test) UnitTest = 65.74 sec*proc (34 tests) Total Test time (real) = 190.90 sec The following tests FAILED: 29 - GmxPreprocessTests (Timeout) 37 - MdrunTests (Failed) 38 - MdrunNonIntegratorTests (Failed) 40 - MdrunMpiTests (Failed) Errors while running CTest make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 make[1]: *** [CMakeFiles/check.dir/rule] Error 2 make: *** [check] Error 2