{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "*This notebook contains material from [PyRosetta](https://RosettaCommons.github.io/PyRosetta.notebooks);\n", "content is available [on Github](https://github.com/RosettaCommons/PyRosetta.notebooks.git).*" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "< [Part I: Parallelized Global Ligand Docking with `pyrosetta.distributed`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.05-Ligand-Docking-dask.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [PyRosettaCluster Tutorial 1B. Reproduce simple protocol](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb) >

\"Open" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# PyRosettaCluster Tutorial 1A. Simple protocol\n", "\n", "PyRosettaCluster Tutorial 1A is a Jupyter Lab that generates a decoy using `PyRosettaCluster`. It is the simplest use case, where one protocol takes one input `.pdb` file and returns one output `.pdb` file. \n", "\n", "All information needed to reproduce the simulation is included in the output `.pdb` file. After completing PyRosettaCluster Tutorial 1A, see PyRosettaCluster Tutorial 1B to learn how to reproduce simulations from PyRosettaCluster Tutorial 1A." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "*Warning*: This notebook uses `pyrosetta.distributed.viewer` code, which runs in `jupyter notebook` and might not run if you're using `jupyterlab`." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "*Note:* This Jupyter notebook uses parallelization and is **not** meant to be executed within a Google Colab environment." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "*Note:* This Jupyter notebook requires the PyRosetta distributed layer which is obtained by building PyRosetta with the `--serialization` flag or installing PyRosetta from the RosettaCommons conda channel \n", "\n", "**Please see Chapter 16.00 for setup instructions**" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "*Note:* This Jupyter notebook is intended to be run within **Jupyter Lab**, but may still be run as a standalone Jupyter notebook." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 1. Import packages" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [], "source": [ "import bz2\n", "import glob\n", "import logging\n", "import os\n", "import pyrosetta\n", "import pyrosetta.distributed.io as io\n", "import pyrosetta.distributed.viewer as viewer\n", "\n", "from pyrosetta.distributed.cluster import PyRosettaCluster\n", "\n", "logging.basicConfig(level=logging.INFO)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 2. Initialize a compute cluster using `dask`\n", "\n", "1. Click the \"Dask\" tab in Jupyter Lab (arrow, left)\n", "2. Click the \"+ NEW\" button to launch a new compute cluster (arrow, lower)\n", "\n", "![title](Media/dask_labextension_1.png)\n", "\n", "3. Once the cluster has started, click the brackets to \"inject client code\" for the cluster into your notebook\n", "\n", "![title](Media/dask_labextension_2.png)\n", "\n", "Inject client code here, then run the cell:" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "
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" ], "text/plain": [ "" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# This cell is an example of the injected client code. You should delete this cell and instantiate your own client with scheduler IP/port address.\n", "if not os.getenv(\"DEBUG\"):\n", " from dask.distributed import Client\n", "\n", " client = Client(\"tcp://127.0.0.1:40329\")\n", "else:\n", " client = None\n", "client" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Providing a `client` allows you to monitor parallelization diagnostics from within this Jupyter Lab Notebook. However, providing a `client` is only optional for the `PyRosettaCluster` instance and `reproduce` function. If you do not provide a `client`, then `PyRosettaCluster` will instantiate a `LocalCluster` object using the `dask` module by default, or an `SGECluster` or `SLURMCluster` object using the `dask-jobqueue` module if you provide the `scheduler` argument parameter, e.g.:\n", "***\n", "```\n", "PyRosettaCluster(\n", " ...\n", " client=client, # Monitor diagnostics with existing client (see above)\n", " scheduler=None, # Bypasses making a LocalCluster because client is provided\n", " ...\n", ")\n", "```\n", "***\n", "```\n", "PyRosettaCluster(\n", " ...\n", " client=None, # Existing client was not input (default)\n", " scheduler=None, # Runs the simluations on a LocalCluster (default)\n", " ...\n", ")\n", "```\n", "***\n", "```\n", "PyRosettaCluster(\n", " ...\n", " client=None, # Existing client was not input (default)\n", " scheduler=\"sge\", # Runs the simluations on the SGE job scheduler\n", " ...\n", ")\n", "```\n", "***\n", "```\n", "PyRosettaCluster(\n", " ...\n", " client=None, # Existing client was not input (default)\n", " scheduler=\"slurm\", # Runs the simluations on the SLURM job scheduler\n", " ...\n", ")\n", "```" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 3. Define or import the user-provided PyRosetta protocol(s):\n", "\n", "Remember, you *must* import `pyrosetta` locally within each user-provided PyRosetta protocol. Other libraries may not need to be locally imported because they are serializable by the `distributed` module. Although, it is a good practice to locally import all of your modules in each user-provided PyRosetta protocol." ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [], "source": [ "if not os.getenv(\"DEBUG\"):\n", " from additional_scripts.my_protocols import my_protocol" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [], "source": [ "if not os.getenv(\"DEBUG\"):\n", " client.upload_file(\"additional_scripts/my_protocols.py\") # This sends a local file up to all worker nodes." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Let's look at the definition of the user-provided PyRosetta protocol `my_protocol` located in `additional_scripts/my_protocols.py`:" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "```\n", "def my_protocol(input_packed_pose=None, **kwargs):\n", " \"\"\"\n", " Relax the input `PackedPose` object.\n", " \n", " Args:\n", " input_packed_pose: A `PackedPose` object to be repacked. Optional.\n", " **kwargs: PyRosettaCluster task keyword arguments.\n", "\n", " Returns:\n", " A `PackedPose` object.\n", " \"\"\"\n", " import pyrosetta # Local import\n", " import pyrosetta.distributed.io as io # Local import\n", " import pyrosetta.distributed.tasks.rosetta_scripts as rosetta_scripts # Local import\n", " \n", " packed_pose = io.pose_from_file(kwargs[\"s\"])\n", " \n", " xml = \"\"\"\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \"\"\"\n", " \n", " return rosetta_scripts.SingleoutputRosettaScriptsTask(xml)(packed_pose)\n", "```" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 4. Define the user-provided keyword argument(s) (i.e. `kwargs`):\n", "Upon PyRosetta initialization on the remote worker, the \"`options`\" and \"`extra_options`\" `kwargs` get concatenated before initialization. However, specifying the \"`extra_options`\" `kwargs` will override the default `-out:levels all:warning` command line flags, and specifying the \"`options`\" `kwargs` will override the default `-ex1 -ex2aro` command line flags." ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [], "source": [ "def create_kwargs():\n", " yield {\n", " \"options\": \"-ex1\",\n", " \"extra_options\": \"-out:level 300 -multithreading:total_threads 1\", # Used by pyrosetta.init() on disributed workers\n", " \"set_logging_handler\": \"interactive\", # Used by pyrosetta.init() on disributed workers\n", " \"s\": os.path.join(os.getcwd(), \"inputs\", \"1QYS.pdb\"),\n", " }" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Ideally, all pose manipulation is accomplished with the user-provided PyRosetta protocols. If you must manipulate a pose prior to instantiating `PyRosettaCluster`, here are some considerations:\n", "- Avoid passing `Pose` and `PackedPose` objects through `create_kwargs()`. You might notice that the above cell passes the protein structure information to `PyRosettaCluster` as a `str` type locating the `.pdb` file. In this way, the input `PackedPose` object is instantiated from that `str` within `PyRosettaCluster` on the remote workers (using `io.pose_from_file(kwargs[\"s\"])`) using a random seed which is saved by `PyRosettaCluster`. This allows the protocol to be reproduced, and avoids passing redundant large chunks of data over the network.\n", "- It may be tempting to instantiate your pose before `PyRosettaCluster`, and pass a `Pose` or `PackedPose` object into the `create_kwargs()`. However, in this case PyRosetta will be initialized with a random seed outside `PyRosettaCluster`, and that random seed will not be saved by `PyRosettaCluster`. As a consequence, any action taken on the pose (e.g. filling in missing heavy atoms) will not be reproducible.\n", "-If you must instantiate your pose before `PyRosettaCluster`, to ensure reproducibility the user must initialize PyRosetta with the constant seed `1111111` within the Jupyter notebook or standalone python script using:\n", "\n", "```\n", "import pyrosetta\n", "pyrosetta.init(\"-run:constant_seed 1\")\n", "```\n", "\n", "The `-run:constant_seed 1` command line flag defaults to the seed `1111111` ([documentation](https://www.rosettacommons.org/docs/latest/rosetta_basics/options/run-options)). Then, instantiate the pose:\n", "\n", "```\n", "input_packed_pose = pyrosetta.io.pose_from_sequence(\"TEST\")\n", "...Perform any pose manipulation...\n", "```\n", "\n", "and then instantiate `PyRosettaCluster` with the additional `input_packed_pose` parameter argument, e.g.:\n", "\n", "```\n", "PyRosettaCluster(\n", " ...\n", " input_packed_pose=input_packed_pose,\n", " ...\n", ")\n", "```\n", "\n", "For an initialization example, see Tutorial 4.\n", "\n", "In summary, the best practice involves giving `create_kwargs` information which will be used by the distributed protocol to create a pose within `PyRosettaCluster`. In edge cases, the user may provide a `Pose` or `PackedPose` object to the `input_packed_pose` argument of `PyRosettaCluster` and set a constant seed of `1111111` outside of `PyRosettaCluster`." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 5. Launch the original simulation using the `distribute()` method\n", "\n", "The protocol produces an output decoy, the exact coordinates of which we will reproduce in Tutorial 1B." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "If the Jupyter Lab Notebook or standalone PyRosetta script did not yet initialize PyRosetta before instantiating `PyRosettaCluster` (preferred workflow), then `PyRosettaCluster` automatically initializes PyRosetta within the Jupyter Lab Notebook or standalone PyRosetta script with the command line flags `-run:constant_seed 1 -multithreading:total_threads 1 -mute all`. Thus, the master node is initialized with the default constant seed, where the master node acts as the client to the distributed workers. The distributed workers actually run the user-provided PyRosetta protocol(s), and each distributed worker initializes PyRosetta with a random seed, which is the seed saved by PyRosettaCluster for downstream reproducibility. The master node is always initialized with a constant seed as best practices." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "To monitor parallelization diagnostics in real-time, in the \"Dask\" tab, click the various diagnostic tools _(arrows)_ to open new tabs:" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![title](Media/dask_labextension_4.png)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Arrange the diagnostic tool tabs within Jupyter Lab how you best see fit by clicking and dragging them:" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![title](Media/dask_labextension_3.png)" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [], "source": [ "if not os.getenv(\"DEBUG\"):\n", " output_path = os.path.join(os.getcwd(), \"outputs_1A\")\n", "\n", " PyRosettaCluster(\n", " tasks=create_kwargs,\n", " client=client,\n", " scratch_dir=output_path,\n", " output_path=output_path,\n", " nstruct=4, # Run the first user-provided PyRosetta protocol four times in parallel\n", " ).distribute(protocols=[my_protocol])" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "While jobs are running, you may monitor their progress using the dask dashboard diagnostics within Jupyter Lab!" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 7. Visualize the resultant decoy" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Gather the output decoys on disk into poses in memory:" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [], "source": [ "if not os.getenv(\"DEBUG\"):\n", " results = glob.glob(os.path.join(output_path, \"decoys\", \"*\", \"*.pdb.bz2\"))\n", " packed_poses = []\n", " for bz2file in results:\n", " with open(bz2file, \"rb\") as f:\n", " packed_poses.append(io.pose_from_pdbstring(bz2.decompress(f.read()).decode()))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "View the poses in memory by clicking and draging to rotate, and zooming in and out with the mouse scroller." ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "5b71c4df7ea04ee4999578d182de56af", "version_major": 2, "version_minor": 0 }, "text/plain": [ "interactive(children=(IntSlider(value=0, continuous_update=False, description='Decoys', max=3), Output()), _do…" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ ".view(i=0)>" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "if not os.getenv(\"DEBUG\"):\n", " view = viewer.init(packed_poses, window_size=(800, 600))\n", " view.add(viewer.setStyle())\n", " view.add(viewer.setStyle(colorscheme=\"whiteCarbon\", radius=0.25))\n", " view.add(viewer.setHydrogenBonds())\n", " view.add(viewer.setHydrogens(polar_only=True))\n", " view.add(viewer.setDisulfides(radius=0.25))\n", " view()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Using the `pyrosetta.distributed.viewer` macromolecular visualizer, you can visualize your results in real-time as they complete." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![title](Media/viewer_1.png)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Congrats!\n", "\n", "You have successfully performed a PyRosetta simulation using `PyRosettaCluster`! In the next tutorial we will reproduce one of the decoys precisely to make our computational science more reproducible." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "< [Part I: Parallelized Global Ligand Docking with `pyrosetta.distributed`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.05-Ligand-Docking-dask.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [PyRosettaCluster Tutorial 1B. Reproduce simple protocol](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb) >

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