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Using OpenMMTools in Google Colab
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| { | |
| "cells": [ | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "colab_type": "text", | |
| "id": "gPFd5CO2yosb" | |
| }, | |
| "source": [ | |
| "# Install Miniconda\n", | |
| "It's the normal procedure, but:\n", | |
| "- We stick to v4.5.4 because it ships with Python 3.6 (same as Google Colab runtime) for compatibility.\n", | |
| "- We install it in `/usr/local`\n", | |
| "\n", | |
| "__Note 1__: If you want to use GPU acceleration, enable it now (before installing anything). Otherwise you will have to repeat everything after enabling GPU acceleration.\n", | |
| "\n", | |
| "__Note 2__: Solving dependencies in such a convoluted environment (`/usr/lib`) can (sometimes) take _a while_ (20 mins in my last attempt). It might be a better idea to use `constructor` ([check here](https://github.com/conda/constructor)) to prebuild a conda installation with all the packages you want if you intend to use them quite often.\n" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 7, | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 1475 | |
| }, | |
| "colab_type": "code", | |
| "id": "xXGOv9XLO5UL", | |
| "outputId": "d663f0ec-19ec-47d8-8141-c7b3bd7dbae5" | |
| }, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "--2019-04-24 12:38:44-- https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh\n", | |
| "Resolving repo.continuum.io (repo.continuum.io)... 104.18.200.79, 104.18.201.79, 2606:4700::6812:c84f, ...\n", | |
| "Connecting to repo.continuum.io (repo.continuum.io)|104.18.200.79|:443... connected.\n", | |
| "HTTP request sent, awaiting response... 200 OK\n", | |
| "Length: 58468498 (56M) [application/x-sh]\n", | |
| "Saving to: ‘Miniconda3-4.5.4-Linux-x86_64.sh’\n", | |
| "\n", | |
| "Miniconda3-4.5.4-Li 100%[===================>] 55.76M 132MB/s in 0.4s \n", | |
| "\n", | |
| "2019-04-24 12:38:45 (132 MB/s) - ‘Miniconda3-4.5.4-Linux-x86_64.sh’ saved [58468498/58468498]\n", | |
| "\n", | |
| "PREFIX=/usr/local\n", | |
| "installing: python-3.6.5-hc3d631a_2 ...\n", | |
| "Python 3.6.5 :: Anaconda, Inc.\n", | |
| "installing: ca-certificates-2018.03.07-0 ...\n", | |
| "installing: conda-env-2.6.0-h36134e3_1 ...\n", | |
| "installing: libgcc-ng-7.2.0-hdf63c60_3 ...\n", | |
| "installing: libstdcxx-ng-7.2.0-hdf63c60_3 ...\n", | |
| "installing: libffi-3.2.1-hd88cf55_4 ...\n", | |
| "installing: ncurses-6.1-hf484d3e_0 ...\n", | |
| "installing: openssl-1.0.2o-h20670df_0 ...\n", | |
| "installing: tk-8.6.7-hc745277_3 ...\n", | |
| "installing: xz-5.2.4-h14c3975_4 ...\n", | |
| "installing: yaml-0.1.7-had09818_2 ...\n", | |
| "installing: zlib-1.2.11-ha838bed_2 ...\n", | |
| "installing: libedit-3.1.20170329-h6b74fdf_2 ...\n", | |
| "installing: readline-7.0-ha6073c6_4 ...\n", | |
| "installing: sqlite-3.23.1-he433501_0 ...\n", | |
| "installing: asn1crypto-0.24.0-py36_0 ...\n", | |
| "installing: certifi-2018.4.16-py36_0 ...\n", | |
| "installing: chardet-3.0.4-py36h0f667ec_1 ...\n", | |
| "installing: idna-2.6-py36h82fb2a8_1 ...\n", | |
| "installing: pycosat-0.6.3-py36h0a5515d_0 ...\n", | |
| "installing: pycparser-2.18-py36hf9f622e_1 ...\n", | |
| "installing: pysocks-1.6.8-py36_0 ...\n", | |
| "installing: ruamel_yaml-0.15.37-py36h14c3975_2 ...\n", | |
| "installing: six-1.11.0-py36h372c433_1 ...\n", | |
| "installing: cffi-1.11.5-py36h9745a5d_0 ...\n", | |
| "installing: setuptools-39.2.0-py36_0 ...\n", | |
| "installing: cryptography-2.2.2-py36h14c3975_0 ...\n", | |
| "installing: wheel-0.31.1-py36_0 ...\n", | |
| "installing: pip-10.0.1-py36_0 ...\n", | |
| "installing: pyopenssl-18.0.0-py36_0 ...\n", | |
| "installing: urllib3-1.22-py36hbe7ace6_0 ...\n", | |
| "installing: requests-2.18.4-py36he2e5f8d_1 ...\n", | |
| "installing: conda-4.5.4-py36_0 ...\n", | |
| "unlinking: asn1crypto-0.24.0-py37_0\n", | |
| "unlinking: certifi-2018.11.29-py37_0\n", | |
| "unlinking: cffi-1.11.5-py37he75722e_1\n", | |
| "unlinking: chardet-3.0.4-py37_1\n", | |
| "unlinking: conda-4.5.12-py37_0\n", | |
| "unlinking: conda-env-2.6.0-1\n", | |
| "unlinking: cryptography-2.4.2-py37h1ba5d50_0\n", | |
| "unlinking: idna-2.8-py37_0\n", | |
| "unlinking: libgcc-ng-8.2.0-hdf63c60_1\n", | |
| "unlinking: libstdcxx-ng-8.2.0-hdf63c60_1\n", | |
| "unlinking: ncurses-6.1-he6710b0_1\n", | |
| "unlinking: openssl-1.1.1a-h7b6447c_0\n", | |
| "unlinking: pip-18.1-py37_0\n", | |
| "unlinking: pycosat-0.6.3-py37h14c3975_0\n", | |
| "unlinking: pycparser-2.19-py37_0\n", | |
| "unlinking: pyopenssl-18.0.0-py37_0\n", | |
| "unlinking: pysocks-1.6.8-py37_0\n", | |
| "unlinking: python-3.7.1-h0371630_7\n", | |
| "unlinking: readline-7.0-h7b6447c_5\n", | |
| "unlinking: requests-2.21.0-py37_0\n", | |
| "unlinking: ruamel_yaml-0.15.46-py37h14c3975_0\n", | |
| "unlinking: setuptools-40.6.3-py37_0\n", | |
| "unlinking: six-1.12.0-py37_0\n", | |
| "unlinking: sqlite-3.26.0-h7b6447c_0\n", | |
| "unlinking: tk-8.6.8-hbc83047_0\n", | |
| "unlinking: urllib3-1.24.1-py37_0\n", | |
| "unlinking: wheel-0.32.3-py37_0\n", | |
| "unlinking: zlib-1.2.11-h7b6447c_3\n", | |
| "installation finished.\n", | |
| "WARNING:\n", | |
| " You currently have a PYTHONPATH environment variable set. This may cause\n", | |
| " unexpected behavior when running the Python interpreter in Miniconda3.\n", | |
| " For best results, please verify that your PYTHONPATH only points to\n", | |
| " directories of packages that are compatible with the Python interpreter\n", | |
| " in Miniconda3: /usr/local\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "!wget https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh && bash Miniconda3-4.5.4-Linux-x86_64.sh -bfp /usr/local" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 8, | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 2305 | |
| }, | |
| "colab_type": "code", | |
| "id": "v5DCYIOLEptA", | |
| "outputId": "e10230de-edcc-4d05-bb8f-e8a3741f91ed" | |
| }, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "\n", | |
| " active environment : None\n", | |
| " user config file : /root/.condarc\n", | |
| " populated config files : \n", | |
| " conda version : 4.5.4\n", | |
| " conda-build version : not installed\n", | |
| " python version : 3.6.5.final.0\n", | |
| " base environment : /usr/local (writable)\n", | |
| " channel URLs : https://repo.anaconda.com/pkgs/main/linux-64\n", | |
| " https://repo.anaconda.com/pkgs/main/noarch\n", | |
| " https://repo.anaconda.com/pkgs/free/linux-64\n", | |
| " https://repo.anaconda.com/pkgs/free/noarch\n", | |
| " https://repo.anaconda.com/pkgs/r/linux-64\n", | |
| " https://repo.anaconda.com/pkgs/r/noarch\n", | |
| " https://repo.anaconda.com/pkgs/pro/linux-64\n", | |
| " https://repo.anaconda.com/pkgs/pro/noarch\n", | |
| " package cache : /usr/local/pkgs\n", | |
| " /root/.conda/pkgs\n", | |
| " envs directories : /usr/local/envs\n", | |
| " /root/.conda/envs\n", | |
| " platform : linux-64\n", | |
| " user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Linux/4.14.79+ ubuntu/18.04 glibc/2.27\n", | |
| " UID:GID : 0:0\n", | |
| " netrc file : None\n", | |
| " offline mode : False\n", | |
| "\n", | |
| "# conda environments:\n", | |
| "#\n", | |
| "base * /usr/local\n", | |
| "\n", | |
| "sys.version: 3.6.5 |Anaconda, Inc.| (default, Apr 29 ...\n", | |
| "sys.prefix: /usr/local\n", | |
| "sys.executable: /usr/local/bin/python\n", | |
| "conda location: /usr/local/lib/python3.6/site-packages/conda\n", | |
| "conda-build: None\n", | |
| "conda-env: /usr/local/bin/conda-env\n", | |
| "user site dirs: \n", | |
| "\n", | |
| "CIO_TEST: <not set>\n", | |
| "CONDA_ROOT: /usr/local\n", | |
| "LD_LIBRARY_PATH: /usr/lib64-nvidia\n", | |
| "LIBRARY_PATH: /usr/local/cuda/lib64/stubs\n", | |
| "PATH: /usr/local/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/tools/node/bin:/tools/google-cloud-sdk/bin:/opt/bin\n", | |
| "PYTHONPATH: /env/python\n", | |
| "PYTHONWARNINGS: ignore:::pip._internal.cli.base_command\n", | |
| "REQUESTS_CA_BUNDLE: <not set>\n", | |
| "SSL_CERT_FILE: <not set>\n", | |
| "\n", | |
| "\n", | |
| "WARNING: could not import _license.show_info\n", | |
| "# try:\n", | |
| "# $ conda install -n root _license\n", | |
| "# packages in environment at /usr/local:\n", | |
| "#\n", | |
| "# Name Version Build Channel\n", | |
| "asn1crypto 0.24.0 py36_0 \n", | |
| "ca-certificates 2018.03.07 0 \n", | |
| "certifi 2018.4.16 py36_0 \n", | |
| "cffi 1.11.5 py36h9745a5d_0 \n", | |
| "chardet 3.0.4 py36h0f667ec_1 \n", | |
| "conda 4.5.4 py36_0 \n", | |
| "conda-env 2.6.0 h36134e3_1 \n", | |
| "cryptography 2.2.2 py36h14c3975_0 \n", | |
| "idna 2.6 py36h82fb2a8_1 \n", | |
| "libedit 3.1.20170329 h6b74fdf_2 \n", | |
| "libffi 3.2.1 hd88cf55_4 \n", | |
| "libgcc-ng 7.2.0 hdf63c60_3 \n", | |
| "libstdcxx-ng 7.2.0 hdf63c60_3 \n", | |
| "ncurses 6.1 hf484d3e_0 \n", | |
| "openssl 1.0.2o h20670df_0 \n", | |
| "pip 10.0.1 py36_0 \n", | |
| "pycosat 0.6.3 py36h0a5515d_0 \n", | |
| "pycparser 2.18 py36hf9f622e_1 \n", | |
| "pyopenssl 18.0.0 py36_0 \n", | |
| "pysocks 1.6.8 py36_0 \n", | |
| "python 3.6.5 hc3d631a_2 \n", | |
| "readline 7.0 ha6073c6_4 \n", | |
| "requests 2.18.4 py36he2e5f8d_1 \n", | |
| "ruamel_yaml 0.15.37 py36h14c3975_2 \n", | |
| "setuptools 39.2.0 py36_0 \n", | |
| "six 1.11.0 py36h372c433_1 \n", | |
| "sqlite 3.23.1 he433501_0 \n", | |
| "tk 8.6.7 hc745277_3 \n", | |
| "urllib3 1.22 py36hbe7ace6_0 \n", | |
| "wheel 0.31.1 py36_0 \n", | |
| "xz 5.2.4 h14c3975_4 \n", | |
| "yaml 0.1.7 had09818_2 \n", | |
| "zlib 1.2.11 ha838bed_2 \n", | |
| "CLICOLOR=1\n", | |
| "CLOUDSDK_CONFIG=/content/.config\n", | |
| "COLAB_GPU=1\n", | |
| "CUDA_PKG_VERSION=10-0=10.0.130-1\n", | |
| "CUDA_VERSION=10.0.130\n", | |
| "CUDNN_VERSION=7.5.0.56\n", | |
| "DATALAB_SETTINGS_OVERRIDES={\"kernelManagerProxyPort\":6000,\"kernelManagerProxyHost\":\"172.28.0.3\",\"jupyterArgs\":[\"--ip=\\\"172.28.0.2\\\"\"]}\n", | |
| "DEBIAN_FRONTEND=noninteractive\n", | |
| "__EGL_VENDOR_LIBRARY_DIRS=/usr/lib64-nvidia:/usr/share/glvnd/egl_vendor.d/\n", | |
| "ENV=/root/.bashrc\n", | |
| "GCS_READ_CACHE_BLOCK_SIZE_MB=16\n", | |
| "GIT_PAGER=cat\n", | |
| "GLIBCPP_FORCE_NEW=1\n", | |
| "GLIBCXX_FORCE_NEW=1\n", | |
| "HOME=/root\n", | |
| "HOSTNAME=dd67983c307e\n", | |
| "JPY_PARENT_PID=34\n", | |
| "LANG=en_US.UTF-8\n", | |
| "LD_LIBRARY_PATH=/usr/lib64-nvidia\n", | |
| "LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libtcmalloc.so.4\n", | |
| "LIBRARY_PATH=/usr/local/cuda/lib64/stubs\n", | |
| "MPLBACKEND=module://ipykernel.pylab.backend_inline\n", | |
| "NCCL_VERSION=2.4.2\n", | |
| "NO_GCE_CHECK=True\n", | |
| "NVIDIA_DRIVER_CAPABILITIES=compute,utility\n", | |
| "NVIDIA_REQUIRE_CUDA=cuda>=10.0 brand=tesla,driver>=384,driver<385 brand=tesla,driver>=410,driver<411\n", | |
| "NVIDIA_VISIBLE_DEVICES=all\n", | |
| "OLDPWD=/\n", | |
| "PAGER=cat\n", | |
| "PATH=/usr/local/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/tools/node/bin:/tools/google-cloud-sdk/bin:/opt/bin\n", | |
| "PWD=/content\n", | |
| "PYTHONPATH=/env/python\n", | |
| "PYTHONWARNINGS=ignore:::pip._internal.cli.base_command\n", | |
| "SHELL=/bin/bash\n", | |
| "SHLVL=2\n", | |
| "TERM=xterm-color\n", | |
| "TF_FORCE_GPU_ALLOW_GROWTH=true\n", | |
| "_=/usr/bin/env\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "!conda info --all\n", | |
| "!conda list\n", | |
| "!env | sort" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "colab_type": "text", | |
| "id": "hD2dcnR7y8Ry" | |
| }, | |
| "source": [ | |
| "# Install needed packages\n", | |
| "Again the normal procedure, just remember to always use `-y` so `conda` does not wait for confirmation. `-q` is useful to prevent interactive outputs (such as the rolling slash /|\\-/|\\-). Always add `python=3.6` to prevent accidental updates!" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 1, | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 2933 | |
| }, | |
| "colab_type": "code", | |
| "id": "3jZucs0Eufuq", | |
| "outputId": "77b61836-52b1-45fe-af18-3623c57efe23" | |
| }, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "Collecting package metadata (current_repodata.json): ...working... done\n", | |
| "Solving environment: ...working... done\n", | |
| "\n", | |
| "## Package Plan ##\n", | |
| "\n", | |
| " environment location: /home/jaime/.conda/envs/opencaddtest\n", | |
| "\n", | |
| " added / updated specs:\n", | |
| " - openmm\n", | |
| " - python=3.6\n", | |
| "\n", | |
| "\n", | |
| "The following packages will be downloaded:\n", | |
| "\n", | |
| " package | build\n", | |
| " ---------------------------|-----------------\n", | |
| " cffi-1.14.4 | py36hc120d54_1 225 KB conda-forge\n", | |
| " chardet-4.0.0 | py36h5fab9bb_0 219 KB conda-forge\n", | |
| " cryptography-3.3.1 | py36h0a59100_0 624 KB conda-forge\n", | |
| " importlib-metadata-3.3.0 | py36h5fab9bb_2 20 KB conda-forge\n", | |
| " ipykernel-5.4.2 | py36he448a4c_0 165 KB conda-forge\n", | |
| " ipython-7.12.0 | py36h5ca1d4c_0 1.1 MB conda-forge\n", | |
| " jedi-0.17.2 | py36h5fab9bb_1 957 KB conda-forge\n", | |
| " markupsafe-1.1.1 | py36he6145b8_2 27 KB conda-forge\n", | |
| " mistune-0.8.4 |py36h1d69622_1002 54 KB conda-forge\n", | |
| " notebook-5.7.10 | py36h9f0ad1d_0 7.6 MB conda-forge\n", | |
| " numpy-1.19.4 | py36h2aa4a07_2 5.3 MB conda-forge\n", | |
| " ocl-icd-2.2.14 | h7f98852_0 118 KB conda-forge\n", | |
| " openmm-7.5.0 | py36hd44746c_4 10.9 MB conda-forge\n", | |
| " pyrsistent-0.17.3 | py36h1d69622_1 89 KB conda-forge\n", | |
| " setuptools-49.6.0 | py36h9880bd3_2 947 KB conda-forge\n", | |
| " terminado-0.9.1 | py36h5fab9bb_1 25 KB conda-forge\n", | |
| " ------------------------------------------------------------\n", | |
| " Total: 28.2 MB\n", | |
| "\n", | |
| "The following NEW packages will be INSTALLED:\n", | |
| "\n", | |
| " cudatoolkit conda-forge/linux-64::cudatoolkit-11.0.3-h15472ef_6\n", | |
| " fftw conda-forge/linux-64::fftw-3.3.8-nompi_h8cb7ab2_1114\n", | |
| " libblas conda-forge/linux-64::libblas-3.9.0-3_openblas\n", | |
| " libcblas conda-forge/linux-64::libcblas-3.9.0-3_openblas\n", | |
| " libgfortran-ng conda-forge/linux-64::libgfortran-ng-9.3.0-he4bcb1c_17\n", | |
| " libgfortran5 conda-forge/linux-64::libgfortran5-9.3.0-he4bcb1c_17\n", | |
| " liblapack conda-forge/linux-64::liblapack-3.9.0-3_openblas\n", | |
| " libopenblas conda-forge/linux-64::libopenblas-0.3.12-pthreads_h4812303_1\n", | |
| " numpy conda-forge/linux-64::numpy-1.19.4-py36h2aa4a07_2\n", | |
| " ocl-icd conda-forge/linux-64::ocl-icd-2.2.14-h7f98852_0\n", | |
| " ocl-icd-system conda-forge/linux-64::ocl-icd-system-1.0.0-1\n", | |
| " openmm conda-forge/linux-64::openmm-7.5.0-py36hd44746c_4\n", | |
| " prompt_toolkit conda-forge/noarch::prompt_toolkit-3.0.8-hd8ed1ab_0\n", | |
| " typing_extensions conda-forge/noarch::typing_extensions-3.7.4.3-py_0\n", | |
| "\n", | |
| "The following packages will be REMOVED:\n", | |
| "\n", | |
| " argon2-cffi-20.1.0-py38h25fe258_2\n", | |
| "\n", | |
| "The following packages will be UPDATED:\n", | |
| "\n", | |
| " entrypoints conda-forge/linux-64::entrypoints-0.3~ --> conda-forge/noarch::entrypoints-0.3-pyhd8ed1ab_1003\n", | |
| " jsonschema conda-forge/linux-64::jsonschema-3.2.~ --> conda-forge/noarch::jsonschema-3.2.0-py_2\n", | |
| " libstdcxx-ng pkgs/main::libstdcxx-ng-9.1.0-hdf63c6~ --> conda-forge::libstdcxx-ng-9.3.0-h2ae2ef3_17\n", | |
| " pexpect conda-forge/linux-64::pexpect-4.8.0-p~ --> conda-forge/noarch::pexpect-4.8.0-pyh9f0ad1d_2\n", | |
| " pickleshare conda-forge/linux-64::pickleshare-0.7~ --> conda-forge/noarch::pickleshare-0.7.5-py_1003\n", | |
| " pip pkgs/main/linux-64::pip-20.3.1-py38h0~ --> conda-forge/noarch::pip-20.3.3-pyhd8ed1ab_0\n", | |
| "\n", | |
| "The following packages will be SUPERSEDED by a higher-priority channel:\n", | |
| "\n", | |
| " ca-certificates pkgs/main::ca-certificates-2020.12.8-~ --> conda-forge::ca-certificates-2020.12.5-ha878542_0\n", | |
| " pandocfilters pkgs/main/linux-64::pandocfilters-1.4~ --> conda-forge/noarch::pandocfilters-1.4.2-py_1\n", | |
| " setuptools pkgs/main::setuptools-51.0.0-py38h06a~ --> conda-forge::setuptools-49.6.0-py36h9880bd3_2\n", | |
| " traitlets conda-forge/noarch::traitlets-5.0.5-p~ --> conda-forge/linux-64::traitlets-4.3.3-py36h9f0ad1d_1\n", | |
| "\n", | |
| "The following packages will be DOWNGRADED:\n", | |
| "\n", | |
| " brotlipy 0.7.0-py38h8df0ef7_1001 --> 0.7.0-py36he6145b8_1001\n", | |
| " certifi 2020.12.5-py38h578d9bd_0 --> 2020.12.5-py36h5fab9bb_0\n", | |
| " cffi 1.14.4-py38ha65f79e_1 --> 1.14.4-py36hc120d54_1\n", | |
| " chardet 4.0.0-py38h578d9bd_0 --> 4.0.0-py36h5fab9bb_0\n", | |
| " cryptography 3.3.1-py38h2b97feb_0 --> 3.3.1-py36h0a59100_0\n", | |
| " importlib-metadata 3.3.0-py38h578d9bd_2 --> 3.3.0-py36h5fab9bb_2\n", | |
| " ipykernel 5.4.2-py38h81c977d_0 --> 5.4.2-py36he448a4c_0\n", | |
| " ipython 7.19.0-py38h81c977d_0 --> 7.12.0-py36h5ca1d4c_0\n", | |
| " jedi 0.17.2-py38h578d9bd_1 --> 0.17.2-py36h5fab9bb_1\n", | |
| " jupyter_core 4.7.0-py38h578d9bd_0 --> 4.7.0-py36h5fab9bb_0\n", | |
| " markupsafe 1.1.1-py38h8df0ef7_2 --> 1.1.1-py36he6145b8_2\n", | |
| " mistune 0.8.4-py38h25fe258_1002 --> 0.8.4-py36h1d69622_1002\n", | |
| " nbconvert 6.0.7-py38h578d9bd_3 --> 5.6.1-py36h9f0ad1d_1\n", | |
| " notebook 6.1.5-py38h578d9bd_0 --> 5.7.10-py36h9f0ad1d_0\n", | |
| " pyrsistent 0.17.3-py38h25fe258_1 --> 0.17.3-py36h1d69622_1\n", | |
| " pysocks 1.7.1-py38h924ce5b_2 --> 1.7.1-py36h9880bd3_2\n", | |
| " python 3.8.5-h7579374_1 --> 3.6.12-hcff3b4d_2\n", | |
| " python_abi 3.8-1_cp38 --> 3.6-1_cp36m\n", | |
| " pyzmq 20.0.0-py38h1d1b12f_1 --> 20.0.0-py36h2b1bd32_1\n", | |
| " terminado 0.9.1-py38h32f6830_1 --> 0.9.1-py36h5fab9bb_1\n", | |
| " tornado 6.1-py38h25fe258_0 --> 6.1-py36h1d69622_0\n", | |
| "\n", | |
| "\n", | |
| "Preparing transaction: ...working... done\n", | |
| "Verifying transaction: ...working... done\n", | |
| "Executing transaction: ...working... By downloading and using the CUDA Toolkit conda packages, you accept the terms and conditions of the CUDA End User License Agreement (EULA): https://docs.nvidia.com/cuda/eula/index.html\n", | |
| "\n", | |
| "done\n", | |
| "\n", | |
| "real\t0m31.991s\n", | |
| "user\t0m26.057s\n", | |
| "sys\t0m2.397s\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "!time conda install -y -q -c conda-forge openmm python=3.6" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "colab_type": "text", | |
| "id": "Qal84ahazWZt" | |
| }, | |
| "source": [ | |
| "# The trick\n", | |
| "Since Miniconda now lives in `/usr/local` (which incidentally is also a default location to load static libraries), we only need to add the corresponding Python path to `sys.path` to enable imports." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 0, | |
| "metadata": { | |
| "colab": {}, | |
| "colab_type": "code", | |
| "id": "S-x_hxCTvfLR" | |
| }, | |
| "outputs": [], | |
| "source": [ | |
| "import sys\n", | |
| "sys.path.insert(0, '/usr/local/lib/python3.6/site-packages/')" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "colab_type": "text", | |
| "id": "PJfhPWp8AacY" | |
| }, | |
| "source": [ | |
| "# Let's play!\n", | |
| "Now you can just interact with the Notebook as you would normally do locally." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 11, | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 287 | |
| }, | |
| "colab_type": "code", | |
| "id": "MLW86ukM-FQo", | |
| "outputId": "04777a02-f738-428e-d188-6659f1e0d9bb" | |
| }, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "There are 4 Platforms available:\n", | |
| "\n", | |
| "1 Reference - Successfully computed forces\n", | |
| "2 CPU - Successfully computed forces\n", | |
| "3 CUDA - Successfully computed forces\n", | |
| "4 OpenCL - Successfully computed forces\n", | |
| "\n", | |
| "Median difference in forces between platforms:\n", | |
| "\n", | |
| "Reference vs. CPU: 6.3031e-06\n", | |
| "Reference vs. CUDA: 6.73543e-06\n", | |
| "CPU vs. CUDA: 7.81258e-07\n", | |
| "Reference vs. OpenCL: 6.75426e-06\n", | |
| "CPU vs. OpenCL: 8.15821e-07\n", | |
| "CUDA vs. OpenCL: 2.17776e-07\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "import simtk.testInstallation\n", | |
| "simtk.testInstallation.main()" | |
| ] | |
| } | |
| ], | |
| "metadata": { | |
| "accelerator": "GPU", | |
| "colab": { | |
| "collapsed_sections": [], | |
| "name": "CondaExampleWithOpenMMTools.ipynb", | |
| "provenance": [], | |
| "toc_visible": true, | |
| "version": "0.3.2" | |
| }, | |
| "kernelspec": { | |
| "display_name": "Python 3", | |
| "language": "python", | |
| "name": "python3" | |
| }, | |
| "language_info": { | |
| "codemirror_mode": { | |
| "name": "ipython", | |
| "version": 3 | |
| }, | |
| "file_extension": ".py", | |
| "mimetype": "text/x-python", | |
| "name": "python", | |
| "nbconvert_exporter": "python", | |
| "pygments_lexer": "ipython3", | |
| "version": "3.8.5" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 1 | |
| } |
Hi Oliver, if they have migrated to Python 3.7, then you should also download the latest Miniconda (instead of v4.5.4). I will test this later this week and update this notebook. Thanks for the report!
Hi Oliver, if they have migrated to Python 3.7, then you should also download the latest Miniconda (instead of v4.5.4). I will test this later this week and update this notebook. Thanks for the report!
Hello Jaime,
Thank you for your reply!
I have tried again using Anaconda2, and it works!
!wget -c https://repo.anaconda.com/archive/Anaconda2-2019.03-Linux-x86_64.sh
!bash ./Anaconda2-2019.03-Linux-x86_64.sh -b -f -p /usr/local
!conda install -y --prefix /usr/local -c omnia/label/cuda100 -c conda-forge openmm
import sys
sys.path.append('/usr/local/lib/python2.7/site-packages/')
import simtk.testInstallation
simtk.testInstallation.main()
Still, it would be really helpful if you could get it work on Python3 (as OpenMM recommended on their website). I haven't seen any error or issue using Python2 yet.
Sorry I forgot to mention that we have to change the runtime type to Python2 and of course with GPU before get started.
Hi Oliver, a year later, I found out what was happening: the conda solver sneakily updates python, which creates all sorts of problems. Make sure to add python=3.6 to the list of packages passed to conda install and it should work ok!
Hi, my name is Ted. I tried running your code and encountered the following error. Would be grateful if any of you could help me figure it out. I got the error while running simtk.testInstallation.main().
Failed to import OpenMM packages; OpenMM will not work.
Make sure OpenMM is installed and the library path is set correctly.
Error message: cannot import name '_openmm' from 'simtk.openmm' (/usr/local/lib/python3.6/site-packages/simtk/openmm/init.py)
An exception has occurred, use %tb to see the full traceback.
SystemExit: 1
Hi @drcube98-mrss! Colab has changed a bit its internals but I didn't update this notebook. Take a look at my condacolab project for a new updated workflow. You can see an example here.
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Hello Jaime, this is Oliver. I tried to install openmm couple times and it didn't work. So I googled "openmm" and "colab" and found your tutorial. Then I followed every step of your tutorial, but I got totally different result. It still doesn't work for me.
So in this step
import syssys.path.append('/usr/local/lib/python3.6/site-packages/')It seems like they moved "site-packages" under python3.7. Even after appending the site-packages under python3.7, I still get the same issue.
"Error message: No module named '_openmm'"
I wonder if I didn't do it correctly or openmm has changed some setting.
Thank you!