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Refactor shell setup code & update CUDA build #425

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9c99943
Created using Colaboratory
afairley Mar 22, 2024
45e28b7
Update setup.py
afairley Mar 27, 2024
c26d12c
Update setup.py
afairley Mar 27, 2024
c273131
Refactoring
afairley Mar 29, 2024
8527e9a
Clear output cells to make diff more legible
afairley Mar 29, 2024
a0a3fd7
Remove output cell text
afairley Mar 29, 2024
40d7d3d
Correct incorrect colab
afairley Mar 29, 2024
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65 changes: 40 additions & 25 deletions notebooks/OpenFold.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,11 @@
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github"
"id": "view-in-github",
"colab_type": "text"
},
"source": [
"<a href=\"https://colab.research.google.com/github/aqlaboratory/openfold/blob/main/notebooks/OpenFold.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
"<a href=\"https://colab.research.google.com/github/aqlaboratory/openfold/blob/main/notebooks/OpenFold.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
Expand Down Expand Up @@ -109,40 +110,54 @@
"#@markdown **Note**: This installs the software on the Colab\n",
"#@markdown notebook in the cloud and not on your computer.\n",
"\n",
"import os, time\n",
"import os, sys, time\n",
"from IPython.utils import io\n",
"from sys import version_info\n",
"import subprocess\n",
"\n",
"python_version = f\"{version_info.major}.{version_info.minor}\"\n",
"PYTHON_VERSION = f\"{version_info.major}.{version_info.minor}\"\n",
"#Default setting of OPENFOLD_COMMIT at None will work with latest code checked in\n",
"# in OPENFOLD_GIT_REPO. Should switch to a tagged release or a branch\n",
"# per best practices.\n",
"OPENFOLD_COMMIT = None\n",
"# COMMIT at which inline CUDA introduced\n",
"#OPENFOLD_COMMIT = \"e2e19f16676b1a409f9ba3a6f69b11ee7f5887c2\"\n",
"# COMMIT at which changes made to work with new numpy version\n",
"#OPENFOLD_COMMIT = \"15b1bbd667652637ea334a9ddd6b71f393910a0e\"\n",
"OPENFOLD_GIT_PROJECT = \"openfold\"\n",
"# For development purposes you may want to use a different\n",
"# \"fork\" of OpenFold than main aqlaboratory repository\n",
"OPENFOLD_GIT_USER = \"aqlaboratory\"\n",
"OPENFOLD_GIT_REPO =\\\n",
" f'https://github.com/{OPENFOLD_GIT_USER}/{OPENFOLD_GIT_PROJECT}'\n",
"\n",
"\n",
"os.system(\"wget -qnc https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh\")\n",
"os.system(\"bash Mambaforge-Linux-x86_64.sh -bfp /usr/local\")\n",
"os.system(\"mamba config --set auto_update_conda false\")\n",
"os.system(f\"mamba install -y -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 openmm=7.7.0 python={python_version} pdbfixer biopython=1.79\")\n",
"os.system(\"pip install -q torch ml_collections py3Dmol modelcif\")\n",
"\n",
"try:\n",
" with io.capture_output() as captured:\n",
" %shell rm -rf {OPENFOLD_GIT_PROJECT}\n",
" %shell wget -qnc https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh\n",
" %shell bash Mambaforge-Linux-x86_64.sh -bfp /usr/local\n",
" %shell mamba install -y -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 openmm=7.7.0 python={PYTHON_VERSION} pdbfixer biopython=1.79\n",
" %shell pip3 install -q torch ml_collections py3Dmol modelcif matplotlib\n",
" %shell git clone --branch main {OPENFOLD_GIT_REPO} {OPENFOLD_GIT_PROJECT}\n",
" if OPENFOLD_COMMIT:\n",
" %shell cd {OPENFOLD_GIT_PROJECT} && git checkout {OPENFOLD_COMMIT}\n",
" %shell cd {OPENFOLD_GIT_PROJECT} && python setup.py bdist_wheel\n",
" %shell pip3 install --no-dependencies ./{OPENFOLD_GIT_PROJECT}\n",
" %shell wget -q -P /content \\\n",
" https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt\n",
" %shell cp -f \\\n",
" -p /content/stereo_chemical_props.txt /usr/local/lib/python{PYTHON_VERSION}/site-packages/openfold/resources/\n",
"\n",
" # Create a ramdisk to store a database chunk to make Jackhmmer run fast.\n",
" %shell sudo apt install --quiet --yes hmmer\n",
" %shell sudo mkdir -m 777 --parents /tmp/ramdisk\n",
" %shell sudo mount -t tmpfs -o size=9G ramdisk /tmp/ramdisk\n",
"\n",
" %shell wget -q -P /content \\\n",
" https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt\n",
"\n",
" %shell mkdir -p /content/openfold/openfold/resources\n",
"\n",
" commit = \"e2e19f16676b1a409f9ba3a6f69b11ee7f5887c2\"\n",
" os.system(f\"pip install -q git+https://github.com/aqlaboratory/openfold.git@{commit}\")\n",
"\n",
" os.system(f\"cp -f -p /content/stereo_chemical_props.txt /usr/local/lib/python{python_version}/site-packages/openfold/resources/\")\n",
"\n",
"except subprocess.CalledProcessError as captured:\n",
" print(captured)"
" print(captured)\n",
" raise\n",
"\n"
]
},
{
Expand Down Expand Up @@ -210,8 +225,8 @@
"import sys\n",
"from typing import Dict, Sequence\n",
"\n",
"sys.path.insert(0, f'/usr/local/lib/python{python_version}/dist-packages/')\n",
"sys.path.insert(0, f'/usr/local/lib/python{python_version}/site-packages/')\n",
"sys.path.insert(0, f'/usr/local/lib/python{PYTHON_VERSION}/dist-packages/')\n",
"sys.path.insert(0, f'/usr/local/lib/python{PYTHON_VERSION}/site-packages/')\n",
"\n",
"# Allows us to skip installing these packages\n",
"unnecessary_modules = [\n",
Expand Down Expand Up @@ -903,7 +918,7 @@
"colab": {
"provenance": [],
"gpuType": "T4",
"toc_visible": true
"include_colab_link": true
},
"kernelspec": {
"display_name": "Python 3",
Expand All @@ -916,4 +931,4 @@
},
"nbformat": 4,
"nbformat_minor": 0
}
}
4 changes: 2 additions & 2 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@
]

extra_cuda_flags = [
'-std=c++14',
'-std=c++17',
'-maxrregcount=50',
'-U__CUDA_NO_HALF_OPERATORS__',
'-U__CUDA_NO_HALF_CONVERSIONS__',
Expand All @@ -38,7 +38,7 @@
]

def get_cuda_bare_metal_version(cuda_dir):
if cuda_dir==None or torch.version.cuda==None:
if cuda_dir==None or torch.version.cuda==None or not torch.cuda.is_available():
print("CUDA is not found, cpu version is installed")
return None, -1, 0
else:
Expand Down