diff --git a/notebooks/OpenFold.ipynb b/notebooks/OpenFold.ipynb
index 8a844652..38179c3d 100644
--- a/notebooks/OpenFold.ipynb
+++ b/notebooks/OpenFold.ipynb
@@ -3,10 +3,11 @@
{
"cell_type": "markdown",
"metadata": {
- "id": "view-in-github"
+ "id": "view-in-github",
+ "colab_type": "text"
},
"source": [
- "![\"Open](\"https://colab.research.google.com/assets/colab-badge.svg\")
"
+ ""
]
},
{
@@ -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"
]
},
{
@@ -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",
@@ -903,7 +918,7 @@
"colab": {
"provenance": [],
"gpuType": "T4",
- "toc_visible": true
+ "include_colab_link": true
},
"kernelspec": {
"display_name": "Python 3",
@@ -916,4 +931,4 @@
},
"nbformat": 4,
"nbformat_minor": 0
-}
\ No newline at end of file
+}
diff --git a/setup.py b/setup.py
index bec98625..bef8d63c 100644
--- a/setup.py
+++ b/setup.py
@@ -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__',
@@ -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: