From 10101f71ef175bccfa9a688ba73f55936e15c635 Mon Sep 17 00:00:00 2001 From: Jan Kosinski Date: Sun, 19 May 2024 12:49:22 +0200 Subject: [PATCH 1/5] Fix export $LD_LIBRARY_PATH in Installation.md --- docs/source/Installation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/Installation.md b/docs/source/Installation.md index 9e34d5f23..fb9e82681 100644 --- a/docs/source/Installation.md +++ b/docs/source/Installation.md @@ -21,7 +21,7 @@ At this time, only Linux systems are supported. 1. Run the setup script to configure kernels and folding resources. > scripts/install_third_party_dependencies.sh` 1. Prepend the conda environment to the `$LD_LIBRARY_PATH`., e.g. - `export $LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH`. You may optionally set this as a conda environment variable according to the [conda docs](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#saving-environment-variables) to activate each time the environment is used. + `export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH`. You may optionally set this as a conda environment variable according to the [conda docs](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#saving-environment-variables) to activate each time the environment is used. 1. Download parameters. We recommend using a destination as `openfold/resources` as our unittests will look for the weights there. - For AlphaFold2 weights, use > ./scripts/download_alphafold_params.sh From 1d89780f4633a32b87df4b1dca3d3f7df9c7a3cd Mon Sep 17 00:00:00 2001 From: Jan Kosinski Date: Sun, 19 May 2024 12:51:43 +0200 Subject: [PATCH 2/5] Fix that would not render in github markdown in Installation.md --- docs/source/Installation.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source/Installation.md b/docs/source/Installation.md index fb9e82681..c2e562054 100644 --- a/docs/source/Installation.md +++ b/docs/source/Installation.md @@ -24,11 +24,11 @@ At this time, only Linux systems are supported. `export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH`. You may optionally set this as a conda environment variable according to the [conda docs](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#saving-environment-variables) to activate each time the environment is used. 1. Download parameters. We recommend using a destination as `openfold/resources` as our unittests will look for the weights there. - For AlphaFold2 weights, use - > ./scripts/download_alphafold_params.sh + > ./scripts/download_alphafold_params.sh <dest> - For OpenFold weights, use : - > ./scripts/download_openfold_params.sh + > ./scripts/download_openfold_params.sh <dest> - For OpenFold SoloSeq weights, use: - > ./scripts/download_openfold_soloseq_params.sh + > ./scripts/download_openfold_soloseq_params.sh <dest> ### Checking your build with unit tests: From 6deee7220203a3987d24556f1c05d095bb239e11 Mon Sep 17 00:00:00 2001 From: Jan Kosinski Date: Sun, 19 May 2024 13:00:34 +0200 Subject: [PATCH 3/5] just a clarification in Installation.md that was not clear to me --- docs/source/Installation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/Installation.md b/docs/source/Installation.md index c2e562054..6da7e8527 100644 --- a/docs/source/Installation.md +++ b/docs/source/Installation.md @@ -22,7 +22,7 @@ At this time, only Linux systems are supported. > scripts/install_third_party_dependencies.sh` 1. Prepend the conda environment to the `$LD_LIBRARY_PATH`., e.g. `export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH`. You may optionally set this as a conda environment variable according to the [conda docs](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#saving-environment-variables) to activate each time the environment is used. -1. Download parameters. We recommend using a destination as `openfold/resources` as our unittests will look for the weights there. +1. Download parameters. We recommend using a destination as `openfold/resources` as our unittests will look for the weights there. You can download all parameters to the same destination folder as the files will not overwrite each other. - For AlphaFold2 weights, use > ./scripts/download_alphafold_params.sh <dest> - For OpenFold weights, use : From c02a3677e33f296411005f9cac5c447629207ada Mon Sep 17 00:00:00 2001 From: Jan Kosinski Date: Sun, 19 May 2024 13:14:30 +0200 Subject: [PATCH 4/5] Add the actual OpenFold installation step in Installation.md Not sure if this the way you want it but otherwise OpenFold would not be installed... And you'd get error like this: srun --time=1-00:00:00 -p gpu-el8 -G 1 --mem-per-gpu 32000 --qos=highest scripts/run_unit_tests.sh srun: job 4368915 queued and waiting for resources srun: job 4368915 has been allocated resources /g/kosinski/kosinski/software/envs/openfold_env/lib/python3.9/site-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.4 warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}" [2024-05-19 13:02:40,227] [INFO] [real_accelerator.py:161:get_accelerator] Setting ds_accelerator to cuda (auto detect) E.................EEEEEEEEEEEE...EEEEEE ====================================================================== ERROR: tests.test_data_pipeline (unittest.loader._FailedTest) ---------------------------------------------------------------------- ImportError: Failed to import test module: tests.test_data_pipeline Traceback (most recent call last): File "/g/kosinski/kosinski/software/envs/openfold_env/lib/python3.9/unittest/loader.py", line 436, in _find_test_path module = self._get_module_from_name(name) File "/g/kosinski/kosinski/software/envs/openfold_env/lib/python3.9/unittest/loader.py", line 377, in _get_module_from_name __import__(name) File "/g/kosinski/kosinski/software/openfold/tests/test_data_pipeline.py", line 23, in import tests.compare_utils as compare_utils File "/g/kosinski/kosinski/software/openfold/tests/compare_utils.py", line 12, in from openfold.model.model import AlphaFold File "/g/kosinski/kosinski/software/openfold/openfold/model/model.py", line 29, in from openfold.model.embedders import ( File "/g/kosinski/kosinski/software/openfold/openfold/model/embedders.py", line 29, in from openfold.model.primitives import Linear, LayerNorm File "/g/kosinski/kosinski/software/openfold/openfold/model/primitives.py", line 38, in from openfold.utils.kernel.attention_core import attention_core File "/g/kosinski/kosinski/software/openfold/openfold/utils/kernel/attention_core.py", line 20, in attn_core_inplace_cuda = importlib.import_module("attn_core_inplace_cuda") File "/g/kosinski/kosinski/software/envs/openfold_env/lib/python3.9/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) ModuleNotFoundError: No module named 'attn_core_inplace_cuda' --- docs/source/Installation.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/source/Installation.md b/docs/source/Installation.md index 6da7e8527..fd294e939 100644 --- a/docs/source/Installation.md +++ b/docs/source/Installation.md @@ -29,6 +29,8 @@ At this time, only Linux systems are supported. > ./scripts/download_openfold_params.sh <dest> - For OpenFold SoloSeq weights, use: > ./scripts/download_openfold_soloseq_params.sh <dest> +1. Install OpenFold: + > python setup.py install ### Checking your build with unit tests: From 9f2a2f8d1faeff1aaf75f128eb19710781cbddbd Mon Sep 17 00:00:00 2001 From: Jan Kosinski Date: Sun, 19 May 2024 13:16:37 +0200 Subject: [PATCH 5/5] Delete extra ` in Installation.md --- docs/source/Installation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/Installation.md b/docs/source/Installation.md index fd294e939..093f16293 100644 --- a/docs/source/Installation.md +++ b/docs/source/Installation.md @@ -19,7 +19,7 @@ At this time, only Linux systems are supported. Mamba is recommended as the dependencies required by OpenFold are quite large and mamba can speed up the process. - Activate the environment, e.g `conda activate openfold_env` 1. Run the setup script to configure kernels and folding resources. - > scripts/install_third_party_dependencies.sh` + > scripts/install_third_party_dependencies.sh 1. Prepend the conda environment to the `$LD_LIBRARY_PATH`., e.g. `export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH`. You may optionally set this as a conda environment variable according to the [conda docs](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#saving-environment-variables) to activate each time the environment is used. 1. Download parameters. We recommend using a destination as `openfold/resources` as our unittests will look for the weights there. You can download all parameters to the same destination folder as the files will not overwrite each other.