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docker build succeed, but docker run failed #83

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carrisonj opened this issue Nov 20, 2024 · 8 comments
Open

docker build succeed, but docker run failed #83

carrisonj opened this issue Nov 20, 2024 · 8 comments
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setup Problem with installation or setting things up

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@carrisonj
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carrisonj commented Nov 20, 2024 •
edited by Augustin-Zidek
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run docker build -t alphafold3 -f docker/Dockerfile . successfully, alphafold3 docker image created as follow:

REPOSITORY                    TAG                             IMAGE ID       CREATED         SIZE
alphafold3                    latest                          88bb828c99fa   5 hours ago     9.05GB

but docker run failed with error as follow:

docker run -it     --volume $HOME/af_input:/root/af_input     --volume $HOME/af_output:/root/af_output     --volume $MODEL_PARAMETERS_DIR:/root/models     --volume $DB_DIR:/root/public_databases     --gpus all  alphafold3    python3 run_alphafold.py     --json_path=/root/af_input/fold_input.json     --model_dir=/root/models     --output_dir=/root/af_output

OpenBLAS blas_thread_init: pthread_create failed for thread 1 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 2 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 3 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 4 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 5 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 6 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 7 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 8 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 9 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 10 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 11 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 12 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 13 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 14 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 15 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 16 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 17 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 18 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 19 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 20 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 21 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 22 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 23 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 24 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 25 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 26 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 27 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 28 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 29 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 30 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 31 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 32 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 33 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 34 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 35 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 36 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 37 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 38 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 39 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 40 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 41 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 42 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 43 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 44 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 45 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 46 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 47 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 48 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 49 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 50 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 51 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 52 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 53 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 54 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 55 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 56 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 57 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 58 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 59 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 60 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 61 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 62 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 63 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
Traceback (most recent call last):
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/_core/__init__.py", line 23, in <module>
    from . import multiarray
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/_core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/_core/overrides.py", line 8, in <module>
    from numpy._core._multiarray_umath import (
ImportError: PyCapsule_Import could not import module "datetime"

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/__init__.py", line 114, in <module>
    from numpy.__config__ import show as show_config
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/__config__.py", line 4, in <module>
    from numpy._core._multiarray_umath import (
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/_core/__init__.py", line 49, in <module>
    raise ImportError(msg)
ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.11 from "/alphafold3_venv/bin/python3"
  * The NumPy version is: "2.1.3"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: PyCapsule_Import could not import module "datetime"


The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/app/alphafold/run_alphafold.py", line 39, in <module>
    from alphafold3.common import folding_input
  File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/common/folding_input.py", line 23, in <module>
    from alphafold3 import structure
  File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/structure/__init__.py", line 14, in <module>
    from alphafold3.structure.bioassemblies import BioassemblyData
  File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/structure/bioassemblies.py", line 18, in <module>
    from alphafold3.structure import mmcif
  File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/structure/mmcif.py", line 29, in <module>
    import numpy as np
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/__init__.py", line 119, in <module>
    raise ImportError(msg) from e
ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.

Plz help us solve it, thanks a lot.
@Augustin-Zidek Augustin-Zidek added the setup Problem with installation or setting things up label Nov 20, 2024
@Augustin-Zidek
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Have you tried following the tips given at https://numpy.org/devdocs/user/troubleshooting-importerror.html?

@jsspencer
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I think this is an issue with the host you are running the docker container on, rather than the docker image itself or numpy.

I think https://stackoverflow.com/questions/52026652/openblas-blas-thread-init-pthread-create-resource-temporarily-unavailable is relevant.

either

  • setting OPENBLAS_NUM_THREADS to a small (eg 1) value; AlphaFold 3 is not sensitive to OpenBLAS performance, so this should be fine
  • checking ulimit and updating the thread limits

should help. I don't know where you are running this, but if on an HPC facility, you might need assistance from the sysadmins for ulimit. Running on head (login) nodes is typically much more restricted than running on a compute node.

@carrisonj
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thank you, jsspencer,

@carrisonj
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carrisonj commented Nov 21, 2024 •
edited by Augustin-Zidek
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i've add lines below to run_alphafold.py,

import os
os.environ['OPENBLAS_NUM_THREADS'] = '1'
before
import numpy as np

but got same error, how to fix the error ?
more error msg as follow:

OpenBLAS blas_thread_init: pthread_create failed for thread 63 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
Traceback (most recent call last):
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/_core/__init__.py", line 23, in <module>
    from . import multiarray
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/_core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/_core/overrides.py", line 8, in <module>
    from numpy._core._multiarray_umath import (
ImportError: PyCapsule_Import could not import module "datetime"

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/__init__.py", line 114, in <module>
    from numpy.__config__ import show as show_config
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/__config__.py", line 4, in <module>
    from numpy._core._multiarray_umath import (
  File "/alphafold3_venv/lib/python3.11/site-packages/numpy/_core/__init__.py", line 49, in <module>
    raise ImportError(msg)
ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.11 from "/alphafold3_venv/bin/python3"
  * The NumPy version is: "2.1.3"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: PyCapsule_Import could not import module "datetime"

@Augustin-Zidek Augustin-Zidek mentioned this issue Nov 21, 2024
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@Augustin-Zidek
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Could you try running the docker run command with the --privileged flag?

@carrisonj
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carrisonj commented Nov 21, 2024 •
edited by Augustin-Zidek
Loading

add line

ENV OPENBLAS_NUM_THREADS=1

before

CMD ["python3", "run_alphafold.py"]

in Dockerfile, than rebuild and run image, got new error as follwo:

[root@node22 ~]# docker run -it     --volume $HOME/af_input:/root/af_input     --volume $HOME/af_output:/root/af_output     --volume $MODEL_PARAMETERS_DIR:/root/models     --volume $DB_DIR:/root/public_databases     --gpus all  alphafold3    python3 run_alphafold.py     --json_path=/root/af_input/fold_input.json     --model_dir=/root/models     --output_dir=/root/af_output
I1121 09:37:49.169083 140327870522496 folding_input.py:1044] Detected /root/af_input/fold_input.json is an AlphaFold 3 JSON since the top-level is not a list.
Running AlphaFold 3. Please note that standard AlphaFold 3 model parameters are
only available under terms of use provided at
https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md.
If you do not agree to these terms and are using AlphaFold 3 derived model
parameters, cancel execution of AlphaFold 3 inference with CTRL-C, and do not
use the model parameters.
2024-11-21 09:37:49.186558: F external/tsl/tsl/platform/default/env.cc:74] Check failed: ret == 0 (1 vs. 0)Thread tf_XLAEigen creation via pthread_create() failed.
Fatal Python error: Aborted

Current thread 0x00007fa0a0dfe480 (most recent call first):
  File "/alphafold3_venv/lib/python3.11/site-packages/jaxlib/xla_client.py", line 76 in make_cpu_client
  File "/alphafold3_venv/lib/python3.11/site-packages/jax/_src/xla_bridge.py", line 261 in make_cpu_client
  File "/alphafold3_venv/lib/python3.11/site-packages/jax/_src/xla_bridge.py", line 971 in _init_backend
  File "/alphafold3_venv/lib/python3.11/site-packages/jax/_src/xla_bridge.py", line 885 in backends
  File "/alphafold3_venv/lib/python3.11/site-packages/jax/_src/xla_bridge.py", line 996 in _get_backend_uncached
  File "/alphafold3_venv/lib/python3.11/site-packages/jax/_src/xla_bridge.py", line 1017 in get_backend
  File "/alphafold3_venv/lib/python3.11/site-packages/jax/_src/xla_bridge.py", line 1141 in local_devices
  File "/app/alphafold/run_alphafold.py", line 639 in main
  File "/alphafold3_venv/lib/python3.11/site-packages/absl/app.py", line 254 in _run_main
  File "/alphafold3_venv/lib/python3.11/site-packages/absl/app.py", line 308 in run
  File "/app/alphafold/run_alphafold.py", line 674 in <module>

Extension modules: numpy._core._multiarray_umath, numpy.linalg._umath_linalg, rdkit.rdBase, rdkit.DataStructs.cDataStructs, rdkit.Chem.rdchem, rdkit.Geometry.rdGeometry, rdkit.Chem.rdinchi, rdkit.Chem.rdCIPLabeler, rdkit.Chem.rdmolfiles, rdkit.Chem.rdmolops, rdkit.Chem.rdMolInterchange, rdkit.Chem.rdCoordGen, jaxlib.cpu_feature_guard, zstandard.backend_c, rdkit.ForceField.rdForceField, rdkit.Chem.rdChemicalFeatures, rdkit.Chem.rdMolChemicalFeatures, rdkit.Chem.rdDistGeom, rdkit.Chem.rdChemReactions, rdkit.Chem.rdDepictor, rdkit.Chem.rdFingerprintGenerator, rdkit.Chem.rdForceFieldHelpers, rdkit.Chem.rdMolAlign, rdkit.Chem.rdMolDescriptors, rdkit.Chem.rdMolEnumerator, rdkit.Chem.rdMolTransforms, rdkit.Chem.rdPartialCharges, rdkit.Chem.rdqueries, rdkit.Chem.rdReducedGraphs, rdkit.Chem.rdShapeHelpers, rdkit.Chem.rdSLNParse, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation (total: 79)
Fatal Python error: Segmentation fault

Current thread 0x00007fa0a0dfe480 (most recent call first):
  File "/alphafold3_venv/lib/python3.11/site-packages/jaxlib/xla_client.py", line 76 in make_cpu_client
  File "/alphafold3_venv/lib/python3.11/site-packages/jax/_src/xla_bridge.py", line 261 in make_cpu_client
  File "/alphafold3_venv/lib/python3.11/site-packages/jax/_src/xla_bridge.py", line 971 in _init_backend
  File "/alphafold3_venv/lib/python3.11/site-packages/jax/_src/xla_bridge.py", line 885 in backends
  File "/alphafold3_venv/lib/python3.11/site-packages/jax/_src/xla_bridge.py", line 996 in _get_backend_uncached
  File "/alphafold3_venv/lib/python3.11/site-packages/jax/_src/xla_bridge.py", line 1017 in get_backend
  File "/alphafold3_venv/lib/python3.11/site-packages/jax/_src/xla_bridge.py", line 1141 in local_devices
  File "/app/alphafold/run_alphafold.py", line 639 in main
  File "/alphafold3_venv/lib/python3.11/site-packages/absl/app.py", line 254 in _run_main
  File "/alphafold3_venv/lib/python3.11/site-packages/absl/app.py", line 308 in run
  File "/app/alphafold/run_alphafold.py", line 674 in <module>

Extension modules: numpy._core._multiarray_umath, numpy.linalg._umath_linalg, rdkit.rdBase, rdkit.DataStructs.cDataStructs, rdkit.Chem.rdchem, rdkit.Geometry.rdGeometry, rdkit.Chem.rdinchi, rdkit.Chem.rdCIPLabeler, rdkit.Chem.rdmolfiles, rdkit.Chem.rdmolops, rdkit.Chem.rdMolInterchange, rdkit.Chem.rdCoordGen, jaxlib.cpu_feature_guard, zstandard.backend_c, rdkit.ForceField.rdForceField, rdkit.Chem.rdChemicalFeatures, rdkit.Chem.rdMolChemicalFeatures, rdkit.Chem.rdDistGeom, rdkit.Chem.rdChemReactions, rdkit.Chem.rdDepictor, rdkit.Chem.rdFingerprintGenerator, rdkit.Chem.rdForceFieldHelpers, rdkit.Chem.rdMolAlign, rdkit.Chem.rdMolDescriptors, rdkit.Chem.rdMolEnumerator, rdkit.Chem.rdMolTransforms, rdkit.Chem.rdPartialCharges, rdkit.Chem.rdqueries, rdkit.Chem.rdReducedGraphs, rdkit.Chem.rdShapeHelpers, rdkit.Chem.rdSLNParse, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation (total: 79)

@Augustin-Zidek
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Looks similar to tensorflow/tensorflow#41532.

Some things to help investigating this:

  • What system are you running this on? Things like: Linux kernel version, Python version, NVIDIA driver version, CUDA version, gcc version.
  • What GPU do you have on the system?
  • How much RAM do you have on the system?
  • Do you have sufficient permissions to run Docker on the system?

@Augustin-Zidek
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Following up on this one -- did you manage to get AlphaFold 3 installed in the end?

@jsspencer jsspencer mentioned this issue Nov 28, 2024
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@jsspencer @Augustin-Zidek @carrisonj