[Python] Runing alphafold job in singularity

Discussão em 'Python' iniciado por Stack, Fevereiro 28, 2025.

  1. Stack

    Stack Membro Participativo

    I have successfully created a singularity image for running alphafold. I am encountering below-mentioned error.

    How to troubleshoot it?

    singularity run --nv alphafold220.sif --fasta_paths=/home/igib/AF_singualrity/test.fasta


    Error:

    /sbin/ldconfig.real: Can't create temporary cache file /etc/ld.so.cache~: Read-only file system Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 37, in <module>
    from alphafold.model import data File "/app/alphafold/alphafold/model/data.py", line 19, in <module>
    from alphafold.model import utils File "/app/alphafold/alphafold/model/utils.py", line 22, in <module>
    import haiku as hk File "/opt/conda/lib/python3.7/site-packages/haiku/__init__.py", line 17, in <module>
    from haiku import data_structures File "/opt/conda/lib/python3.7/site-packages/haiku/data_structures.py", line 17, in <module>
    from haiku._src.data_structures import to_immutable_dict File "/opt/conda/lib/python3.7/site-packages/haiku/_src/data_structures.py", line 30, in <module>
    from haiku._src import utils File "/opt/conda/lib/python3.7/site-packages/haiku/_src/utils.py", line 24, in <module>
    import jax File "/opt/conda/lib/python3.7/site-packages/jax/__init__.py", line 108, in <module>
    from .experimental.maps import soft_pmap File "/opt/conda/lib/python3.7/site-packages/jax/experimental/maps.py", line 25, in <module>
    from .. import numpy as jnp File "/opt/conda/lib/python3.7/site-packages/jax/numpy/__init__.py", line 16, in <module>
    from . import fft File "/opt/conda/lib/python3.7/site-packages/jax/numpy/fft.py", line 17, in <module>
    from jax._src.numpy.fft import ( File "/opt/conda/lib/python3.7/site-packages/jax/_src/numpy/fft.py", line 19, in <module>
    from jax import lax File "/opt/conda/lib/python3.7/site-packages/jax/lax/__init__.py", line 330, in <module>
    from jax._src.lax.fft import ( File "/opt/conda/lib/python3.7/site-packages/jax/_src/lax/fft.py", line 144, in <module>
    xla.backend_specific_translations['cpu'][fft_p] = pocketfft.pocketfft AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft'

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