CODEWITHSUNDEEP
pythonpython-3.xanacondajob-schedulingsingularity-container
comp-era
comp-era

Reputation: 21

Runing alphafold job in singularity

I am new to singularity concept but successfully created singularity image for running alpha fold tool. I am encountering below-mentioned error. I would like to request if anyone could explain how to troubleshoot the error or any related information that may help to combat it. Thank you in advance.

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

**

*> /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 from alphafold.model import data File "/app/alphafold/alphafold/model/data.py", line 19, in from alphafold.model import utils File "/app/alphafold/alphafold/model/utils.py", line 22, in import haiku as hk File "/opt/conda/lib/python3.7/site-packages/haiku/init.py", line 17, in from haiku import data_structures File "/opt/conda/lib/python3.7/site-packages/haiku/data_structures.py", line 17, in 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 from haiku._src import utils File "/opt/conda/lib/python3.7/site-packages/haiku/_src/utils.py", line 24, in import jax File "/opt/conda/lib/python3.7/site-packages/jax/init.py", line 108, in from .experimental.maps import soft_pmap File "/opt/conda/lib/python3.7/site-packages/jax/experimental/maps.py", line 25, in from .. import numpy as jnp File "/opt/conda/lib/python3.7/site-packages/jax/numpy/init.py", line 16, in from . import fft File "/opt/conda/lib/python3.7/site-packages/jax/numpy/fft.py", line 17, in from jax._src.numpy.fft import ( File "/opt/conda/lib/python3.7/site-packages/jax/_src/numpy/fft.py", line 19, in from jax import lax File "/opt/conda/lib/python3.7/site-packages/jax/lax/init.py", line 330, in from jax._src.lax.fft import ( File "/opt/conda/lib/python3.7/site-packages/jax/_src/lax/fft.py", line 144, in xla.backend_specific_translations['cpu'][fft_p] = pocketfft.pocketfft AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft'*

**

Upvotes: 0

Views: 560

Answers (1)

tsnowlan
tsnowlan

Reputation: 3772

Singularity images run on a read-only file system, with the exception being directories that have been mounted from the host OS.

You can enable a tmpfs overlay when running by using the --writable-tmpfs flag. Note that the max size of the tmpfs overlay is the size of /dev/shm, which can be smaller than expected in some cloud VMs.

Upvotes: 0

Related Questions