Runing alphafold job in singularity
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.
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
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*> /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'*

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