Read only file system error
Closed this issue · 9 comments
What happened?
Erroring out because of read only file system:
Traceback (most recent call last):
File "/opt/conda/bin/nnUNet_predict", line 33, in
sys.exit(load_entry_point('nnunet', 'console_scripts', 'nnUNet_predict')())
File "/opt/conda/bin/nnUNet_predict", line 25, in importlib_load_entry_point
return next(matches).load()
File "/opt/conda/lib/python3.8/importlib/metadata.py", line 77, in load
module = import_module(match.group('module'))
File "/opt/conda/lib/python3.8/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1014, in _gcd_import
File "", line 991, in _find_and_load
File "", line 975, in _find_and_load_unlocked
File "", line 671, in _load_unlocked
File "", line 843, in exec_module
File "", line 219, in _call_with_frames_removed
File "/home/cabinet/nnUNet/nnunet/inference/predict_simple.py", line 19, in
from nnunet.inference.predict import predict_from_folder
File "/home/cabinet/nnUNet/nnunet/inference/predict.py", line 21, in
from batchgenerators.augmentations.utils import resize_segmentation
File "/opt/conda/lib/python3.8/site-packages/batchgenerators/augmentations/utils.py", line 22, in
from skimage.transform import resize
File "/opt/conda/lib/python3.8/site-packages/skimage/init.py", line 141, in
from .data import data_dir
File "", line 1039, in _handle_fromlist
File "/opt/conda/lib/python3.8/site-packages/lazy_loader/init.py", line 76, in getattr
submod = importlib.import_module(submod_path)
File "/opt/conda/lib/python3.8/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/opt/conda/lib/python3.8/site-packages/skimage/data/_fetchers.py", line 270, in
_init_pooch()
File "/opt/conda/lib/python3.8/site-packages/skimage/data/_fetchers.py", line 247, in _init_pooch
os.makedirs(data_dir, exist_ok=True)
File "/opt/conda/lib/python3.8/os.py", line 213, in makedirs
makedirs(head, exist_ok=exist_ok)
File "/opt/conda/lib/python3.8/os.py", line 213, in makedirs
makedirs(head, exist_ok=exist_ok)
File "/opt/conda/lib/python3.8/os.py", line 213, in makedirs
makedirs(head, exist_ok=exist_ok)
[Previous line repeated 1 more time]
File "/opt/conda/lib/python3.8/os.py", line 223, in makedirs
mkdir(name, mode)
OSError: [Errno 30] Read-only file system: '/home/adp9359'
What command did you use?
#!/bin/bash
#SBATCH --account=p31681 ## YOUR ACCOUNT pXXXX or bXXXX
#SBATCH --partition=gengpu
#SBATCH --nodes=1 ## how many computers do you need
#SBATCH --ntasks-per-node=1 ## how many cpus or processors do you need on each computer
#SBATCH --gres=gpu:a100:1 ## type of GPU requested, and number of GPU cards to run on
#SBATCH --time=04:00:00 ## how long does this need to run (remember different partitions have restrictions on this param)
#SBATCH --mem=40G ## how much RAM do you need per CPU (this effects your FairShare score so be careful to not ask for more than you need))
#SBATCH --job-name=run_ibeat ## When you run squeue -u NETID this is how you can identify the job
#SBATCH --output=cabinet_test_1007.log ## standard out and standard error goes to this file
module purge
module load singularity
singularity run --nv --cleanenv --no-home \
-B /projects/b1174/cabinet_test/bidsdir:/input \
-B /projects/b1174/cabinet_test/outdir:/output \
-B /projects/b1174/cabinet_test/param_files/param_file.json:/param_file.json \
/projects/b1174/singularity_images/cabinet:latest.sif \
/input /output participant -jargs /param_file.json -end postbibsnet -v -participant 1007What version of CABINET are you using?
latest from singularity
Relevant log output
Traceback (most recent call last):
File "/opt/conda/bin/nnUNet_predict", line 33, in <module>
sys.exit(load_entry_point('nnunet', 'console_scripts', 'nnUNet_predict')())
File "/opt/conda/bin/nnUNet_predict", line 25, in importlib_load_entry_point
return next(matches).load()
File "/opt/conda/lib/python3.8/importlib/metadata.py", line 77, in load
module = import_module(match.group('module'))
File "/opt/conda/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 843, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/home/cabinet/nnUNet/nnunet/inference/predict_simple.py", line 19, in <module>
from nnunet.inference.predict import predict_from_folder
File "/home/cabinet/nnUNet/nnunet/inference/predict.py", line 21, in <module>
from batchgenerators.augmentations.utils import resize_segmentation
File "/opt/conda/lib/python3.8/site-packages/batchgenerators/augmentations/utils.py", line 22, in <module>
from skimage.transform import resize
File "/opt/conda/lib/python3.8/site-packages/skimage/__init__.py", line 141, in <module>
from .data import data_dir
File "<frozen importlib._bootstrap>", line 1039, in _handle_fromlist
File "/opt/conda/lib/python3.8/site-packages/lazy_loader/__init__.py", line 76, in __getattr__
submod = importlib.import_module(submod_path)
File "/opt/conda/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/opt/conda/lib/python3.8/site-packages/skimage/data/_fetchers.py", line 270, in <module>
_init_pooch()
File "/opt/conda/lib/python3.8/site-packages/skimage/data/_fetchers.py", line 247, in _init_pooch
os.makedirs(data_dir, exist_ok=True)
File "/opt/conda/lib/python3.8/os.py", line 213, in makedirs
makedirs(head, exist_ok=exist_ok)
File "/opt/conda/lib/python3.8/os.py", line 213, in makedirs
makedirs(head, exist_ok=exist_ok)
File "/opt/conda/lib/python3.8/os.py", line 213, in makedirs
makedirs(head, exist_ok=exist_ok)
[Previous line repeated 1 more time]
File "/opt/conda/lib/python3.8/os.py", line 223, in makedirs
mkdir(name, mode)
OSError: [Errno 30] Read-only file system: '/home/adp9359'Add any additional information or context about the problem here.
Thank you!
Hi @ajdneuro - I suggest pulling the tagged 2.4.0 version of cabinet. This was an older bug. If that doesn't fix it, specify a working directory, and that should do the trick.
Thanks trying now!
Thank you for your response, I pulled 2.4.0 and adding a working dir and I am still getting the read only file system error, any thoughts?
Are you giving relative paths, or are those absolute? Also, are you getting the exact same error?
Hi,
These are absolute and yes it is saying my home directory (/home/adp9359) is read only, thank you!:
It looks like you need to make the directory you bind as the working dir writeable.
@ajdneuro - someone on our team said they get this error when using the --no-home flag. Try removing that and see if that fixes it. Thanks!
@ajdneuro - I am going to close off this issue. Please re-open it if the problem persists.