question-mark

Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Cannot run ants.registration in HPC (slurm)

See original GitHub issue

Issue Description

Describe the bug When I submit running command of the bash file to the HPC, the process got stuck at ants.registration step. It seems that the forward transformation and other output of registration cannot be saved. I created a tmp folder (default for ANTsPy) to save these outputs, but it still did not work. Does anyone have ideas about this issue? Thanks in advance.

HPC Python Virtual Environment:

antspyx==0.3.3
certifi==2022.6.15
charset-normalizer==2.0.12
chart-studio==1.1.0
configparser==5.2.0
cycler==0.11.0
fonttools==4.33.3
idna==3.3
imageio==2.19.3
joblib==1.1.0
kiwisolver==1.4.3
matplotlib==3.5.2
networkx==2.6.3
nibabel==3.2.2
numpy==1.21.6
packaging==21.3
pandas==1.3.5
patsy==0.5.2
Pillow==9.1.1
plotly==5.8.2
PyMySQL==1.0.2
pynrrd==0.4.3
pyparsing==3.0.9
python-dateutil==2.8.2
pytz==2022.1
PyWavelets==1.3.0
PyYAML==6.0
requests==2.28.0
retrying==1.3.3
scikit-image==0.19.3
scikit-learn==1.0.2
scipy==1.7.3
shutils==0.1.0
six==1.16.0
slicerio==0.1.3
statsmodels==0.13.2
tenacity==8.0.1
threadpoolctl==3.1.0
tifffile==2021.11.2
typing_extensions==4.2.0
urllib3==1.26.9
webcolors==1.12

Issue Analytics

  • State:open
  • Created 4 months ago
  • Comments:14 (4 by maintainers)

github_iconTop GitHub Comments

2reactions
gdevenyicommented, Sep 29, 2022

Ans use sbatch sbatch --cpus-per-task=8 unittest.sh to run, but it is always in the Pending Status instead of Running, do you have any idea about this?

This is exactly the time to ask your HPC support, this is unrelated to ANTs

1reaction
gdevenyicommented, Sep 29, 2022

This sounds to me like resource restrictions on the jobs as being submitted to SLURM (low CPU count and RAM). I suggest contacting your HPC support for help with requesting appropriate resources.

Read more comments on GitHub >

github_iconTop Results From Across the Web

ANTs on Biowulf - NIH HPC
ANTs extracts information from complex datasets that include imaging (Word Cloud). Paired with ANTsR (answer), ANTs is useful for managing, ...
Read more >
missing *h.inflated / antsRegistration error: segmentation fault ...
Hello, I have been trying to get a BIDS data set analyzed with fmriprep. I have initially been using a local Mac OSX...
Read more >
Advanced Normalization Tools ( ANTs ) Discussion
I am running this on a SLURM cluster. ... FSL's registration would not give the best outcome, so I like to use ANTs...
Read more >
HPC for Neuroimaging
Introduction¶. This page provides the neuroimaging community with a tutorial for getting started with the HPC (High Performance Computing) ...
Read more >
HPC Documentation Documentation - Read the Docs
These jobs will run before normal but the walltime is limited. An example of Slurm GPU job script. #!/bin/bash. #SBATCH --job-name=MyJob.
Read more >

github_iconTop Related Medium Post

No results found

github_iconTop Related StackOverflow Question

No results found

github_iconTroubleshoot Live Code

Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free

github_iconTop Related Reddit Thread

No results found

github_iconTop Related Hackernoon Post

No results found

github_iconTop Related Tweet

No results found

github_iconTop Related Dev.to Post

No results found

github_iconTop Related Hashnode Post

No results found