Khan Computational Imaging Lab
Replies: 3 comments
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Dear Dr. Khan,
Thank you for your email, I appreciate your help.
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Can you verify that the TAR_OPTIONS env var is being set inside your docker environment? Using 'exec env' can do that
Best,
Ali
…________________________________
From: Halil Aziz ***@***.***>
Sent: Sunday, September 29, 2024 11:47:17 AM
To: khanlab/khanlab ***@***.***>
Cc: Ali Khan ***@***.***>; Comment ***@***.***>
Subject: Re: [khanlab/khanlab] Hippunfold (Discussion #2)
I added the -e TAR_OPTIONS='--no-same-owner' option to my command but unfortunately still got the same error.
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Reply to this email directly, view it on GitHub<#2 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACXV2XKR3QSIERJYLPQW7PLZZAOILAVCNFSM6AAAAABPBE2SZGVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANZYHE4DQMI>.
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Hi all,
I am repeatedly getting an error when I run Hippunfold. It is not related to memory space. Basically, I tried the example dataset (ds002168) but it gave the same error.
Can you advise me on a solution?
Thanks
The part of the error is below:
input: work/sub-s0101/anat/sub-s0101_hemi-R_space-corobl_desc-preproc_T1w.nii.gz, /root/.cache/hippunfold/model/trained_model.3d_fullres.Task101_hcp1200_T1w.nnUNetTrainerV2.model_best.tar
output: work/sub-s0101/anat/sub-s0101_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz
log: logs/sub-s0101/sub-s0101_hemi-R_space-corobl_nnunet.txt (check log file(s) for error details)
shell:
mkdir -p tempmodel tempimg templbl && cp work/sub-s0101/anat/sub-s0101_hemi-R_space-corobl_desc-preproc_T1w.nii.gz tempimg/temp_0000.nii.gz && tar -xf /root/.cache/hippunfold/model/trained_model.3d_fullres.Task101_hcp1200_T1w.nnUNetTrainerV2.model_best.tar -C tempmodel && export RESULTS_FOLDER=tempmodel && export nnUNet_n_proc_DA=16 && nnUNet_predict -i tempimg -o templbl -t Task101_hcp1200_T1w -chk model_best -tr nnUNetTrainerV2 --disable_tta &> logs/sub-s0101/sub-s0101_hemi-R_space-corobl_nnunet.txt && cp templbl/temp.nii.gz work/sub-s0101/anat/sub-s0101_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-09-28T174342.928237.snakemake.log
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