UID Issue on Linux

[imolax]

Hi There!

We are having an issue with hippunfold on Docker for Linux. We can get it running, however, it exits when it tries to tar the models.

Here's what we're running:

docker run -it --rm -v /data/BILCOR/BIDS:/bids -v /data/BILCOR/BIDS/derivatives/hippunfold:/output khanlab/hippunfold:latest /bids /output participant --participant-label 02 --modality T1w -p --cores all

And here is the error (note: the error below is just the last uid issue; there are many that come before it).

Config file config/snakebids.yml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 64
Rules claiming more threads will be scaled down.
Provided resources: gpus=0, mem_mb=16000, mem_mib=15259, time=60
Singularity containers: ignored
Select jobs to execute...
mkdir -p tempmodel tempimg templbl && cp work/sub-02/anat/sub-02_hemi-R_space-corobl_desc-preproc_T1w.nii.gz tempimg/temp_0000.nii.gz && tar -xf /root/.cache/hippunfold/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-02/sub-02_hemi-R_space-corobl_nnunet.txt && cp templbl/temp.nii.gz work/sub-02/anat/sub-02_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz
Changing to shadow directory: /output/.snakemake/shadow/tmp7ataqbav
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 64
Rules claiming more threads will be scaled down.
Provided resources: gpus=0, mem_mb=16000, mem_mib=15259, time=60
Singularity containers: ignored
Select jobs to execute...
mkdir -p tempmodel tempimg templbl && cp work/sub-02/anat/sub-02_hemi-Lflip_space-corobl_desc-preproc_T1w.nii.gz tempimg/temp_0000.nii.gz && tar -xf /root/.cache/hippunfold/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-02/sub-02_hemi-Lflip_space-corobl_nnunet.txt && cp templbl/temp.nii.gz work/sub-02/anat/sub-02_hemi-Lflip_space-corobl_desc-nnunet_dseg.nii.gz
Changing to shadow directory: /output/.snakemake/shadow/tmp0ynzy08r
tar: nnUNet/3d_fullres/Task101_hcp1200_T1w/nnUNetTrainerV2__nnUNetPlansv2.1/fold_3/debug.json: Cannot change ownership to uid 3050834, gid 6007967: Invalid argument

and it continues with many tar uid errors, then ends with:

tar: nnUNet/3d_fullres/Task101_hcp1200_T1w/nnUNetTrainerV2__nnUNetPlansv2.1: Cannot change ownership to uid 3050834, gid 6007967: Invalid argument
tar: Exiting with failure status due to previous errors
[Tue May 28 14:05:18 2024]
Error in rule run_inference:
    jobid: 0
    input: work/sub-02/anat/sub-02_hemi-Lflip_space-corobl_desc-preproc_T1w.nii.gz, /root/.cache/hippunfold/trained_model.3d_fullres.Task101_hcp1200_T1w.nnUNetTrainerV2.model_best.tar
    output: work/sub-02/anat/sub-02_hemi-Lflip_space-corobl_desc-nnunet_dseg.nii.gz
    log: logs/sub-02/sub-02_hemi-Lflip_space-corobl_nnunet.txt (check log file(s) for error details)
    shell:
        mkdir -p tempmodel tempimg templbl && cp work/sub-02/anat/sub-02_hemi-Lflip_space-corobl_desc-preproc_T1w.nii.gz tempimg/temp_0000.nii.gz && tar -xf /root/.cache/hippunfold/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-02/sub-02_hemi-Lflip_space-corobl_nnunet.txt && cp templbl/temp.nii.gz work/sub-02/anat/sub-02_hemi-Lflip_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/2024-05-28T135729.251009.snakemake.log

Any advice would be appreciated!

[akhanf]

Ah looks like a weird root+docker issue:
https://superuser.com/questions/1435437/how-to-get-around-this-error-when-untarring-an-archive-tar-cannot-change-owner

But it looks like there is a fix with a tar option (--no-same-owner), and apparently tar options can be set with env vars, so this should hopefully resolve the problem:

docker run -it --rm -e TAR_OPTIONS='--no-same-owner'  -v /data/BILCOR/BIDS:/bids -v /data/BILCOR/BIDS/derivatives/hippunfold:/output khanlab/hippunfold:latest /bids /output participant --participant-label 02 --modality T1w -p --cores all```

[imolax]

Thank you so much! It's running now.