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brainlife / app-endpointMapGeneration

This app will generate endpoint maps for all tracts in an input classification structure. User can specify what sort of decay/smoothing algorithm can be used (or none) and whether the output is to be normalized (e.g. max density voxel in tract endpoint mask = 1).
MIT License
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Error in extracting CTF file #2

Open DanNBullock opened 3 years ago

DanNBullock commented 3 years ago

Error when running recently:

  • '[' -z 'hayashis@iu.edu 29511 *CPmh9xvKQKHE FSg0ijTusqaQc' ']'
    • echo hayashis@iu.edu 29511 '*CPmh9xvKQKHE' FSg0ijTusqaQc
    • '[' '!' -f gm_mask.nii.gz ']' ++ pwd
    • singularity exec -e -B /export/prod/60a417d72da9f0bc39c3c988/60a417d72da9f01d79c3c98e/license.txt:/usr/local/freesurfer/license.txt docker://brainlife/freesurfer_on_mcr:6.0.0 ./convertgmmask.sh INFO: Using cached SIF image reading colortable from MGH file... colortable with 14176 entries read (originally /usr/local/freesurfer/FreeSurferColorLUT.txt)

real 0m35.183s user 0m5.200s sys 0m0.626s

  • mkdir -p freesurfer
  • cp gm_mask.nii.gz freesurfer
  • singularity exec -e docker://brainlife/mcr:neurodebian1604-r2017a ./compiled/bsc_classifiedStreamEndpointCortex_BL INFO: Using cached SIF image Error in extracting CTF file to '/export/prod/60a417d72da9f0bc39c3c988/60a417d72da9f01d79c3c98e/.mcrCache9.2/bsc_cl0'. Details: 'Could not create the destination parent directory: File exists' du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/compiler': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/.matlab': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/N': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/java': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/bin': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/bin': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/distcomp': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/getDistcompConfigurationNames.m': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/gpu/+parallel': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/distcomp_evaluate_filetask.m': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/distcomp_evaluate_filetask_core.m': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/parallel/@codistributed/hMldivideTranspose.m': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/parallel/@codistributed/head.m': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/parallel/@codistributed/hBuildFromTemplate.m': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/images/images/+images/+internal': No such file or directory Could not access the MATLAB Runtime component cache. Details: Some error has occurred in the file: core/mclCtfFileExtractor.cpp, at line: 64. The error message is: Error in extracting CTF file to '/export/prod/60a417d72da9f0bc39c3c988/60a417d72da9f01d79c3c98e/.mcrCache9.2/bsc_cl0'. Details: 'Could not create the destination parent directory: File exists'

real 197m4.009s user 0m6.026s sys 0m11.492s`

soichih commented 3 years ago

Which resource did this run on?

Also, are you seeing this error message on other jobs (all on the same resource)?

On Thu, May 20, 2021 at 1:12 PM Daniel Bullock @.***> wrote:

Error when running recently:

  • '[' -z @.** 29511 CPmh9xvKQKHE FSg0ijTusqaQc' ']'
  • echo @.** 29511 'CPmh9xvKQKHE' FSg0ijTusqaQc
  • '[' '!' -f gm_mask.nii.gz ']' ++ pwd
  • singularity exec -e -B /export/prod/60a417d72da9f0bc39c3c988/60a417d72da9f01d79c3c98e/license.txt:/usr/local/freesurfer/license.txt docker://brainlife/freesurfer_on_mcr:6.0.0 ./convertgmmask.sh INFO: Using cached SIF image reading colortable from MGH file... colortable with 14176 entries read (originally /usr/local/freesurfer/FreeSurferColorLUT.txt)

real 0m35.183s user 0m5.200s sys 0m0.626s

  • mkdir -p freesurfer
  • cp gm_mask.nii.gz freesurfer
  • singularity exec -e docker://brainlife/mcr:neurodebian1604-r2017a ./compiled/bsc_classifiedStreamEndpointCortex_BL INFO: Using cached SIF image Error in extracting CTF file to '/export/prod/60a417d72da9f0bc39c3c988/60a417d72da9f01d79c3c98e/.mcrCache9.2/bsc_cl0'. Details: 'Could not create the destination parent directory: File exists' du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/compiler': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/.matlab': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/N': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/java': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/bin': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/bin': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/distcomp': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/getDistcompConfigurationNames.m': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/gpu/+parallel': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/distcomp_evaluate_filetask.m': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/distcomp/distcomp_evaluate_filetask_core.m': No such file or directory du: cannot access @./hMldivideTranspose.m': No such file or directory du: cannot access @./head.m': No such file or directory du: cannot access @.***/hBuildFromTemplate.m': No such file or directory du: cannot access './.mcrCache9.2/bsc_cl0/toolbox/images/images/+images/+internal': No such file or directory Could not access the MATLAB Runtime component cache. Details: Some error has occurred in the file: core/mclCtfFileExtractor.cpp, at line: 64. The error message is: Error in extracting CTF file to '/export/prod/60a417d72da9f0bc39c3c988/60a417d72da9f01d79c3c98e/.mcrCache9.2/bsc_cl0'. Details: 'Could not create the destination parent directory: File exists'

real 197m4.009s user 0m6.026s sys 0m11.492s`

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DanNBullock commented 3 years ago

Unfortunately, I reran those jobs and lost the logs, I'll be sure to include those next time. I saw it on a few other jobs, not sure if they were on the same resource. The jobs seem to be running a bit slowly (i.e. fewer at a time than expected). Also, some of them are hitting wall time, not sure what that's about.