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missing settings files #5

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mattcieslak opened this issue May 8, 2023 · 15 comments
Closed

missing settings files #5

mattcieslak opened this issue May 8, 2023 · 15 comments

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@mattcieslak
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Hi Okan,

I'm seeing a new error on some HBCD runs:

Stderr:
        terminate called after throwing an instance of 'boost::filesystem::filesystem_error'
          what():  boost::filesystem::status: Function not implemented: "/src/TORTOISEV4/bin/../settings/system_settings/default_system_settings.
json"
        Aborted (core dumped)

Are there files outside of bin that should be keeping for TORTOISE to work?
@eurotomania
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eurotomania commented May 8, 2023 via email

@mattcieslak
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This came from a DRBUDDI run, very strange

@eurotomania
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eurotomania commented May 8, 2023 via email

@mattcieslak
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In the docker build I was only copying over the bin directory. I'm copying the settings directory into the image now too, maybe that will solve it

@eurotomania
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eurotomania commented May 8, 2023 via email

@eurotomania
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eurotomania commented May 8, 2023 via email

@mattcieslak
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Currently 1.76.0:
https://github.com/PennLINC/qsiprep_build/blob/main/Dockerfile_TORTOISE#L28

@eurotomania
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eurotomania commented May 8, 2023 via email

@mattcieslak
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ok, this may be a false alarm. It looks like there was an unrelated issue with memory that was showing up as this sometimes :(

@mattcieslak mattcieslak reopened this May 9, 2023
@mattcieslak
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mattcieslak commented May 9, 2023 •
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The memory issue was unrelated, this unfortunately came up again.

background: being run on a centos7 machine via apptainer (rebranded singularity) from the pennbbl/qsiprep:unstable image that has the most recent TORTOISE installed (commmit 9fb5296).

The actual error message is

terminate called after throwing an instance of 'boost::filesystem::filesystem_error'
  what():  boost::filesystem::status: Function not implemented: "/src/TORTOISEV4/bin/../settings/system_settings/default_system_settings.json"
command.txt: line 1: 151819 Aborted                 DRBUDDI -d /cbica/comp_space/abcd_qsiprep/job-4698856-sub-326427/.git/wkdir/qsiprep_wf/single_subject_326427_wf/dwi_preproc_ses_V02_run_1_wf/hmc_sdc_wf/drbuddi_sdc_wf/drbuddi/drbuddi_down_dwi.nii -u /cbica/comp_space/abcd_qsiprep/job-4698856-sub-326427/.git/wkdir/qsiprep_wf/single_subject_326427_wf/dwi_preproc_ses_V02_run_1_wf/hmc_sdc_wf/drbuddi_sdc_wf/drbuddi/drbuddi_up_dwi.nii --up_json /cbica/comp_space/abcd_qsiprep/job-4698856-sub-326427/.git/wkdir/qsiprep_wf/single_subject_326427_wf/dwi_preproc_ses_V02_run_1_wf/hmc_sdc_wf/drbuddi_sdc_wf/drbuddi/blip_up.json -s /cbica/comp_space/abcd_qsiprep/job-4698856-sub-326427/.git/wkdir/qsiprep_wf/single_subject_326427_wf/anat_preproc_wf/rigid_acpc_resample_unfatsat/sub-326427_ses-V02_run-1_T2w_lps_desaturated_trans.nii

I can see that the settings file is available in the container:

Apptainer> ls /src/TORTOISEV4/bin/../settings/system_settings/default_system_settings.json
/src/TORTOISEV4/bin/../settings/system_settings/default_system_settings.json
Apptainer> cat /src/TORTOISEV4/bin/../settings/system_settings/default_system_settings.json
{
    "_comment": "Percentage of CPU cores to be used by TORTOISE as a float. Ex, 1: use all cores  0.1: use 10% of max cores",
    "PercentOfCpuCoresToUse": 1
}

I wonder if this could be related to boostorg/filesystem#172, popping up also in PointCloudLibrary/pcl#5197 and microsoft/WSL#6994.

@eurotomania
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eurotomania commented May 9, 2023 via email

@mattcieslak
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I'm currently trying out using boost 1.77, do you think that could work? https://app.circleci.com/pipelines/github/PennLINC/qsiprep_build/145/workflows/b022dcbd-f7fc-43a4-972a-0b742c2123fa/jobs/1087

@eurotomania
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eurotomania commented May 9, 2023 via email

@mattcieslak
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boost 1.77 fixed it!

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eurotomania commented May 9, 2023 via email

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@mattcieslak @eurotomania