singularity build 1.3.1 fails immediately #1534
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Hi. Apologies for the noisy warnings. There was a recent change that we'd hoped would rein them in somewhat, but it looks like we'll need to look more closely. However, these warnings are not errors; did you run into an actual failure at some point? |
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The job just failed after 7 seconds and that error log is all that was
produced. I'll try again with an increased verbosity.
--
Joseph M. Orr, Ph.D.
Assistant Professor
Department of Psychological and Brain Sciences
Texas A&M Institute for Neuroscience
Texas A&M University
College Station, TX
…On Mon, Mar 11, 2019 at 1:02 PM Chris Markiewicz ***@***.***> wrote:
Hi. Apologies for the noisy warnings. There was a recent change that we'd
hoped would rein them in somewhat, but it looks like we'll need to look
more closely. However, these warnings are not errors; did you run into an
actual failure at some point?
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Ok here's the error: |
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Thanks for the full error. I believe @oesteban can comment on how this is supposed to be handled. |
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What is your exact command line? |
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Thanks! Can you try the following? export TEMPLATEFLOW_HOME=/opt/templateflow
srun singularity run -B $HOME/.templateflow:/opt/templateflow $image $bidsdir $outdir \
participant -w $workdir\
--participant_label $subject --nthreads 30 --omp-nthreads 30 --mem-mb 60000\
--low-mem --ignore slicetiming --output-space T1w fsnative template\
--use-aroma --aroma-melodic-dimensionality -150 \
--fs-license-file $outdir/license.txt -vv --notrackBasically, 1) setting the Once that is tested, you could also give a try to this newer image @chrisfilo just baked last week: https://neurostars.org/t/filenotfounderror-errno-2-no-such-file-or-directory-home-fmriprep-cache/3770/7?u=oesteban In principle, that should work for you as well (and your tests will give us confidence that we really fixed these problems). |
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That gave an error
I tried making a .templateflow directory in my home directory and in the singularity image, but kept getting the same message. |
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Interesting. It seems that singularity does not like that the target path does not exist previously in the image. What about this?: unset TEMPLATEFLOW_HOME
srun singularity run -B $HOME/.templateflow:/home/fmriprep/.cache/templateflow \
$image $bidsdir $outdir participant -w $workdir\
--participant_label $subject --nthreads 30 --omp-nthreads 30 --mem-mb 60000\
--low-mem --ignore slicetiming --output-space T1w fsnative template\
--use-aroma --aroma-melodic-dimensionality -150 \
--fs-license-file $outdir/license.txt -vv --notrack |
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Same thing again, and I confirmed that /home/fmriprep/.cache/templateflow is in the container image, so unfortunately that doesn't seem to be the hang-up. |
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Can you try Chris' image, that could be the only solution
…On Mon, Mar 11, 2019, 13:18 Joseph M. Orr ***@***.***> wrote:
Same thing again, and I confirmed that /home/fmriprep/.cache/templateflow
is in the container image, so unfortunately that doesn't seem to be the
hang-up.
***@***.*** fmriprep$ singularity shell -B /home/.templateflow:/home/fmriprep/.cache/templateflow /apps/psyc/containers/fmriprep/1.3.1
ERROR : Failed to get real path of /var/singularity/mnt/final/home/fmriprep/.cache/templateflow: No such file or directory
ABORT : Retval = 255
***@***.*** fmriprep$ ls -al /apps/psyc/containers/fmriprep/1.3.1/home/fmriprep/.cache/
total 35
drwxr-xrwx 5 joseph.orr psyc 5 Mar 6 12:05 .
drwxr-xrwx 7 joseph.orr psyc 10 Mar 7 15:42 ..
drwxr-xrwx 2 joseph.orr psyc 3 Mar 7 15:42 matplotlib
drwxr-xrwx 2 joseph.orr psyc 3 Mar 7 15:42 pip
drwxr-xrwx 9 joseph.orr psyc 9 Mar 6 12:05 templateflow
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<#1534 (comment)>,
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Sure, I'll try that tonight |
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I installed Chris's image, but I'm getting a new error now regarding git configuration for templateflow |
oesteban
added
impact: high
oesteban
added a commit
to templateflow/python-client
that referenced
this issue
Mar 13, 2019
This PR adds a check on ``TEMPLATEFLOW_USE_DATALAD`` (default unset or false) which needs to evaluate to ``True`` in order to use DataLad. This fix addresses nipreps/fmriprep#1534.
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I think I fixed this problem with the latest update to TemplateFlow. @oricon, could you build a singularity image from poldracklab/fmriprep:templateflow-0.1.2 ? |
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Sorry, different error this time, looks like a S3 AMS issue |
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what is your command line? |
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I was using |
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Okay, that would be expected. Can you check without the templateflow boilerplate? |
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I realized that as soon as you asked about command line. The job is currently running (>4 minutes) without errors and has actually progressed to processing the data. Thanks! |
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We'll be rolling a new release out very soon! Thanks for your precious feedback! |
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Looks like there are some issues with the 1.3.1 build in singularity. I get a TemplateFlow warning and a bunch of DeprecationWarnings as soon as I submit. The standard output shows that BIDS compliance was checked, but there's nothing else in the log. The error log is below. My system has singularity v. 2.6.1.
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