External Email - Use Caution
Hello,
I have a question related to the singularity container to run a bash script that includes freesurfer commends.
The issue is
I have built a singularity container and included the freesurfer license in the container.
Recalling and executing the script were run successfully as a root user login (without any errors), while as a general user (non-root) login, it showed an error with nu_correct; however, mri_convert seems to run fine as a step before nu_correct. The nu_correct used in the script four times. For the first to third nu_correct, it showed a full iteration (50/50) for each one and showed the following error:
---Error message---
evaluate_field: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed.
nu_evaluate: crashed while running evaluate_field (termination status=134)
nu_correct: crashed while running nu_evaluate (termination status=65280)
--------------------------------------------------------------------
Then, at the fourth nu_correct it stopped after 48 iterations then showed the following error:
---Error message---
ncvarput: ncid 4: No space left on device mivarput1: MINC package entry point nu_evaluate: crashed while running minccalc (termination status=768) nu_correct: crashed while running nu_evaluate (termination status=768)
--------------------------------------------------------------------
Note: I am using
Linux Redhat 7.9 and the singularity installed using YUM command.
Singularity version 3.6.0
For generating the container, I have used the following:
singularity build -F xxx.sif xxx.def
For running the container, I have used the following:
singularity run -e -C -H /home/Ahmed/aaa/s:/opt/data xxx.sif bash /opt/s/s1_WMH.sh
Would you advise please, I want to run the container on other computers, but in this case, it will not work.
Thanks,
Ahmed