External Email - Use Caution
Hello Ahmed, There is one error message indicating you are running out of disk space to write to. Not clear to me if that is inside or outside the container, but either files need to be deleted and/or your disk partition needs to be larger. I would strongly discourage running as userid root. Root has privileges that non-root users don’t have, so if something is not setup correctly privilege wise in the machine image, then you will not find out when running as root. And once you run something as root, then non-root user may subsequently have issues running the same commands because they cannot delete/create temporary files previously created in subdirectories and/or owned by root, and commands as those non-root users will fail. As part of building the container image (as root), it should be possible to create a normal non-root userid and then select that non-root userid to be the userid when the container runs (or at least that works in docker). - R.
On Jul 8, 2020, at 16:37, Bahrani, Ahmed A. <ahmed..bahrani@uky.edu> wrote: 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 isI 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 devicemivarput1: MINC package entry pointnu_evaluate: crashed while running minccalc (termination status=768)nu_correct: crashed while running nu_evaluate (termination status=768)-------------------------------------------------------------------- Note: I am usingLinux 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_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer