fs_time will not affect any processing, so you could replace it with a
stub. But why do you think it is fs_time?
On 3/19/2021 10:54 AM, Yakupov, Renat /DZNE wrote:
External Email - Use Caution
Dear Freesurfer developers,
I am trying to run the longitudinal processing pipeline of our data on
our HPC cluster (SGE based) and it crashes at the 3rd step -
generating the longitudinal runs. The exact command is 'recon-all
-long tp1dir basedir -all'. There is no error message on the screen,
it just says that it exited with errors.
The recon-all.log file has no error information either, other than the
statement that it exited with errors. It seems to have stopped after
mri_nu_correct.mni step and looking further it looks like it crashed
at the beginning of orig_nu step, since orig_nu.log has this error
message:
/usr/bin/time: /dev/stdout: Not a directory
Please see attached log files.
Additional information:
Freesurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
uname -a:
Linux compute-0-2.local 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22
06:48:29 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
lsb_release -a:
LSB Version:
:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: CentOS
Description: CentOS release 6.6 (Final)
Release: 6.6
Codename: Final
What is interesting is that running it on the headnode directly
without qsub works fine. The headnode has the same OS and tcsh versions.
In my rather poorly informed opinion, it looks like fs_time is the
culprit. For a quick fix, is it safe to assume that using fs_time from
Freesurfer 6 wont affect the processing pipeline in any way?
Thank you!
Best regards,
Renat.
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