Hello,
I'm running bedpostx_seychelles from the seychelles prompt (via trac-all -bedp -c $SUBJECTSDIR/[dmrircfile]) with vers. v5.1.0-20110514. The processes are generated and run correctly, as far as I can see, until the post-processing job. I receive and email stating:
PBS Job Id: 1535470.seychelles.nmr.mgh.harvard.edu Job Name: bedpostx_post Execution terminated Exit_status=0 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:00
Why might the process be terminated?
-Sean
Hi Sean,
You should look at the Exit_status. If it is '0', then your job ran successfully. If it is '1' or something else, then there is an error. So it looks like your job ran correctly.
Priti
Hello,
I'm running bedpostx_seychelles from the seychelles prompt (via trac-all -bedp -c $SUBJECTSDIR/[dmrircfile]) with vers. v5.1.0-20110514. The processes are generated and run correctly, as far as I can see, until the post-processing job. I receive and email stating:
PBS Job Id: 1535470.seychelles.nmr.mgh.harvard.edu Job Name: bedpostx_post Execution terminated Exit_status=0 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:00
Why might the process be terminated?
-Sean
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Priti,
Thanks, but would seem that despite the 0 status, something didn't run correctly. trac-all -path cannot find the file merged_ph1samples.nii.gz. Actually none of expected bedpostx files, other than nodif_brain_mask have been created in the dmri.bedpostx folder.
-Sean
Hi Sean,
You should look at the Exit_status. If it is '0', then your job ran
successfully. If it is '1' or something else, then there is an error. So it looks like your job ran correctly.
Priti
Hello, I'm running bedpostx_seychelles from the seychelles prompt (via
trac-all
-bedp -c $SUBJECTSDIR/[dmrircfile]) with vers. v5.1.0-20110514. The
processes are generated and run correctly, as far as I can see, until the
post-processing job. I receive and email stating: PBS Job Id: 1535470.seychelles.nmr.mgh.harvard.edu Job Name: bedpostx_post Execution terminated Exit_status=0 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:00 Why might the process be terminated? -Sean _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Do not run your jobs on seychelles. Most nodes are still CentOS4 and I think a lot of the tools are simply not going to run on CentOS4 anymore. Run them on launchpad and if you still get errors then we need to investigate.
-- Paul Raines (http://help.nmr.mgh.harvard.edu)
On Mon, 4 Jun 2012 2:52pm, stobyne@nmr.mgh.harvard.edu wrote:
Hi Priti,
Thanks, but would seem that despite the 0 status, something didn't run correctly. trac-all -path cannot find the file merged_ph1samples.nii.gz. Actually none of expected bedpostx files, other than nodif_brain_mask have been created in the dmri.bedpostx folder.
-Sean
Hi Sean,
You should look at the Exit_status. If it is '0', then your job ran
successfully. If it is '1' or something else, then there is an error. So it looks like your job ran correctly.
Priti
Hello, I'm running bedpostx_seychelles from the seychelles prompt (via
trac-all
-bedp -c $SUBJECTSDIR/[dmrircfile]) with vers. v5.1.0-20110514. The
processes are generated and run correctly, as far as I can see, until the
post-processing job. I receive and email stating: PBS Job Id: 1535470.seychelles.nmr.mgh.harvard.edu Job Name: bedpostx_post Execution terminated Exit_status=0 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:00 Why might the process be terminated? -Sean _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Sean,
Are you sourcing Freesurfer stable 5.1 in seychelles? trac-all -bedp is supposed to submit multiple jobs (one job for each slice, in addition to bedpostx_pre and bedpostx_post).. When you ran trac-all -bedp did it submit all of those jobs?
Priti
Hi Priti,
Thanks, but would seem that despite the 0 status, something didn't run correctly. trac-all -path cannot find the file merged_ph1samples.nii.gz. Actually none of expected bedpostx files, other than nodif_brain_mask have been created in the dmri.bedpostx folder.
-Sean
Hi Sean,
You should look at the Exit_status. If it is '0', then your job ran
successfully. If it is '1' or something else, then there is an error. So it looks like your job ran correctly.
Priti
Hello, I'm running bedpostx_seychelles from the seychelles prompt (via
trac-all
-bedp -c $SUBJECTSDIR/[dmrircfile]) with vers. v5.1.0-20110514. The
processes are generated and run correctly, as far as I can see, until the
post-processing job. I receive and email stating: PBS Job Id: 1535470.seychelles.nmr.mgh.harvard.edu Job Name: bedpostx_post Execution terminated Exit_status=0 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:00 Why might the process be terminated? -Sean _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Paul Raines -
Priti Srinivasan -
stobyne＠nmr.mgh.harvard.edu