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Frances Alvarez
May 27, 2016, 12:47:53 PM5/27/16
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Hi,
My spring version is spring-0.84.1470 and eman version is EMAN 2.1.
When I submit a job wherein I indicate use of 1 node (24 cpus) in my qsub script, Spring proceeds with the command (e.g. segment, segclassreconstruct, etc). But if I indicate use of more than 1 node, Spring generates the correct mpirun command (e.g. node=2 should be mpirun -np 48), but the job exits normally without Spring doing anything. Is there something wrong in my qsub script or parameter file? I am attaching the qsub script I used and the resulting report.log generated by Spring (which also contains the parameters I requested for segclassreconstruct). Any help is much appreciated.
Thank you.
Frances Alvarez
Postdoctoral Scholar
Zhang Lab
Department of Structural Biology
University of Pittsburgh
My spring version is spring-0.84.1470 and eman version is EMAN 2.1.
When I submit a job wherein I indicate use of 1 node (24 cpus) in my qsub script, Spring proceeds with the command (e.g. segment, segclassreconstruct, etc). But if I indicate use of more than 1 node, Spring generates the correct mpirun command (e.g. node=2 should be mpirun -np 48), but the job exits normally without Spring doing anything. Is there something wrong in my qsub script or parameter file? I am attaching the qsub script I used and the resulting report.log generated by Spring (which also contains the parameters I requested for segclassreconstruct). Any help is much appreciated.
Thank you.
Frances Alvarez
Postdoctoral Scholar
Zhang Lab
Department of Structural Biology
University of Pittsburgh
Carsten Sachse
May 28, 2016, 3:45:42 AM5/28/16
to emspring
Dear Frances,
From your description, I understand that you're running PBS submission system on your cluster. It appears that internode communication is not working. Have you introduced passwordless ssh to your environment as described (http://www.sachse.embl.de/emspring/notes.html#computer-cluster-with-multi-cpu-nodes)? Double check the FAQ notes on OpenMPI for more details.
I hope this solves the problem.
Best wishes,
Carsten
Frances Alvarez
Jun 1, 2016, 9:09:21 AM6/1/16
to emspring
Hi Carsten,
Yes, we are running PBS and passwordless SSH but it turns out that there is something wrong in my account upon double-checking. Thank you for pointing me to the right direction. The issue has now been resolved.
Thank you so much!
Frances
Yes, we are running PBS and passwordless SSH but it turns out that there is something wrong in my account upon double-checking. Thank you for pointing me to the right direction. The issue has now been resolved.
Thank you so much!
Frances
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