Dear Amber community:
I am running Amber10 on a Beowulf cluster using Intel Xeon E5520
processors, Infiniband interconnects, Suse, MPICH2. Amber10 was compiled
with the Intel Compilers.
I find that Amber pmemd jobs (submitted via PBS) run fine if I use 64 or
fewer processors (4 nodes x 16 ppn). However, if I use more processors,
Amber10 runs for 50-100 time steps and then the job hangs and goes no
further. The system monitor shows that the processors remain active.
There is no error message in the printed amber.out file or the amber.info
file. When the job is cancelled, there are no error messages in the pbs.o
or pbs.e files, other than that the job was terminated.
If anyone could help me understand what is going on, or how to figure out
what is going on, I would greatly appreciate it. Am I unaware of a flag
that needs to be set?
Thanks,
Ed Pate
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 26 2010 - 18:00:03 PDT
