[AMBER] PMEMD 9 on MVAPICH / Infiniband problem

From: Nick Holway <nick.holway.gmail.com>
Date: Fri, 27 Mar 2009 15:55:38 +0000

Dear all.

We've compiled PMEMD 9 using ifort 10, MVAPICH2 1.2 and OFED 1.4 on
64bit Rocks 5.1 (ie Centos 5.2 and SGE 6.1u5). I'm able to launch
single pmemd jobs via qsub using mpirun_rsh and they run well. The
problem we see is when two jobs are launched at once is that some of
the jobs disappear from qstat in SGE as well as continue to run

I'm calling PMEMD with this line - $MPIHOME/bin/mpirun_rsh -np $NSLOTS
-hostfile $TMPDIR/machines $AMBERHOME/pmemd -O -i xxxx.inp -c
xxxx_min.rest -o xxxx.out -p xxxx.top -r xxxx_eqt.rest -x xxxx.trj

Does anyone know what I've got to do to make the PMEMD jobs run properly?

Thanks for any help.


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Received on Sun Mar 29 2009 - 01:09:06 PDT
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