AMBER Archive (2009)

Subject: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem

From: Nick Holway (nick.holway_at_gmail.com)
Date: Fri Mar 27 2009 - 10:55:38 CDT

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
indefinitely.

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.

Nick

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