[gmx-users] jobs in parallel

Patricia Soto Becerra psoto at ultra.chem.ucsb.edu
Wed Aug 11 01:54:12 CEST 2004

Hi gmx-users!,
I have some difficulties to run parallel jobs in a new cluster (128 dual
CPU Xeon 3.06 Ghz processors with a Myrinet high-speed interconnect).

When I submit my job:

mpirun -np 2 mdrun_mpi -s topol.tpr

It is reported to be running on a specific node. For example, when I
type *qstat* it is reported to run on node10.

If I check the md0.log and md1.log files, the processes are running on
other nodes (say node01 and node02)!!. When I connect to the nodes
reported in md0.log and md1.log indeed the jobs are running there (node01
and node02), and nothing in node10 (the one that is reported by
*qstat*). The performace is so low under these conditions that for any 
benchmark of gromacs the parallel jobs turn to be a lot slower than a
single node job.

My guess is that there is a problem with PBS (?) but at the moment I
cannot find a solution.

Does anybody have any idea on how to solve this???!


Dr. Patricia Soto
Post-doctoral Researcher
Department of Chemistry and Biochemistry
University of California, Santa Barbara CA 93106 - 9510 
United States

**Como bien nos ensena la vida, la verdad es una aspiracion inalcanzable
que, en todo caso, habita al otro lado del muro que forman las
innumerables verdades que cada uno sostenemos por convencimiento o por
intereses mas o menos legitimos**  Jesus A. Nunez Villaverde, 03-08-04


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