[gmx-users] Problems with REMD in Gromacs 4.6.3
gigo at ibb.waw.pl
Fri Jul 12 04:59:44 CEST 2013
With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were
separate MPI jobs of course (OpenMPI 1.6.4). Each replica I run on 4
cores with OpenMP. There is Torque installed on the cluster build of
12-cores nodes, so I used the following script:
#PBS -S /bin/tcsh
#PBS -N test
#PBS -l nodes=48:ppn=12
#PBS -l walltime=300:00:00
#PBS -l mem=288Gb
#PBS -r n
mpiexec -np 144 --loadbalance mdrun_mpi -v -cpt 20 -multi 144 -ntomp 4
It was working just great with 4.6.2. It does not work with 4.6.3. The
new version was compiled with the same options in the same environment.
Mpiexec spreads the replicas evenly over the cluster. Each replica forks
4 threads, but only one of them uses any cpu. Logs end at the citations.
Some empty energy and trajectory files are created, nothing is written
Please let me know if you have any immediate suggestion on how to make
it work (maybe based on some differences between versions), or if I
should fill the bug report with all the technical details.
Ps. I'm sending this message for the 3rd time - it did not appear on
the list the last 2 times. Just in case - sorry for the spam.
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