DimitryASuplatov wrote:
Hello,
I have installed gromacs-4 on Solaris 8 with mpi support.
I was very disappointed by the lack of -np option in grompp and mdrun.
The -np option is absent in grompp, as it is no longer necessary. The -np flag
is indeed present for mdrun, however.
After reading the manual and the site I came to a conclusion that now we
do not need to specify number of nodes via gromacs status file but
instead use mpirun option only.
Executing (for gromacs benchmarking set)
grompp
mpirun c0-5 mdrun_mpi -v
starts six threads on six processors though output speed is the same as
for a single-node run. No errors, no warnings.
I didn't think threading was supported yet, maybe I'm wrong. But you can
definitely use -np 6 with mdrun_mpi.
-Justin
So, am I doing wrong with gromacs parallelization or is this the problem
of the Solaris MPI?
Thank you.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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