On 11/19/12 12:09 PM, Parisa Rahmani wrote:
Dear gmx users
I have a problem with running parallel jobs on my Debian system(Openmpi
installed on it),
**Linux debian 3.2.0-1-amd64 #1 SMP , UTC 2012 x86_64 GNU/Linux**
I am using gmx 3.3.3, because of the *lambda dynamics* method which is
implemented in it.
AS I know ,in gmx 3.x, the number of processors supplied for the subsequent
mdrun needed to match the input file. but when i use **grompp -np 6 &
mpirun -np 6 mdrun** the following error appears :
ERROR : run input file md.tpr was made for 6 nodes,
while mdrun expected it to be for 1 nodes.
through search of mailing list i found similar problems, but non of
the solutions worked for my case.
wihtout -np option in grompp the error disappears, and then with each
of these commands
**
1)mpirun -np 6 mdrun -deffnm md
2)mpirun -np 6 mdrun -deffnm md -N 6
3)mpirun -np 6 mdrun -np 6 -deffnm md
4)mdrun -np 6 -s md -N 6
**it uses 6 processors(each one at nearly 100%), but the simulation
time is the same as for 1 processor.
I have no problem with parallel jobs on our cluster(gmx 3.3.3 &
openmpi), with following command:
**
grompp -np 6 -f ...
mpiexec mdrun ...(number of processors is specified in the bash file)
**
,
but i can't run it on my 6 core system.
Also, I have no problem with newer version of gmx (4.5.x), but i
should use this version, and Hope someone can help me.
Have you properly compiled an MPI-enabled mdrun? The default executable name
should be mdrun_mpi. It should be linked against libmpi, so running ldd on the
mdrun executable should tell you.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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