I would like to run one simulation in parallel so that it utilises all the
available nodes and cores. For that,
I have compiled gromacs with mpi enabled and also installed openmpi on my
machine.
I am using the following command:
mpirun -np 4 mdrun_mpi -v -s *.tpr
When i use top command, I get:
Hi,
Is it a local work station or cluster with multiple CPUs? Which gromacs
version did you install?
On Mon, Oct 7, 2013 at 1:55 PM, pratibha kapoor
kapoorpratib...@gmail.comwrote:
I would like to run one simulation in parallel so that it utilises all the
available nodes and cores. For that,
On 21/04/2010 11:29 PM, Hsin-Lin wrote:
Hi,
I compare the run times.
The calculation of two processors is faster than one.
And I saw the utility of the two cores large than 85% separately.
I can sure it's exactly parallel simulation in my PC now.
Another question is:
someone told me the
Did you preprocess the .tpr file for 2 cores with grompp? Also, I believe
you have to have an additional -np 2 after the mdrun_mpi command: mpirun -np
2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log
-c 200ns.gro -np 2
-- at least this is what I understand from what my prof told me.
Arden Perkins wrote:
Did you preprocess the .tpr file for 2 cores with grompp? Also, I
believe you have to have an additional -np 2 after the mdrun_mpi
command: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr
-g 200ns.log
-c 200ns.gro -np 2
-- at least this is what I
On 22/04/2010 3:12 AM, Arden Perkins wrote:
Did you preprocess the .tpr file for 2 cores with grompp?
This was only necessary for GROMACS 3.
Also, I
believe you have to have an additional -np 2 after the mdrun_mpi
This was only necessary with early versions of MPI libraries.
command:
Hi,
I want to use my dual core PC to do the simulation.
The version of GROMACS installed is version 4.0.5.
According the message post by others on mailing list before.
I type lamboot first, and type the commend:
mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log
-c
On 21/04/2010 12:55 AM, Hsin-Lin wrote:
Hi,
I want to use my dual core PC to do the simulation.
The version of GROMACS installed is version 4.0.5.
According the message post by others on mailing list before.
I type lamboot first, and type the commend:
mpirun -np 2 mdrun_mpi -s 200ns.tpr -e
I tried to run a gromacs simulation (gromacs 3.3.1, MD, 18000 atoms) on 2
systems:
Intel(R) Pentium(R) CPU 2.40GHz with 100Mbit network
and
AMD Opteron(tm) Processor 250 with 1Gbit network
On both systems I had a crash when I tried to run with more then 5 processors.
From 1-5 there was no
servaas michielssens wrote:
I tried to run a gromacs simulation (gromacs 3.3.1, MD, 18000 atoms) on
2 systems:
Intel(R) Pentium(R) CPU 2.40GHz with 100Mbit network
and
AMD Opteron(tm) Processor 250 with 1Gbit network
On both systems I had a crash when I tried to run with more then 5
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