Mahnam wrote:
In God We Trust
Hello GMX users
I am trying to run one gromacs simulation in parallel. I have
successfully compiled gromacs 4 with mpi support on a cluster with
x86_64 architecture with 4 cpus (intel core 2 Quad 6600).
when I run mdrun with single-processor ,it works f
In God We Trust
Hello GMX users
I am trying to run one gromacs simulation in parallel. I have successfully
compiled gromacs 4 with mpi support on a cluster with x86_64 architecture
with 4 cpus (intel core 2 Quad 6600).
when I run mdrun with single-processor ,it works fine and everything i
I decided to recompile mdrun with mpi support again and restart the
simulation again.
I also checked for lam running on the nodes and it was still running
nevertheless I tried to halt lam.
Now everything seems to be running ok.
On Tue, 2008-01-15 at 12:24 -0500, [EMAIL PROTECTED] wrote:
> > Wha
What i was trying to do is to run a parallel simulation. I have
successfully compiled mdrun with mpi support.
This is my grompp command
grompp -f md.mdp -c rec_pr.gro -p rec.top -o rec.tpr -np 12
And this is the script I sent to the cluster:
#!/bin/bash
cd /home/yunierkis/MD
export LAMRSH="ss
What i was trying to do is to run a parallel simulation. I have
successfully compiled mdrun with mpi support.
This is my grompp command
grompp -f md.mdp -c rec_pr.gro -p rec.top -o rec.tpr -np 12
And this is the script I sent to the cluster:
#!/bin/bash
cd /home/yunierkis/MD
export LAMRSH="ss
i reckon that you have not built in mpi support to mdrun in GROMACS so
each instance of mdrun produces one trajectory rather than running in
parallel and produce only one trajectory.
Mark Abraham wrote:
Yunierkis Perez Castillo wrote:
Hi all, I'm new to gromacs. I have setup a protein MD simul
Yunierkis Perez Castillo wrote:
Hi all, I'm new to gromacs. I have setup a protein MD simulation in a
cluster, I'm using 6 computers with 2 CPUs each one.
After gromacs begun running I had 12 trajectory files in the folder the
output is written:
md.trr
#md.trr.1#
#md.trr.2#
#m
Hi all, I'm new to gromacs. I have setup a protein MD simulation in a
cluster, I'm using 6 computers with 2 CPUs each one.
After gromacs begun running I had 12 trajectory files in the folder the
output is written:
md.trr
#md.trr.1#
#md.trr.2#
#md.trr.11#
It seems like the traject
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