On 15/03/2012 2:50 PM, cuong nguyen wrote:
Dear Gromacs users,
I prepare to run my simulations on the supercomputer on single node
with 64 CPUs. Although I have seen on Gromacs Mannual suggesting to
use MPI to parellel, I still haven't understood how to use this
application and which commands
If you are to run on a single node, then there's no need for mpi nowadays.
mdrun uses all cores it can find anyway. If you need to split your calculation
over many machines, however, you will need mpi.
Best,
Erik
15 mar 2012 kl. 04.50 skrev cuong nguyen:
> Dear Gromacs users,
>
> I prepare
Thanks Erik,
In case I run my simulations on 4 nodes, please let me know what do I have
to add to the command to start "MPI"? I have used the commands:
*grompp -f NVT_50ns.mdp -o NVT_50ns.tpr -c NVT_20ns.g96 -p topol.top
mdrun -s NVT_50ns -o NVT_50ns -c NVT_50ns -x NVT_50ns -e NVT_50ns -g
NVT_50ns
On 29/03/2012 12:25 PM, cuong nguyen wrote:
Thanks Erik,
In case I run my simulations on 4 nodes, please let me know what do I
have to add to the command to start "MPI"? I have used the commands:
/grompp -f NVT_50ns.mdp -o NVT_50ns.tpr -c NVT_20ns.g96 -p topol.top
mdrun -s NVT_50ns -o NVT_50ns
Hi, all,
I was wondering if there was anyone out there that has successfully
used Gromacs, MPI, and CONDOR. One thing that would be particularly
useful would be submit scripts. I have installed MPI on my own
account, but I haven't figured out how to use MPI with condor. I
would appreci
Hi Arthur,
In our group we do use Gromacs, MPI and Condor. I will leave you some
tips of how to use it but if you still have some doubts you can contact
me off the list.
Sara Campos
Submission script:
Universe = parallel
Executable = exec.sh
# 2 processors will be used
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