[gmx-users] Clusters

[Lucas Dadalt Morero]

I have a script teste.sh which contains:
#!/bin/bash
#$ -S /bin/bash


#PBS -l nodes=8:ppn=6
  



source /home/dadalt/gmx-5.0.4/bin/

grompp -f md.mdp -c 1UBQ_400_npt.gro -t 1UBQ_400_npt.cpt -p topol.top -o product.tpr
/usr/lib64/openmpi/bin/mpirun -np 8 mdrun_mpi -v -deffnm product

I use the command qsub to run teste.sh :
qsub -cwd -pe mpi 4 teste.sh


   Through this steps the simulation is perfomed using just ONE node, but I want to use 8 nodes. 
What I am doing wrong? What I need to change? 

I am using Rock Cluster distribution.

Thanks in advance

Lucas


> Date: Tue, 14 Apr 2015 16:14:18 +0200
> From: pall.szilard at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Clusters
> 
> On Tue, Apr 14, 2015 at 2:45 AM, Lucas Dadalt Morero <ldm_w at hotmail.com> wrote:
> > Sorry, it's 8 cores. Network is good.
> 
> Good for what? I was hoping to hear that it's e.g IB QDR. Otherwise
> it's unlikely that you'll scale to all nodes.
> 
> > The hardware setup is ok, I just want to know how to perform a gromacs simulation using all the nodes..
> 
> Compile with MPI and run just like you'd run any MPI application. See
> if it scales at all on your network, if it does you can try tweaking
> the performance (e.g. PP-PME ratio, mutiple OpenMP threads per rank,
> nstlist, etc.)
> I suggest you check out that following page:
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization
> 
> --
> Szilárd
> 
> >
> >
> > Lucas
> >
> >> Date: Tue, 14 Apr 2015 02:06:49 +0200
> >> From: pall.szilard at gmail.com
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Clusters
> >>
> >> What network do you have? Unless it's fast (that is low latency) you
> >> won't be able to run across nodes. Are you sure about 9 cores, that
> >> number seems strange?
> >> --
> >> Szilárd
> >>
> >>
> >> On Mon, Apr 13, 2015 at 11:52 PM, Lucas Dadalt Morero <ldm_w at hotmail.com> wrote:
> >> > Are there any tutorial or tips to use cluster in Gromacs?
> >> > I have 5 nodes  with 9 cores each node and want use all them in one simulation, is that possible?
> >> > I've read something about gromacs MPI but I don't know how to use.
> >> > Can someone suggest some text or some tutorial for me?
> >> >
> >> > Thanks in advance,
> >> > Lucas
> >> >
> >> > --
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