[gmx-users] parallel simulation

2013-10-07 Thread pratibha kapoor
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:

Re: [gmx-users] parallel simulation

2013-10-07 Thread Venkat Reddy
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,

Re: [gmx-users] parallel simulation in dual core PC

2010-04-21 Thread Mark Abraham
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

Re: [gmx-users] parallel simulation in dual core PC

2010-04-21 Thread Arden Perkins
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.

Re: [gmx-users] parallel simulation in dual core PC

2010-04-21 Thread Justin A. Lemkul
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

Re: [gmx-users] parallel simulation in dual core PC

2010-04-21 Thread Mark Abraham
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:

[gmx-users] parallel simulation in dual core PC

2010-04-20 Thread Hsin-Lin
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

Re: [gmx-users] parallel simulation in dual core PC

2010-04-20 Thread Mark Abraham
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

[gmx-users] parallel simulation crash on 6 processors

2007-11-28 Thread servaas michielssens
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

Re: [gmx-users] parallel simulation crash on 6 processors

2007-11-28 Thread David van der Spoel
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