[gmx-users] using MPI

[Mark Abraham]

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 -c NVT_50ns -x NVT_50ns -e NVT_50ns -g 
> NVT_50ns -v/
> however, the speed was still the same.

You need to find out what MPI you have installed and consult the 
available documentation for that. We cannot help you with that.

Mark

> Best regards,
>
> Cuong
>
> 2012/3/15 Erik Marklund <erikm at xray.bmc.uu.se 
> <mailto:erikm at xray.bmc.uu.se>>
>
>     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 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 I have to use. Please
>>     help me to deal with this?
>>     Many thanks and regards,
>>     Cuong
>>
>>     -- 
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>     -----------------------------------------------
>     Erik Marklund, PhD
>     Dept. of Cell and Molecular Biology, Uppsala University.
>     Husargatan 3, Box 596,    75124 Uppsala, Sweden
>     phone: +46 18 471 6688 <tel:%2B46%2018%20471%206688>        fax:
>     +46 18 511 755 <tel:%2B46%2018%20511%20755>
>     erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
>     http://www2.icm.uu.se/molbio/elflab/index.html
>
>
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>
> -- 
> Nguyen Van Cuong
> PhD student - Curtin University of Technology
> Mobile: (+61) 452213981
>
>
>

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