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 <[email protected]
<mailto:[email protected]>>
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
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-----------------------------------------------
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>
[email protected] <mailto:[email protected]>
http://www2.icm.uu.se/molbio/elflab/index.html
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
