Play with the domain decomposition, lincs itr/order, -ntomp and -ntmpi, etc... I was able to get a 4 day simulation which often gave that error to speed up to 12 hours on 24 CPU/3 nodes/144 cores but it took 2 days of submitting, checking speed, and killing jobs to try another grid routine. My problem related to this is it wont go any faster (more nodes, cpu's or cores and starts to hit limits where there are only 100 atoms in a unit cell) if anyone knows a way to make it go faster.
Sincerely,
Stephan Watkins
Gesendet: Freitag, 26. Juli 2013 um 22:13 Uhr
Von: "Quintin Sheridan" <qsher...@nd.edu>
An: "gmx-users@gromacs.org" <gmx-users@gromacs.org>
Betreff: [gmx-users] Free Energy Simulations in Parallel
Von: "Quintin Sheridan" <qsher...@nd.edu>
An: "gmx-users@gromacs.org" <gmx-users@gromacs.org>
Betreff: [gmx-users] Free Energy Simulations in Parallel
Dear Gromacs Users,
Is it possible to run free energy calculations in parallel using mpirun?
If not, what is the fastest way to run free energy calculations. I am
trying to us the Bennet's Accepetance Ratio (g_bar) to get the free energy
of solvation for an ionic liquid based on the tutorial by Justin Lemkul. I
hav tried to decouple an ion pair as well as individual ions. In either
case the simulations run locally but when I try to run them in parrallel I
get the error:
Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 2.26125 nm
Thank You
Quintin Sheridan
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Is it possible to run free energy calculations in parallel using mpirun?
If not, what is the fastest way to run free energy calculations. I am
trying to us the Bennet's Accepetance Ratio (g_bar) to get the free energy
of solvation for an ionic liquid based on the tutorial by Justin Lemkul. I
hav tried to decouple an ion pair as well as individual ions. In either
case the simulations run locally but when I try to run them in parrallel I
get the error:
Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 2.26125 nm
Thank You
Quintin Sheridan
--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
