Selina Nawaz skrev 2011-03-02 11.54:
Hi, I am a Phd student studying polymer membranes.
I have installed Gromacs version 4.5.2 on our department cluster and
attempted to run a simulations on a DPPC bilayer membranes taken from
the tielleman website.
I have set the system up in an NPT ensemble using a semi-isotropic
pressure coupling.
The simulation seems to run perfect in serial however I am having
problems to run the simulation in parallel.
I understand that this version of Gromacs uses threading to
parallelise the system. I wanted to know whether it is possible to run
this using openmpi and if not how do i use this thread base
parallelisation.
Many Thanks
Selina
Hi,
It's slightly different than you think. Gromacs uses a thread based MPI
implementation for communications between cores on the same machine. If
you compile without threads it would use e.g. OpenMPI instead of threads
as far as I know. Note that it will still use OpenMPI (or equivalent)
for inter-node communication.
Cheers,
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
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
