Both are probably using 4 cores, the first one as threads, the second via mpi.
However, in the second one you are using 16 threads to run 4 copies of
the same simulation, 4 threads each, thus getting performance similar
(or less) to using only one core. When using mpi, you should use
mdrun_mpi
If you install package 1 on your list, the second one will be
installed as well (ie you need both of them).
// Linus
On Mon, Jul 30, 2012 at 10:56 AM, rama david ramadavidgr...@gmail.com wrote:
Hi GROMACS FRIENDS,
I have dell T3500 precision, 64 bits, 6C workstation with fedora
Quite sure it's just different syntax in topology and mdp file. Compare to C;
#define POSRES // expressed as -DPOSRES in the mdp file
#ifdef POSRES // when working in the topology file
// Linus
On Thu, Jul 26, 2012 at 1:52 PM,
reising...@rostlab.informatik.tu-muenchen.de wrote:
On 7/26/12
In order to use MPI on Ubuntu with the distribution-supplied package,
you need to use a combination of mpirun and mdrun_mpi, e.g.
mpirun -np 2 mdrun_mpi -deffnm md
to run on two cores.
On Mon, Dec 27, 2010 at 7:04 PM, Justin A. Lemkul jalem...@vt.edu wrote:
גדעון לפידות wrote:
Hi all,
I
The nicelevel is simply the priority of the process, where 19 is the
lowest priority (ie most other programs will use the cpu before the
gromacs process does) and -20 the highest.
See man nice.
// Linus
On Tue, Dec 7, 2010 at 10:13 PM, GZ Zhang zgz...@gmail.com wrote:
Hi, ALL
I'm using
What did you try to do? To use dssp, you must select entire residues,
e.g. 1 (protein). That error sounds a bit like my problem when trying
to do dssp using only the backbone.
// Linus Östberg
On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote:
Hi,
Thanks for your
Use grompp normally, without the -np flag. Then run mdrun_mpi with your
normal parameters as mpirun -np x mdrun_mpi -deffnm xx
On Mon, Jun 21, 2010 at 2:00 PM, Amin Arabbagheri amin_a...@yahoo.comwrote:
Hi all,
I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic
package
7 matches
Mail list logo
