On Wed, Jun 5, 2013 at 4:35 PM, João Henriques
joao.henriques.32...@gmail.com wrote:
Just to wrap up this thread, it does work when the mpirun is properly
configured. I knew it had to be my fault :)
Something like this works like a charm:
mpirun -npernode 2 mdrun_mpi -ntomp 8 -gpu_id 01
Thank you very much for both contributions. I will conduct some tests to
assess which approach works best for my system.
Much appreciated,
Best regards,
João Henriques
On Tue, Jun 4, 2013 at 6:30 PM, Szilárd Páll szilard.p...@cbr.su.se wrote:
mdrun is not blind, just the current design does
Sorry to keep bugging you guys, but even after considering all you
suggested and reading the bugzilla thread Mark pointed out, I'm still
unable to make the simulation run over multiple nodes.
*Here is a template of a simple submission over 2 nodes:*
--- START ---
#!/bin/sh
#
# - - - - - - - - - -
On Wed, Jun 5, 2013 at 2:53 PM, João Henriques
joao.henriques.32...@gmail.com wrote:
Sorry to keep bugging you guys, but even after considering all you
suggested and reading the bugzilla thread Mark pointed out, I'm still
unable to make the simulation run over multiple nodes.
*Here is a
Ok, thanks once again. I will do my best to overcome this issue.
Best regards,
João Henriques
On Wed, Jun 5, 2013 at 3:33 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Wed, Jun 5, 2013 at 2:53 PM, João Henriques
joao.henriques.32...@gmail.com wrote:
Sorry to keep bugging you guys,
Just to wrap up this thread, it does work when the mpirun is properly
configured. I knew it had to be my fault :)
Something like this works like a charm:
mpirun -npernode 2 mdrun_mpi -ntomp 8 -gpu_id 01 -deffnm md -v
Thank you Mark and Szilárd for your invaluable expertise.
Best regards,
João
Dear all,
Since gmx-4.6 came out, I've been particularly interested in taking
advantage of the native GPU acceleration for my simulations. Luckily, I
have access to a cluster with the following specs PER NODE:
CPU
2 E5-2650 (2.0 Ghz, 8-core)
GPU
2 Nvidia K20
I've become quite familiar with the
Yes, documentation and output is not optimal. Resources are limited, sorry.
Some of these issues are discussed in
http://bugzilla.gromacs.org/issues/1135. The good news is that it sounds
like you are having a non-problem. The output tacitly assumes
heterogeneity. If your performance results are
mdrun is not blind, just the current design does report the hardware
of all compute nodes used. Whatever CPU/GPU hardware mdrun reports in
the log/std output is *only* what rank 0, i.e. the first MPI process,
detects. If you have a heterogeneous hardware configuration, in most
cases you should be
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