On 26/05/2011 8:50 AM, Joshua L. Phillips wrote:
You will need a file formatted like the following:
node0 slots=4 max_slots=4
node1 slots=4 max_slots=4
...
node9 slots=4 max_slots=4
You will then need to use the -hostfile option to supply the filename to
either mpiexec or mpirun (not mdrun).
Indeed. Details will vary with the nature of the MPI installation - but
it's an MPI issue, not a GROMACS issue. The only relevant detail is that
you wish every pair of cores assigned to a replica to be on the same
machine. The above approach will generally achieve that.
Mark
-- Josh
On Wed, 2011-05-25 at 11:50 -0700, Sanku M wrote:
Hi,
I am planning to run replica exchange simulation using gromacs
4.0.7 . I have read the manual about REMD. Only thing I wanted to know
is that how I can specify the name of host-machines where I am
planning to run the simulations.
I have 10 different quad-core computers each intra-connected with the
other each running OPENMPI. I want to run 20 replica each using 2
cores in parallel.
So, I was wondering whether I have to create any file containing the
names of those machines . If so, can someone give an example of format
of the file which contain those names ? Finally, what keyword I should
use in mdrun to specify that file for running replica exchange.
Also, I am not using any PBS for submitting jobs.
Sanku
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