> I am not sure about it we have successfully run amber 14 from PBS
> without any PBS_NODEFILE variable, but I will try to use it.
Any mpirun command needs a list of the nodes to run on, otherwise it
defaults to the node the command was run from. There must be some way on
your cluster to specify which nodes are assigned to the current job; the
mpirun command itself does not have the built in intelligence to
automatically figure it out. Usually this comes from the queuing system;
if you are not running a queuing system, then you can create the
"nodelist" by hand. Searching google for "mpirun tutorial" shows some
examples...
> What about Intel MPI?
>
> >> Can AMBER 14 work with Intel MPI generally?
Yes, or even with the built-in MPI version that comes with AMBER 14 or
mpich; the AMBER reference manual has clear discussion of this. For the
Intel compile, there is an extra flag to configure, -intelmpi
All of the compiles assume you have the matching mpicc and mpif90 in your
path, and as mentioned previously, you want all the MPI commands to match.
You showed this with the openmpi compile, just neglected to specify the
host_file that lists what nodes to run on. If running PBS, as Ross Walker
mentioned, this is usually set to the variable $PBS_NODEFILE
--tec3
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 28 2014 - 11:30:03 PST
