My suggestion would be to just use a queueing system. I don't currently
use one myself, but classics NQS and PBS stem from the supercomputer
center building I worked at at NASA while I was the secretary and Leap
programmer for AMBER, and they were a natural fit even before clusters
came along.
Vis a vis clusters, GPUs seem to be the thing these days - noting that
there is now peer-to-peering with them, they could be schedulable as
singles or doubles (granularity a queuing system would help with). E.g.
if you have the advertised hardware to create the need:
http://ambermd.org/news.html#4Ux8GPU
The more that is invested in hardware, the more likely it is shared
and/or optimized with a queueing system.
Bill
On 12/28/2014 11:07 AM, Thomas Cheatham wrote:
>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 28 2014 - 20:30:03 PST
