[gmx-users] Can we convert one job into many serial jobs?

Mark Abraham mark.j.abraham at gmail.com
Mon May 25 18:10:41 CEST 2015


On Mon, May 25, 2015 at 4:08 PM Zhang, Cheng <c.zhang.11 at ucl.ac.uk> wrote:

> I am now using openmpi nodes to run GROMACS (e.g. mdrun_mpi) on our
> cluster. When the nodes required are too many (e.g. more than 8), jobs
> always take a long time to wait in the queue. So I wonder if there is a
> possibility that we can
> 1) convert the job into many serial jobs?

Only if you are prepared to run a separate simulation in every concurrent
single-node job, or you can get better throughput by chaining single-node
jobs than you can get by running in parallel. If you have measured this,
you should complain bitterly - people probably paid good money for the
network, and you would have evidence that it got bought for the
pre-production benchmarks, and is now being wasted in practice. If they
wanted to build a single-node throughput cluster, then they should do that
and e.g. not bother to install MPI on it. ;-)

2) convert the job into several openmpi jobs but with only 1 node in each
> job?

No. All the cores synchronize every few milliseconds. Nothing can start
until all the nodes are ready.

> When serial jobs are submitted, hundreds of jobs can be run within just a
> few minutes.

Sounds like you will be able to generate a good complaint :-)


> Thank you very much.
> Yours sincerely
> Cheng
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