[gmx-users] several runs

Victor Rosas Garcia rosas.victor at gmail.com
Tue Feb 24 22:54:51 CET 2015

Perhaps I can be of help here.

Except for the smallest systems, GROMACS simulations are very
compute-intensive, so a single machine is needed for a single job. In
many instances, several machines are required for a single job
(provided you have a fast enough network).

If you give a single machine more than one compute job, or if you
require of it more computing power than if physically has (like asking
for 8 cpus when the machine only has 6) that's called oversubscribing
the machine. It causes severe performance degradation, as the machine
has more work than it can handle. Not only in terms of CPU, but also
because the input/output channels will saturate

So, if a single simulation requires all the resources in your machine,
running several will make it unusable.

It is a lot better to run a single job per machine.

Hope this helps.


2015-02-24 13:40 GMT-06:00 mah maz <mahmaz71 at gmail.com>:
> Hi Justin,
> Thank you for your answer! If you may help with any of these questions I
> would be greatly grateful;
> How can I understand if they were interfered? How is pinning? Any other
> ways you can recommend?
> Thanks a lot
> On Tue, Feb 24, 2015 at 10:14 PM, mah maz <mahmaz71 at gmail.com> wrote:
>> Is running simulations in several terminals problematic?
>> On Tue, Feb 24, 2015 at 8:42 PM, mah maz <mahmaz71 at gmail.com> wrote:
>>> Dear all,
>>> How can I perform several simulations simultaneously (in linux)?
>>> thank you!
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