[gmx-users] Running Gromacs on clusters

[Mark Abraham]

Hi,

By default, an MPI enabled binary will not be called gmx, so yours probably
is not.

Mark

On Mon, 28 Mar 2016 04:18 Ray Chao <xiaoainisa at gmail.com> wrote:

> H
> ​i, gmx users,
>
> I am trying to run Gromacs on clusters using different nodes but failed.
> The Gromacs version on cluster is 5.0 and 5.1, and MPI stack is OpenMPI.
> Initially I wrote my script as:
> "mpirun -np 64 gmx mdrun -deffnm md"
> However, the job was aborted becasue "unable to write checkpoint file.
> maybe you are out of disk space" when I definitely have enough disk space.
> Then I consulted the cluster staff. They did not know why either and said
> maybe it's because multiple nodes were trying to write the the same file.
> So I tried
> "gmx mdrun -deffnm md"
> In this case, it is running well. But, the problem is that it can only use
> 1 single node even if there are 4 nodes available.
> Can anybody help me fix this? Thank you guys so much.
>
> Ray​
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.