[gmx-users] Running Gromacs on clusters

Mark Abraham mark.j.abraham at gmail.com
Mon Mar 28 08:23:12 CEST 2016


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


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​
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