[gmx-users] Running Gromacs on clusters

Ray Chao xiaoainisa at gmail.com
Mon Mar 28 03:18:23 CEST 2016

​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.


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