[gmx-users] Simulation Terminated on Clusters Due to "cannot rename checkpoint file"

Mark Abraham mark.j.abraham at gmail.com
Sun Feb 14 19:24:13 CET 2016


GROMACS works correctly if you have permissions to read and write and
enough space to do so. But I expect that you can't try to run from $WORK
using mdrun -cpi $HOME/old.cpt if $HOME is full.

I suggest you consult the docs for the cluster, and consult your sysadmins
for any help with your script.


On Sun, Feb 14, 2016 at 7:17 PM Ray Chao <xiaoainisa at gmail.com> wrote:

> Hi, Mark,
> Thank you for your response. I am not sure if this is the right way to
> reply, because I cannot see the content of gmx maillist emails.
> I am running in my own space. Here is the story. Everybody has a $HOME and
> $WORK directory on the cluster. The $HOME is for permanent storage with
> 100GB disk space and $WORK is for temporary storage with 1TB storage.
> Initially I was running my case on $HOME. Since the files begin to pile up,
> the space is running out, I turned to the $WORK directory. At that time, I
> began to receive such an error message. Even I then move my cases back to
> $HOME, it did not work either.
> Best regards,
> Lei Zhao
> Ph.D Student in Mechanical Engineering, Virginia Tech
> Mobile:+1-540-750-9042
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