[gmx-users] simulation termination problem

[Justin Lemkul]

On 8/29/19 12:31 PM, Prabir Khatua wrote:
> Hello Gromacs users,
>
> I am trying to simulate a system of atom size 3,58,973 in gromacs 5.1.5.
> However, my simulation is being terminated in between with the following
> error.
>
> File input/output error:
> Cannot rename checkpoint file; maybe you are out of disk space?
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> I did not find any solution with respect to the error I was having in the
> mentioned website. What I found was related to memory issue. I do not know
> whether this is the same issue.

The issue is not related to memory, it is (potentially) related to disk 
space. Do you have enough space on the filesystem to write output files? 
This can also happen sometimes when the filesystem blips. There's not 
much you can do about that except complain to your sysadmin about 
integrity of the filesystem.

-Justin

> Please note that I was successfully able to run another simulation of a
> system having relatively less number of atoms with same script. The run
> command that I used for the simulation was
>
> mpirun -np 48 gmx_mpi mdrun -ntomp 1 -deffnm npt
>
> I ran both the simulations on two nodes having 24 cpu cores in each one of
> the nodes.
> I am also not able to figure out one issue. The log file of the system
> where the simulation was successfully completed showed
>
> Running on 2 nodes with total 48 cores, 48 logical cores, 0 compatible GPUs
>    Cores per node:           24
>    Logical cores per node:   24
>    Compatible GPUs per node:  0
>
> However, in the unsuccessful case, the log file showed
>
> Running on 1 node with total 24 cores, 24 logical cores
>
> Thus, it looks like the simulation was running on single node although I
> asked it to run on two nodes. I have no idea how to fix this issue. Please
> help me fix this issue or what I am doing wrong.
>
> Thanks in advance,
>
> Prabir
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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