[gmx-users] simulation termination problem

[Prabir Khatua]

Thanks Justin. The problem has been fixed.

On Fri, Aug 30, 2019 at 7:31 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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-- 

*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*