[gmx-users] simulation termination problem

[Prabir Khatua]

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.
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

-- 

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