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.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
