[gmx-users] Can't allocate memory problem

[Yunlong Liu]

Hi,


I am currently experiencing a "Can't allocate memory" problem on Gromacs 4.6.5 with GPU acceleration.

Actually, I am running my simulations on Stampede/TACC supercomputers with their GPU queue. My first experience is when the simulation length longer than 10 ns, the system starts to throw out the "Can't allocate memory" problem as follows:


Fatal error:
Not enough memory. Failed to realloc 1403808 bytes for f_t->f, f_t->f=0xa912a010
(called from file /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c, line 3840)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"These Gromacs Guys Really Rock" (P.J. Meulenhoff)
: Cannot allocate memory
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi_gpu on CPU 0 out of 4

-------------------------------------------------------
Program mdrun_mpi_gpu, VERSION 4.6.5
Source code file: /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/smalloc.c, line: 241

Fatal error:
Not enough memory. Failed to realloc 1403808 bytes for f_t->f, f_t->f=0xaa516e90
(called from file /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c, line 3840)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Recently, this error occurs even I run a short NVT equilibrium. This problem also exists when I use Gromacs 5.0 with GPU acceleration. I looked up the Gromacs errors website to check the reasons for this. But it seems that none of those reasons will fit in this situation. I use a very good computer, the Stampede and I run short simulations. And I know gromacs use nanometers as unit. I tried all the solutions that I can figure out but the problem becomes more severe.

Is there anybody that has an idea on solving this issue?

Thank you.

Yunlong








Davis Yunlong Liu

BCMB - Second Year PhD Candidate

School of Medicine

The Johns Hopkins University

E-mail: yliu120 at jhmi.edu<mailto:yliu120 at jhmi.edu>