[gmx-users] Error: Lost Particles while sorting

Smith, Micholas D. smithmd at ornl.gov
Thu Mar 31 20:40:27 CEST 2016

Dear other users (and developers)

I moved some simulations that were working pretty well on one supercomputer to another (the previous one did not have gpu nodes) to take advantage of some gpus, but I am now getting a sporadic error:


Program gmx_mpi, VERSION 5.0
Source code file: /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom
acs/mdlib/nbnxn_search.c, line: 728

Software inconsistency error:
Lost particles while sorting
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


in one of my simulations (but not the others), when I start to use more 16 MPI processes per simulation. I should note that I am using mdrun -multidir in order to launch these simulations at the same time, and it doesn't seem to be a specific simulation that it causing the issue. Additionally, it is rather sporadic, sometimes the simulations will run with no problems, other times it run for 2 minutes and then fails (and I get stuck back in the queue). Any ideas?

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

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