[gmx-users] intermittent crashes running on multiple nodes

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 7 22:34:54 CET 2009

Ron Hills wrote:
> Dear GMX Users,
> I have been running gromacs-4.0.2 and gromacs-4.0_rc3 in parallel on 
> various 8-cores-per-node and 16-cores-per-node 64-bit linux clusters. 
> While I am able to run mpi without any problems on a single node (8 or 
> 16 processes, respectively), when running larger jobs on more than one 
> node I invariably get a crash either immediately or after several hours 
> of correct simulation output. Below are errors and compile 
> options/details. The nodes seem to stop communicating and stop producing 
> output after some time even if I use mpirun -q 0. These were mostly 
> small simulations (40 angstrom cubic box containing peptide(s) and 
> water). Thanks, Ron Hills

This looks like a broken MPI installation, rather than a GROMACS 
problem. Please see if you can get other MPI programs to work.


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