[gmx-users] gromacs hanging at end of parallel run

J Kendrick J.Kendrick at Bradford.ac.uk
Tue Apr 12 12:46:15 CEST 2005

I'd be grateful of some pointers as to where to look for this problem.
I am running gromacs under mpi on an intel cluster.
The single node version of the program works
The parallel version (3.2.1) appears to finish the calculation but then
leaves all of the processes running.  The trajectory file is written and a
summary of the performance on each of the nodes is written, but it doesn't
finish.  This behaviour seems to depend on the calculation and the number of
I have switched debug on, with scripts to work under gridengine.  This
example (methanol/water from the tutorial) will run on 2 and 4 nodes.  At
one point I thought it was fftw causing the problem so I have compiled and
linked with both fftw2.1.3 and fftw2.1.5.
I currently think that the code is in MPI_Finalize and waiting for IO
completion, but I am not sure what to look at next.
Any help gratefully received.

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