[gmx-users] PME on BlueGene

Jakob Wohlert jw685 at cornell.edu
Wed Jun 3 03:30:33 CEST 2009


I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the
configuration options from the wiki I have succeeded insofar that I have a
working program as long as I don't use PME.

I have tried many different variants of fftw - 2.1.5, 3.2.1, single
precision, double precision, different compiler optimizations and so on,
but it all ends the same: mdrun getting stuck somewhere in the
initialization process.

However, by using the built in fft library FFTPACK instead of FFTW, PME
will work, but that is not really an alternative.

In at least a few cases I have been able to pinpoint the location where it
hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls
MPI_Sendrecv, but then nothing else happens as far as I can tell.

I'm confused and I have sort of ran out of ideas right now. Has anyone
else encountered a problem like this, or has anyone any suggestions how to
proceed from here?

Jakob Wohlert

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