Mark Abraham wrote:
Jakob Wohlert wrote:
Hi,
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?
Thanks for your answer!
That looks to me like the separate PME nodes are dying through some
linking problem and the problem is only manifest on node 0 when its
sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when
all the nodes die at the first point they refer to a symbol in the FFT
library.
Otherwise, looking at warnings/errors from the linker will be required.
Ok, can you be a little more specific? Do you mean when compiling fftw,
gromacs or both? I'm not very experienced with these kind of things.
Are you compiling an FFT library version for the back end, or the
front end?
I'm trying to get it to work on the back end, on the front end it works
fine! (So, I have fftw libraries for both).
/Jakob
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