________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Tuesday, June 02, 2009 7:55 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PME on BlueGene
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? 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. Are you compiling an FFT library version for the back end, or the front end? Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php