That all looks fine so far. The core file processor won't help unless you've compiled with -g. Hopefully cmake -DCMAKE_BUILD_TYPE=Debug will do that, but I haven't actually checked that really works. If not, you might have to hack cmake/Platform/BlueGeneP-static-XL-C.cmake.
Anyway, if you can compile with -g, then the core file will tell us in what function it is dying, which might help locate the problem. Mark On Tue, Aug 6, 2013 at 11:43 PM, Prentice Bisbal <prentice.bis...@rutgers.edu> wrote: > Dear GMX-users, > > I need some assistance running Gromacs 4.6.3 on a Blue Gene/P. Although I > have a background in Chemistry, I'm an experienced professional HPC admin > who's relatively new to supporting Blue Genes and Gromacs. My first Gromacs > user is having trouble running Gromacs on our BG/P. His jobs die and dump > core, with no obvious signs (not to me, at least) of where the problem lies. > > I compiled Gromacs 4.6.3 with the following options: > > ------------------------------------------snip------------------------------------------- > > cmake .. \ > -DCMAKE_TOOLCHAIN_FILE=../cmake/Platform/BlueGeneP-static-XL-C.cmake \ > -DBUILD_SHARED_LIBS=OFF \ > -DGMX_MPI=ON \ > -DCMAKE_C_FLAGS="-O3 -qarch=450d -qtune=450" \ > -DCMAKE_INSTALL_PREFIX=/scratch/bgapps/gromacs-4.6.2 \ > -DGMX_CPU_ACCELERATION=None \ > -DGMX_THREAD_MPI=OFF \ > -DGMX_OPENMP=OFF \ > -DGMX_DEFAULT_SUFFIX=ON \ > -DCMAKE_PREFIX_PATH=/scratch/bgapps/fftw-3.3.2 \ > 2>&1 | tee cmake.log > > ------------------------------------------snip------------------------------------------- > > When one of my users submits a job, it dumps core. My scheduler is > LoadLeveler, and I used this JCF file to replicate the problem. I added the > '-debug 1' flag after searching the gmx-users archives: > > ------------------------------------------snip------------------------------------------- > > #!/bin/bash > # @ job_name = xiang > # @ job_type = bluegene > # @ bg_size = 64 > # @ class = small > # @ wall_clock_limit = 01:00:00,00:50:00 > # @ error = job.$(Cluster).$(Process).err > # @ output = job.$(Cluster).$(Process).out > # @ environment = COPY_ALL; > # @ queue > > source /scratch/bgapps/gromacs-4.6.2/bin/GMXRC.bash > > ------------------------------------------snip------------------------------------------- > > /bgsys/drivers/ppcfloor/bin/mpirun > /scratch/bgapps/gromacs-4.6.2/bin/mdrun_mpi -pin off -deffnm sbm-b_dyn3 -v > -dlb yes -debug 1 > > The stderr file shows this at the bottom, which isn't too helpful: > > ------------------------------------------snip------------------------------------------- > > Reading file sbm-b_dyn3.tpr, VERSION 4.6.2 (single precision) > > Will use 48 particle-particle and 16 PME only nodes > This is a guess, check the performance at the end of the log file > Using 64 MPI processes > <Aug 06 17:25:55.303879> BE_MPI (ERROR): The error message in the job record > is as follows: > <Aug 06 17:25:55.303940> BE_MPI (ERROR): "killed with signal 6" > > -----------------------------------------snip----------------------------------------------- > > I have a bunch of core files which I can analyze with the IBM Core file > processor, and I also have bunch of debug files from mdrun. I went through > about 12/64 of them, and didn't see anything that looked like an error. > > Can anyone offer me any suggestions of what to look for, or additional > debugging steps I can take? Please keep in mind I'm the system administrator > and not an expert-user of gromacs, so I'm not sure if the inputs are > correct, or are at correct for my BG/P configuration. Any help will be > greatly appreciated. > > Thanks, > Prentice > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
