[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

[Mark Abraham]

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.bisbal at 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
>
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