[gmx-developers] Regarding Gromacs VERSION 5.2-dev multiprocess segfault

[Justin Lemkul]

On 1/5/16 6:28 AM, Mark Abraham wrote:
> Hi,
>
> Mentioning that this is produced by Justin's drude branch would have been
> considerate. ;-) I presume you can't reproduce the problem with master, 5.1.1
> (or another released version)?
>

If it is confirmed that the problem is unique to the Drude branch, I will look 
into it if provided a .tpr file.  It would also be a very useful test to know if 
a normal (non-polarizable) system runs with those binaries, to help narrow it 
down.  It's extremely easy to crash a polarizable system by simply running it wrong.

-Justin

> Mark
>
> On Tue, Jan 5, 2016 at 11:09 AM Puneet Singh <singh.punit1990 at gmail.com
> <mailto:singh.punit1990 at gmail.com>> wrote:
>
>     Dear Sir/Madam,
>     I am facing issues with gromacs development version,
>
>     *CC="mpicc" CXX="mpicxx" CFLAGS="-fPIC" CPPFLAGS="-I$FFTW_INCLUDE_DIR"
>     LDFLAGS="-L$FFTW_LIBRARY_DIR" CMAKE_INCLUDE_PATH="" CMAKE_LIBRARY_PATH=""
>     cmake
>     -DCMAKE_INSTALL_PREFIX:PATH=/home/cc/vfaculty/puneets.vfaculty/Gromacs-dev/gmx
>     -DGMX_MPI=ON  -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/home/soft/cuda-7.0
>     -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
>     -DCMAKE_PREFIX_PATH=/home/cc/vfaculty/puneets.vfaculty/caffe/CaffeDependencies/
>     -DGMX_FFT_LIBRARY=fftw3  -DGMX_PREFER_STATIC_LIBS=ON
>     -DGMX_CPU_ACCELERATION=NONE -DGMX_LAPACK_USER="-L/usr/lib64 -llapack -lblas
>     -lgfortran" -DGMX_BLAS_USER="-L/usr/lib64 -lblas -lgfortran"
>     -DFFTW_INCLUDE_DIR="/home/apps/FFTW/3.3.4/gnu/include"
>     -DFFTW_LIBRARIES="/home/apps/FFTW/3.3.4/gnu/lib/libfftw3.a"
>     -DCMAKE_PREFIX_PATH="/home/apps/FFTW/3.3.4/gnu/" .. 2>&1|tee cmake_config.log*
>
>
>
>
>     config_log
>     https://drive.google.com/open?id=0B2ywpNeYZkgyX2xVektsYXdKOEk
>     make_log
>     https://drive.google.com/open?id=0B2ywpNeYZkgyM3g2X1M2U1hWY0U
>
>     now when i run the executable with:
>     export OMP_NUM_THREADS=2
>     mpirun -np 1 gmx_mpi --ntomp 2
>
>     it runs fine(gmx_run.log_1), but with
>     mpirun -np 2 gmx_mpi --ntomp 2,
>
>     i get segfault (gmx_run.log)
>     Any help/hint will be very useful,
>     Awaiting your reply,
>
>     Regards,
>     Puneet Singh
>
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>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================