[gmx-users] parallel job

[Alexander Alexander]

Hello,

Thanks for your response. I guess it is thread-MPI and I do not know why I
just get only one single gmx although I use for example 56 slots.

Please find below some information printed out in log file as well as part
of the submission scripts:
------
GROMACS:      gmx mdrun, VERSION 5.1.2
Executable:   /home/itman/bin/gromacs-5.1.2/bin/gmx
Data prefix:  /home/itman/bin/gromacs-5.1.2
Command line:
  gmx mdrun -deffnm prd -s prd.tpr -ntomp 8 -ntmpi 7

GROMACS version:    VERSION 5.1.2
Precision:          single
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:        disabled
OpenCL support:     disabled
invsqrt routine:    gmx_software_invsqrt(x)
SIMD instructions:  AVX_128_FMA
FFT library:        fftw-3.3.4-sse2-avx
RDTSCP usage:       enabled
C++11 compilation:  disabled
TNG support:        enabled
Tracing support:    disabled
Built on:           Mon Feb 15 17:14:35 CET 2016
Built by:           itman at univ.m [CMAKE]
Build OS/arch:      Linux 2.6.32-431.29.2.el6.x86_64 x86_64
Build CPU vendor:   AuthenticAMD
Build CPU brand:    AMD Opteron(TM) Processor 6276
Build CPU family:   21   Model: 1   Stepping: 2
Build CPU features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf_lm
misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2
sse3 sse4a sse4.1 sse4.2 ssse3 xop
C compiler:         /usr/lib64/ccache/cc GNU 4.4.7
C compiler flags:    -mavx -mfma4 -mxop    -Wundef -Wextra
-Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall
-Wno-unused -Wunused-value -Wunused-parameter  -O3 -DNDEBUG
-funroll-all-loops  -Wno-array-bounds
C++ compiler:       /usr/lib64/ccache/c++ GNU 4.4.7
C++ compiler flags:  -mavx -mfma4 -mxop    -Wundef -Wextra
-Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function
-O3 -DNDEBUG -funroll-all-loops  -Wno-array-bounds
Boost version:      1.55.0 (internal)

---------

#$ -A gromacs_parallel
#$ -pe smp 56
trap '' usr1
trap '' usr2
FB_CHEMIE=/home/fb_chem
export PATH=/home/itman/bin/gromacs-5.1.2/bin:$PATH
export
LD_LIBRARY_PATH=/home/itman/bin/gromacs-5.1.2${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}

gmx mdrun -deffnm prd -s prd.tpr -ntomp 8 -ntmpi 7 >D.log 2>&1

joberror=$?
exit $joberror
------
Thanks,
Regards,
Alex

On Sat, Jun 18, 2016 at 4:53 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Depends what you mean by parallel. The top utility will show you processes,
> and whether via MPI or thread-MPI, there will generally be multiple GROMACS
> processes started from one call of gmx mdrun.
>
> Mark
>
> On Sat, Jun 18, 2016 at 4:30 PM Alexander Alexander <
> alexanderwien2k at gmail.com> wrote:
>
> > Dear Gromacs user,
> >
> > For a gromacs parallel job, I was wondering if gmx would show up as just
> a
> > single bonded "gmx" when one invoked "top" in command or its distributon
> > over cpu's shows up as a series of "gmx" in top command inside the node.
> >
> > Regards,
> > Alex
> > --
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