[gmx-users] problem of submitting job in HPC

[Albert]

hello Mark:

 thanks a lot for kind advices. Here is my log file for output of mdrun
-version, There are always some duplicate informations and files



Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Gromacs version:    VERSION 4.6.3
Precision:          single
Memory model:       64 bit
MPI library:        MPI
OpenMP support:     enabled
GPU support:        disabled
invsqrt routine:    (1.0/__sqrt(x))
CPU acceleration:   NONE
FFT library:        fftw-3.3.2-fma
Large file support: enabled
RDTSCP usage:       disabled
Built on:           Thu Aug 29 02:03:12 CEST 2013
Built by:           sheed at c2n25-hf0 [CMAKE]
Gromacs version:    VERSION 4.6.3
Precision:          single
Memory model:       64 bit
MPI library:        MPI
OpenMP support:     enabled
GPU support:        disabled
invsqrt routine:    (1.0/__sqrt(x))
CPU acceleration:   NONE
FFT library:        fftw-3.3.2-fma
Large file support: enabled
RDTSCP usage:       disabled
Built on:           Thu Aug 29 02:03:12 CEST 2013
Built by:           sheed at c2n25-hf0 [CMAKE]
Build OS/arch:      AIX 1 00CCE0564C00
Build CPU vendor:   Unknown
Build CPU brand:    Unknown CPU brand
Build CPU family:   0   Model: 0   Stepping: 0
Build CPU features: CannotDetect
C compiler:         /usr/bin/mpcc_r XL mpcc_r
C compiler flags:      -qlanglvl=extc99 -qarch=auto -qtune=auto
-qthreaded -qalias=noansi -qhalt=e  -O3 -qstrict -qsimd=auto -qmaxmem=-1 -qa
rch=pwr7 -qtune=pwr7
Build OS/arch:      AIX 1 00CCE0564C00
Build CPU vendor:   Unknown
Build CPU brand:    Unknown CPU brand
Build CPU family:   0   Model: 0   Stepping: 0
Build CPU features: CannotDetect
C compiler:         /usr/bin/mpcc_r XL mpcc_r
C compiler flags:      -qlanglvl=extc99 -qarch=auto -qtune=auto
-qthreaded -qalias=noansi -qhalt=e  -O3 -qstrict -qsimd=auto -qmaxmem=-1 -qa
rch=pwr7 -qtune=pwr7
Gromacs version:    VERSION 4.6.3
Precision:          single
Memory model:       64 bit
MPI library:        MPI
OpenMP support:     enabled
GPU support:        disabled
invsqrt routine:    (1.0/__sqrt(x))
CPU acceleration:   NONE
FFT library:        fftw-3.3.2-fma
Large file support: enabled
RDTSCP usage:       disabled
Built on:           Thu Aug 29 02:03:12 CEST 2013
Built by:           sheed at c2n25-hf0 [CMAKE]
Build OS/arch:      AIX 1 00CCE0564C00
Build CPU vendor:   Unknown
Build CPU brand:    Unknown CPU brand
Build CPU family:   0   Model: 0   Stepping: 0
Build CPU features: CannotDetect
C compiler:         /usr/bin/mpcc_r XL mpcc_r
C compiler flags:      -qlanglvl=extc99 -qarch=auto -qtune=auto
-qthreaded -qalias=noansi -qhalt=e  -O3 -qstrict -qsimd=auto -qmaxmem=-1 -qa
rch=pwr7 -qtune=pwr7
Gromacs version:    VERSION 4.6.3
Precision:          single
Memory model:       64 bit
MPI library:        MPI
OpenMP support:     enabled
GPU support:        disabled
invsqrt routine:    (1.0/__sqrt(x))
CPU acceleration:   NONE
FFT library:        fftw-3.3.2-fma
Large file support: enabled
RDTSCP usage:       disabled
Built on:           Thu Aug 29 02:03:12 CEST 2013
Built by:           sheed at c2n25-hf0 [CMAKE]
Build OS/arch:      AIX 1 00CCE0564C00
Build CPU vendor:   Unknown
Build CPU brand:    Unknown CPU brand
Build CPU family:   0   Model: 0   Stepping: 0
Build CPU features: CannotDetect
C compiler:         /usr/bin/mpcc_r XL mpcc_r
C compiler flags:      -qlanglvl=extc99 -qarch=auto -qtune=auto
-qthreaded -qalias=noansi -qhalt=e  -O3 -qstrict -qsimd=auto -qmaxmem=-1 -qa
rch=pwr7 -qtune=pwr7
Gromacs version:    VERSION 4.6.3
Precision:          single
Memory model:       64 bit
MPI library:        MPI
.
.
.





2013/8/28 Mark Abraham <mark.j.abraham at gmail.com>

> On Wed, Aug 28, 2013 at 7:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> > On 8/28/13 12:39 PM, Albert wrote:
> >>
> >> Hello:
> >>
> >>   I am trying to use following command to run 4.6.3 in a HPC cluster:
> >>
> >> mpiexec -n 32 /opt/gromacs/4.6.3/bin/mdrun_mpi  -dlb yes -v -s md.tpr -x
> >> md.xtc
> >> -o md.trr -g md.log -e md.edr  >& md.info
> >>
> >> the 4.5.5 works fine in this machine with command:
> >>
> >> mpiexec -n 32 mdrun -nosum -dlb yes -v -s md.tpr -x md.xtc -o md.trr -g
> >> md.log
> >> -e md.edr  >& md.info
> >>
> >> the difference is that the option "-nosum" is not available in 4.6.3
> >>
> >> but 4.6.3 always failed. It generate a lot of similar files and log
> >> informations. It looks like use mpiexec evoke serial mdrun.....
> >>
> >> Does anybody have any idea?
> >>
> >
> > Have you verified that the 4.6.3 mdrun was correctly installed such that
> it
> > can make use of MPI?
>
> i.e. by inspecting the top of the .log file, or the output of mdrun
> -version?
>
> Mark
> --
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