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@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@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@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@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.abra...@gmail.com> > On Wed, Aug 28, 2013 at 7:06 PM, Justin Lemkul <jalem...@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 > -- > 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? 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