Re: [gmx-users] mdrun on multiple nodes

On Thu, Apr 21, 2016 at 2:20 AM, Husen R wrote: > Hi, > > > Thank a lot for the information. > > in my gromacs installation, 'gmx_mpi' is works while 'mdrun_mpi' is not > recognized as a gromacs command. Just as expected; the binary is suffixed, not the comand and you built a

Re: [gmx-users] mdrun on multiple nodes

Hi, Thank a lot for the information. in my gromacs installation, 'gmx_mpi' is works while 'mdrun_mpi' is not recognized as a gromacs command. Regards, Husen On Wed, Apr 20, 2016 at 6:42 PM, Mark Abraham wrote: > Hi, > > Well spotted. These should all be along

Re: [gmx-users] mdrun on multiple nodes

Hi, Well spotted. These should all be along the lines of mpirun -np 2 gmx_mpi mdrun or mpirun -np 2 mdrun_mpi if the admins have done an mdrun-only installation. I'll fix that for future versions Mark On Wed, 20 Apr 2016 13:34 Husen R wrote: > Hi Mark, > > I'm wondering

Re: [gmx-users] mdrun on multiple nodes

Hi Mark, I'm wondering why in this link http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html 'gmx' is used to run mdrun on more than one node instead of 'gmx_mpi' ? Regards, Husen On Wed, Apr 20, 2016 at 3:48 PM, Mark Abraham wrote: > Hi,

Re: [gmx-users] mdrun on multiple nodes

Hi Mark, I have configured gromacs with mpi support (using -DGMX_MPI=on): tar xfz gromacs-5.1.2.tar.gz cd gromacs-5.1.2 mkdir build cd build cmake .. -DGMX_MPI=on -DGMX_BUILD_OWN_FFTW=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Currently, I tried to use gmx_mpi (as

Re: [gmx-users] mdrun on multiple nodes

Hi Mark, I have configured gromacs with mpi support (using -DGMX_MPI=on): tar xfz gromacs-5.1.2.tar.gz cd gromacs-5.1.2 mkdir build cd build cmake .. -DGMX=on -DGMX_BUILD_OWN_FFTW=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Currently, I tried to use gmx_mpi (as you

Re: [gmx-users] mdrun on multiple nodes

Hi, Probably you haven't built gromacs with MPI support, else the name of the binary would be gmx_mpi. You can get that confirmed if you look further down the output .log files. Mark On Wed, 20 Apr 2016 10:09 Husen R wrote: > Hi all, > > I tried to run mdrun on more than one

[gmx-users] mdrun on multiple nodes

Hi all, I tried to run mdrun on more than one node using the command available in this url http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html . The following is my sbatch job : ###SBATCH #!/bin/bash #SBATCH -J sim #SBATCH -o