Hi, On Oct 17, 2013, at 2:25 PM, pratibha kapoor <kapoorpratib...@gmail.com> wrote:
> Dear gromacs users > > I would like to run my simulations on all nodes(8) with full utilisation of > all cores(2 each). I have compiled gromacs version 4.6.3 using both thread > mpi and open mpi. I am using following command: > mpirun -np 8 mdrun_mpi -v -s -nt 2 -s *.tpr -c *.gro > But I am getting following error: > Setting the total number of threads is only supported with thread-MPI and > Gromacs was compiled without thread-MPI . > Although during compilation I have used: > cmake .. -DGMX_MPI=ON -DGMX_THREAD_MPI=ON you can either use MPI or thread_mpi. But you can use MPI and OpenMP with -DGMX_MPI=ON -DGMX_OPENMP=ON > If I dont use -nt option, I could see that all the processors(8) are > utilised but I am not sure whether all cores are being utilised. For You can run with mpirun -np 16 mdrun_mpi -v -s -nt 2 -s *.tpr -c *.gro to use all 16 available cores. > version 4.6.3 without mpi, I Know by default gromacs uses all the threads > but not sure if mpi version uses all threads or not. Take a look at the md.log output file, there it should be written what Groamcs did use! Best, Carsten > Any help is appreciated. > -- > 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? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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? Read http://www.gromacs.org/Support/Mailing_Lists