Hi, If you're running GROMACS compiled with MPI support, then your command line should start e.g. mpirun -np gmx mdrun. Consult your cluster documentation for details.
Mark On Mon, 21 Dec 2015 16:39 Live King <vikasdubey1...@gmail.com> wrote: > Hi everyone, > > I am running free energy calculations on my cluster using GROMACS 5.0.5. I > have 21 windows so, I run my simulations parallely. I am fairly new to > GROMACS 5.0.5 and had used version 4.5.5 before. In that case I used "-np > 2" or "-np 1 " option of mdrun to run parallel simulations. GROMACS 5.0.5 > doesn't seem to recognize -np option. I tried -nt 1 and -nt 2 then It > gives this error. > > > > > > *Fatal error:Setting the total number of threads is only supported with > thread-MPI and Gromacs was compiled without thread-MPI* > so, I tried removing both options and now whenever I run my simulations on > cluster they are really really slow. Is this a problem of GROMACS > installation ? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.