It says that "The number of cores must be a multiple of the number of replicas (given with -multi, which must equal the number of .tpr<http://www.gromacs.org/Documentation/File_Formats/Topology_%28.tpr%29_File>files i.e., 10 for the above general example using prefix_0.tpr through prefix_9.tpr)"
I gave the options -multi 5 . But still I am getting the same error. Can you please explain, why is it so. Do I need to have the same no. of cores as the no. of .tpr files ?? On Thu, Jan 12, 2012 at 3:38 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 12/01/2012 5:29 PM, bharat gupta wrote: > > Thanks for the advice I re-complied everything again with static libraries > and the installation went fine. But while executing the following command I > am again getting error :- > > > mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 500 -v > > > Fatal error: > The number of nodes (1) is not a multiple of the number of simulations (3) > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff) > > Halting program mdrun_mpi > > gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff) > > application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 > > > I am trying to simulate 5 replicas and I have 4 cpu . > > > See http://www.gromacs.org/Documentation/How-tos/REMD Execution Steps > point 2. You cannot simulate an arbitrary number of replicas on an > arbitrary number of processors. > > Mark > > > > > > On Thu, Jan 12, 2012 at 1:37 PM, lina <lina.lastn...@gmail.com> wrote: > >> On Thursday 12,January,2012 08:54 AM, bharat gupta wrote: >> >>> Hi, >>> >>> I am trying to run a REMD of a peptide. But while executing the >>> following command after nvt and npt equilibration , I am getting the >>> following error:- >>> >>> mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000 >>> mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot >>> enable executable stack as shared object requires: Permission denied >>> >> >> Can you run a normal md smoothly? >> try: >> mdrun_mpi mdrun -deffnm prefix_0 >> >> if it works, then some of your trajectories not sound. means system does >> not equilibrium well. >> >> >>> >>> Can anybody suggest me how could I rectify this error. >>> >>> -- >>> Bharat >>> >>> >> -- >> 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 >> > > > > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > Mobile no. - 010-5818-3680 > E-mail : monu46...@yahoo.com > > > > > > -- > 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 > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com
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