The command I used this time :- mdrun_mpi mdrun -s prefix_.tpr -multi 5 -replex 100
Here's the error that I got :- Fatal error: The number of nodes (1) is not a multiple of the number of simulations (5) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Look at these, my work-strong arms" (P.J. Harvey) Halting program mdrun_mpi gcq#345: "Look at these, my work-strong arms" (P.J. Harvey) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 On Thu, Jan 12, 2012 at 3:53 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 12/01/2012 5:45 PM, bharat gupta wrote: > > 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 ?? > > > You can't be getting an identical error, the numbers are different now. > > If mdrun is reporting the number of nodes is 1, then you have not > configured your MPI environment correctly so that it knows how many > processors you have available. You will need to solve this by reading your > MPI documentation. > > If you have only four processors, you will not be able to run efficient > REMD on five replicas, even if you can work out how to get MPI to > over-allocate MPI processes to your physical processors. > > Please copy and paste command line and error together, so that people who > might help don't feel like they might be wasting their time guessing. They > have other things to do. Your example input below did not produce your > error below, because 20 != 3. > > > Mark > > > 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 > > > > > > -- > 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
