Dear Gromacs Users, We normally run gromacs 4.0.x mdrun with OpenMPI in a 24 core shared-memory server (SunFire X4450). i. e. the command we use for a 12 core run is : mpirun -np 12 mdrun -v -c output_md.gro This is working great so far.
Now we are trying to use gromacs 4.5.x and I found this on the release notes (http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x) : “Running on a multi-core node now uses thread-based parallelization to automatically spawn the optimum number of threads in the default build. MPI is now only required for parallelization over the network.” So, I guess now instead of “mpirun -np 12 mdrun -v -c output_md.gro” we should use “mdrun -nt 12 -v -c output_md.gro” and expect the same performance. Am I right? Also, is this “automatically spawn the optimum number of threads” reliable ? Does that mean that if the recommended number is 4 cores (threads) there’s no way to make it run faster even if specifying -nt 12 or 24 ? Any advice will be welcome. Thanks in advance. Best Regards, Arnau Cordomí -- 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
