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How do I compile GROMACS for parallel runs? |
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Friday, 09 September 2005 |
On most systems you only have to add the option --enable-mpi to the configure script, and then compile GROMACS the normal way. For this to work you need to have MPI communication libraries install, and some kind of wrapper script like mpicc or mpcc to use when compiling MPI programs. MPI should always be present on supercomputers, and if you are running on workstations we recommend LAM MPI, www.lam-mpi.org. On Linux it's even simpler - just install the RPM packages we provide!
On most supercomputers you can only run MPI programs on dedicated nodes, so in this case you probably want all the analysis programs compiled without MPI first. Since you normally only need the mdrun program with MPI support you can type "make mdrun; make install-mdrun" instead, but remember to type "make distclean" if you have previously compiled GROMACS without MPI. It is also possible to put a suffix on the MPI-version programs, or just start MPI runs when an environment variable is set. Check the options to the configure script with "./configure --help".
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