Dear GROMACS users,<div>I successfully installed GROMACS 4.5.1 several months ago on a Mac Pro with 12 CPUs, and the "mdrun" command (not "mpirun mdrun_mpi") allows parallel simulations--it automatically uses multiple processors, while the number of processors can be manually specified as N with the flag "mdrun -nt N". I understand that this is a feature of GROMACS 4 and later. Now I am making minor changes to the mdrun source code, and I want to recompile such that the parallel version of mdrun is updated with my changes. But when I run:</div>
<div><br></div><div> make mdrun (or just make)</div><div> make install-mdrun (or just make install)</div><div><br></div><div>from the top-level source directory, the only executables that are updated are the ones with the _mpi suffix, such as mdrun_mpi. The version of mdrun in src/kernel/ is updated, but this one has no -nt flag and cannot seem to run on multiple processors. And when I run</div>
<div><br></div><div> mpirun -np N mdrun_mpi [options],</div><div><br></div><div>the same simulation is started separately on each processor, leading to a crash. If I use</div><div><br></div><div> mpirun -np 1 -cpus-per-proc N mdrun_mpi [options],</div>
<div><br></div><div>I get an error message that this is not supported on my computer ("An attempt to set processor affinity has failed").</div><div><br></div><div>I can't configure the input .tpr file for parallel because grompp doesn't have the -np flag in GROMACS 4.</div>
<div><br></div><div>How can I update the parallel-capable "mdrun" executable with my changes?</div><div>Thanks in advance,</div><div><br></div><div>Adam</div>