mdrun -s nm.tpr -mtx nm.mtx -v -deffnm nm
on a system with 637 atoms you end up with:
...Finish step 636 out of 637and it hangs there with all cores running at 100%
For some reason the normal mode analysis of at least this particular system won't run on multiple cores.
Use an mpi compiled version of mdrun (see previous posts on compiling _dd, _mpi and _ddmpi versions of gromacs) and force the use of ONE core.
mpd --ncpus=4 &
mpdrun -n 1 mdrun_mpi -s nm.tpr -mtx nm.mtx -v -deffm nm
This was confimed by running it on four computers:
64 bit: a six core AMD 64 using a compiled version of gromacs. Hangs.
64 bit: a four core intel i5 using both the debian version and a compiled version of gromacs. Hangs.
64 bit: an older four core intel using a compiled version of gromacs. Hangs.
32 bit: an old single-core laptop using the debian version of gromacs. Works.
Next, three single-core virtual machines were set up -- a stable 32 bit, a testing 32 bit and a testing 64 bit machine, all with the debian version of gromacs (sudo apt-get install gromac). They all worked, as they only had a single core.