[Dock-fans] dock6.mpi is running in serial on 48 CPUs?

Scott Brozell sbrozell at rci.rutgers.edu
Thu Mar 24 00:27:02 PDT 2016


On Wed, Mar 23, 2016 at 04:56:50PM -0400, Jonathan Gough wrote:
> I'm guessing that this may be some sort of input error or something simple.
> I compiled dock6 and dock6.mpi without any real problems.  the path to
> mpirun is correct, all the other paths seem to be correct.
> When I run a basic screen on a set of compounds using the serial version or
> using the mpi version, dock is taking the exact amount of time. I would
> have to believe if I am looking at 100 compounds using 48 cpu's, that I
> would see some sort of speed increase.
> The only other thing that I can think of is that the cluster we have has
> been set up using openmpi-1.8.5.  However, I installed and compiled against
> a local version of mpich-3.1.4 and I'm executing it from the full path.

Does your dock output file contain, eg:
Parallel dock running 48 MPI processes

How many ligands are in the file specified by ligand_atom_file ?

What happens when you run the mpi test:
cd dock6/install/test; make parallel

If you need more help then please send verbose and verbatim details.


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