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

Jonathan Gough jonathan.d.gough at gmail.com
Wed Mar 23 13:56:50 PDT 2016


Hi all,

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.

I was wondering if anyone has any other advice on trouble shooting this.

Thanks.
Jonathan
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