[gmx-users] IRIX PROBLEMS
r.k.badhan at stud.man.ac.uk
Tue Dec 9 10:46:02 CET 2003
Firstly thank you too all who have passed on suggestions for my
EM runs with ATP, I'm half way there now, but I'm sure I will be
bugging you all again for more assistance.
Secondly, we are having troubles running our simulations on the
Universities high performance computer system.
They have installed Gromacs in double precision for us, and I can
quite happily run my simulations using a single processor (-np 1)
by issuing the MPIRUN command. But when we try to run in
parallel on 4 processors, we get an error message back stating
that the run input files were designed 256 nodes and were
expecting to be for 4 nodes.
This occurs when initiating the MDRUN command for the first set of
energy minimisations on out protein.
We are not allowed interactive access to the server, and must
submit batch jobs of each commands. Now, these commands
seem to be fine as we can run the sims. on a single processor, but
there is always a problem when running in parallel.
Could this be a conflict with some of the libraries, something like
FFTW and LAM-MPI??
I'm not an expert on this, and the technicians at the university dont
seem to know why this is happening.
Any suggestions would be appreciated.
School of Pharmacy and Pharmacetical Science
The University of Manchester
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