[gmx-users] IRIX PROBLEMS

Raj Badhan r.k.badhan at stud.man.ac.uk
Tue Dec 9 10:46:02 CET 2003

Dear Users,
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 
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.
Many thanks
Raj Badhan
Postgraduate researcher
School of Pharmacy and Pharmacetical Science
The University of Manchester
Manchester, UK.

More information about the gromacs.org_gmx-users mailing list