[gmx-users] Parallel running problem

Alan Dodd anoddlad at yahoo.com
Wed Sep 7 14:18:05 CEST 2005

Hello Gromacs users,
I gather this problem is similar to many previous, but
can't see an obvious solution in the replies to any of
them.  I've been trying to get GROMACS to run on this
sample dual-core, dual-socket opteron box that we have
on loan.  Despite my best efforts, I seem unable to
get mdrun to understand that it's supposed to run on
more than one node.  I'm telling it to do so, and it
even appreciates it's supposed to in the output (see
below), but then decides I've told it to run on just
the one and dies.  Has anyone any idea what's going
wrong?  Is it just some kind of incompatibility with
mpich/the hardware?

mpirun -np 4 -machinefile machines mdrun -np 4 

mdrun output:
for all file options
         -np    int      4  Number of nodes, must be
the same as used for
         -nt    int      1  Number of threads to start
on each node
      -[no]v   bool     no  Be loud and noisy
-[no]compact   bool    yes  Write a compact log file
  -[no]multi   bool     no  Do multiple simulations in
parallel (only with
                            -np > 1)
   -[no]glas   bool     no  Do glass simulation with
special long range
 -[no]ionize   bool     no  Do a simulation including
the effect of an X-Ray
                            bombardment on your system

Back Off! I just backed up md.log to ./#md.log.5#
Reading file short.tpr, VERSION 3.2.1 (single
Fatal error: run input file short.tpr was made for 4
             while mdrun expected it to be for 1

Alan Dodd (University of Bristol)

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