SV: Re: [gmx-users] mpi problems: "topol.tpr made for 2 nodes .."

[Soren Enemark]

Mark Abraham <Mark.Abraham at anu.edu.au> skrev:    Soren Enemark wrote:
> Dear all,
> we are currently trying to set up Gromacs to run in parallel on a 3 
> dual-core machines with centOS ver. 4 .
> 
> But we face the following error message when we try to run mdrun_mpi:
> 
> Program mdrun_mpi, VERSION 3.3
> Source code file: init.c, line: 69
> 
> Fatal error:
> run input file topol.tpr was made for 2 nodes,
> while mdrun_mpi expected it to be for 1 nodes.
> -------------------------------------------------------
> 
> Can anybody help us with this?
> 
> The error message came after running:
> grompp -f md.mdp -c b.gro -p topol.top -v -np 2
> followed by:
> mpirun -np 2 mdrun_mpi -s -v -np 2

The second -np 2 is only needed for old versions of MPI, but I don't 
know if this will help your problem.

   
   
  Thanks for taking the time to answer, I really appreciate this!
  I tried:
  grompp -f md.mdp -c b.gro -p topol.top -v -np 2
  followed by:
mpirun -np 2 mdrun_mpi -s -v
   
  with the same result as previously. Was this what you meant?
  If so, are there any other flags that I could try to set?
   
  For some reason it seems that mpirun does not send the information 
  (that 2 processors are to be used) to mdrun_mpi, or that mdrun_mpi does not receive the information from mpirun. What could be the reason for that?
   
  Thanks,
  Søren Enemark
   
   
   
   
  
Mark
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