[gmx-users] parallel problem

Arvid Soederhaell arvid at fmp-berlin.de
Tue Sep 2 14:17:00 CEST 2003

I am about to start to use mdrun on 2 nodes, but I have some problems. 

I create a file mpi_rw-run.tpr using grompp -np 2. This seems ok and i get
no errors. Then I have a version of mdrun compiled with --enable-mpi. This
executable is called mdrun_mpi. When I do 

mdrun_mpi -np 2 -s mpi_rw-run.itp.....etc.

I get the message   
bla bla bla.....

 -pd pull.pdo Output, Opt.  Pull data output
 -pn pull.ndx Input, Opt.  Index file 
 -mtx nm.mtx Output, Opt.  Hessian matrix

      Option Type Value Description
      -[no]h bool no Print help info and quit
      -[no]X bool no Use dialog box GUI to edit command line options
       -nice int  19 Set the nicelevel
     -deffnm string  Set the default filename for all file options
         -np int   2 Number of nodes, must be the same as used for grompp
      -[no]v bool yes 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 mpi_dyn6_nt_anisoP_rw.log to
./#mpi_dyn6_nt_anisoP_rw.log.6# Getting Loaded... Reading file
mpi_rw-run.tpr, VERSION 3.1.4 (single precision) Reading file
mpi_rw-run.tpr, VERSION 3.1.4 (single precision)  Fatal error: run input
file mpi_rw-run.tpr was made for 2 nodes,
             while mdrun_mpi expected it to be for 1 nodes. 

Note that mdrun_mpi seems to understand that I have written -np 2 in the
"Option Type Value Description" section, but not in the end, where
mdrun_mpi expect 1 node input from grompp. This seems unlogic to me...
What do I do wrong??? 

Thanx in advance 
   Arvid Soderhall

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