[gmx-users] expected it to be for 1 nodes

Jeroen Mesters mesters at biochem.uni-luebeck.de
Thu Sep 29 14:05:56 CEST 2005

Machine: *dual* processor dell precision 650 with SuSE linux 9.2
Software: *1)* mpich installed, machines file constructed, mpd started 
*2)* compiled gromacs twice, once with and once without --enable-mpi 
(using mpich). So, I ended up with two programmes, mdrun_mpi and mdrun. 
The program versions are different in size which I would expect... 
Indeed, one program was compiled with cc and the other with mpicc (no 
errors during compilation).

Step 1: grompp -np 2 -f full.mdp -c after_pr_CA.gro -p ph5.top -n 
index.ndx -o 2cpu.tpr
Step 2: mdrun_mpi -np 2 -s 2cpu.tpr  >>>> Fatal error: run input file 
2cpu.tpr was made for 2 nodes, while mdrun_mpi expected it to be for 1 

Question 1. Are my commands correct i.e. is this the proper why to start?
Question 2. Can this work at all or do I really need *2* computers (2 

Thanx for any hints, Jeroen.

Jeroen Raymundus Mesters, Ph.D.
Institut fuer Biochemie, Universitaet zu Luebeck
Ratzeburger Allee 160, D-23538 Luebeck
Tel: +49-451-5004070, Fax: +49-451-5004068
E-mail: mesters at biochem.uni-luebeck.de
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me  (Macbeth)

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