[gmx-users] parallel problem

[Itamar Kass]

befor the mdrun command you should invoke the mpi using 
mpirun -np 2 mdrun -np 2 ...


Quoting Arvid Soederhaell <arvid at fmp-berlin.de>:

> Hi, 
> 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
>                             corrections
>  -[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. 
> quantix:/home/arvid/gmx-rw-mem> 
> *************************************************************************
> 
> 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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********************************************
Computers are like airconditioners... They don't work well with Windows
open.
********************************************

===========================================
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585146
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Homepage: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
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