[gmx-users] parallel problem
Arvid Soederhaell
arvid at fmp-berlin.de
Tue Sep 2 14:17:00 CEST 2003
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
More information about the gromacs.org_gmx-users
mailing list