[gmx-users] Error in running parallel GROMACS

[David van der Spoel]

On Sat, 2005-01-29 at 10:48 +0530, quanta at chem.unipune.ernet.in wrote:
> Hi all,
> 
> I am getting some problem in running parallel GROMACS.
> I have made the .tpr file for four nodes using grompp as
> /usr/local/bin/i686-pc-linux-gnu/bin/grompp_d -f $1.mdp -c $1.gro -p
> $1.top -o $1.tpr -v -np $2
> However, during mdrun its giving error in reading the .tpr file, which I
> am unable to understand. It writes output as:
> 
> Getting Loaded...
> Reading file cappr.tpr, VERSION 3.2.1 (double precision)
> Fatal error: 0: size=996, len=1032, rx_count=0
> 
> p1_1811:  p4_error: : -1
> [1] MPI Abort by user Aborting program !
> [1] Aborting program!
>     p4_error: latest msg from perror: No such file or directory
>  /usr/bin/mpirun: line 1: 15277 Broken pipe
> /usr/local/bin/i686-pc-linux-gnu/bin/mdrun_d "-np" "2" "-s" "cappr.tpr"
>  "-o" "cappr.trr" "-c" "cappr.gro" "-g" "cappr.log" "-v" "-N" "2" -p4pg
> /home/quanta/nfs/gromacs/PI15197 -p4wd /home/quanta/nfs/gromacs
> 
> so, what could be the problem? Can some one help me?
> Thanks in advance..
this should be a FAQ.

mpirun -np 4 mdrun
no -np after the mdrun command.

> 
> best wishes,
> 
> Rashmi
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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