[gmx-users] parallel run errors

Andrey V. Golovin golovin at genebee.msu.su
Thu May 5 18:07:10 CEST 2005


Hello Ramachandra,

try: mpirun -np 2

5/5/2005, 7:46 PM you wrote:

Ramachandra Rao Gullapalli> Dear GMX ers
Ramachandra Rao Gullapalli> I have been having trouble with running
the Gromacs program in parallel. I have
Ramachandra Rao Gullapalli> been trying to run the example speptide
simulation of the website on a parallel
Ramachandra Rao Gullapalli> cluster as a test and am getting the same
error every time. 

Ramachandra Rao Gullapalli> 1) My MPI script is as follows...

Ramachandra Rao Gullapalli> #PBS -l nodes=2:myrinet:ppn=2
Ramachandra Rao Gullapalli> #PBS -l walltime=2:00:00
Ramachandra Rao Gullapalli> #PBS -j oe
Ramachandra Rao Gullapalli> #PBS -q lionxm-mcd18

Ramachandra Rao Gullapalli> # change the current working directory to
the directory where
Ramachandra Rao Gullapalli> # the executable file 'foo' can be found
Ramachandra Rao Gullapalli> cd ~rrg142/gromacs/testfiles/speptide300/

Ramachandra Rao Gullapalli> # run the executable file 'foo' using the
qmpirun script
Ramachandra Rao Gullapalli> mpirun
/usr/global/gromacs/i686-pc-linux-gnu/bin/mdrun -v -s full.tpr -o
Ramachandra Rao Gullapalli> full.trr -c after_em.gro -np 2 -g
after_md.log

Ramachandra Rao Gullapalli> 2) I Grompp it for two nodes to prepare
the input tpr file using the following
Ramachandra Rao Gullapalli> command

Ramachandra Rao Gullapalli> grompp -v -f full -o full -c after_em -p
speptide -np 2

Ramachandra Rao Gullapalli> 3) The error message i have been receving
consistently is as follows

Ramachandra Rao Gullapalli> Reading file full.tpr, VERSION 3.2.1
(single precision)
Ramachandra Rao Gullapalli> Reading file full.tpr, VERSION 3.2.1
(single precision)
Ramachandra Rao Gullapalli> Fatal error: run input file full.tpr was
made for 2 nodes,
Ramachandra Rao Gullapalli>              while mdrun expected it to
be for 1 nodes.
Ramachandra Rao Gullapalli> Fatal error: run input file full.tpr was
made for 2 nodes,
Ramachandra Rao Gullapalli>              while mdrun expected it to
be for 1 nodes.
Ramachandra Rao Gullapalli> Fatal error: run input file full.tpr was
made for 2 nodes,
Ramachandra Rao Gullapalli>              while mdrun expected it to
be for 1 nodes.
Ramachandra Rao Gullapalli> Fatal error: run input file full.tpr was
made for 2 nodes,
Ramachandra Rao Gullapalli>              while mdrun expected it to
be for 1 nodes.
Ramachandra Rao Gullapalli>
/var/spool/pbs/mom_priv/jobs/610948.lion.SC: full.trr: command not
found


Ramachandra Rao Gullapalli> Can anyone please help me with the
mistake i have been doing?
Ramachandra Rao Gullapalli> The cluster has a MPIGM kind of network

Ramachandra Rao Gullapalli> I shall be very thankful for any kind of
suggestions.

Ramachandra Rao Gullapalli> Sincerely
Ramachandra Rao Gullapalli> Regards
Ramachandra Rao Gullapalli> Rama






Ramachandra Rao Gullapalli> The important thing is not to stop
questioning. Curiosity has its own reason for existing...
Ramachandra Rao Gullapalli> -Einstein 
Ramachandra Rao Gullapalli>
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Ramachandra Rao Gullapalli>
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--
Best regards,

----------------------------------------------------------------- 
Andrey V. Golovin 
Ph.D,Professor assistant    tel: (095) 939-5305  
Bioengineering and 
Bioinformatics Department              
Moscow State University     fax: (095) 939-3181 
119899 Moscow            E-mail: golovin at genebee.msu.su 
Russia                      web: http://rnp-group.genebee.msu.su 
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