[gmx-users] parallel run errors

[Sandeep Somani]

hi rama 

below is the submission script i use after grompp for 8 procs. 
might help..

-sandeep

==============================================
#! to set   : nodes , ppn (procs per node) 
#! to submit: qsub <thisFile> -N <name> 
#! to monitor: qstat -ans 
#PBS -l nodes=4:ppn=2
#PBS -l mem=200mb
#PBS -j oe
NPROCS=`wc -l < $PBS_NODEFILE`

echo ------------------------------------------
#goto current directory (cd $PWD doesnt work!) 
cd $PBS_O_WORKDIR
echo NAMD job in $PWD submitted by ssomani on 
date
echo This shell is $PBS_O_SHELL
echo This job has been allocated $NPROCS nodes:
echo `cat $PBS_NODEFILE`
echo ------------------------------------------

gmx=/usr/local/gromacs3.2.1/i686-pc-linux-gnu/bin/mdrun_mpi
MOL=mymol 

echo -------------production -------------------------
/usr/local/mpich-gm/bin/mpirun -machinefile $PBS_NODEFILE -np $NPROCS
${gmx} -s ${MOL}_md.tpr -o ${MOL}7 -c ${MOL}7.gro -g md_md.log

==============================================













> -----Original Message-----
> From: gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of 
> Ramachandra Rao Gullapalli
> Sent: Thursday, May 05, 2005 11:46 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] parallel run errors
> 
> 
> Dear GMX ers
> I have been having trouble with running the Gromacs program 
> in parallel. I have been trying to run the example speptide 
> simulation of the website on a parallel cluster as a test and 
> am getting the same error every time. 
> 
> 1) My MPI script is as follows...
> 
> #PBS -l nodes=2:myrinet:ppn=2
> #PBS -l walltime=2:00:00
> #PBS -j oe
> #PBS -q lionxm-mcd18
> 
> # change the current working directory to the directory where
> # the executable file 'foo' can be found
> cd ~rrg142/gromacs/testfiles/speptide300/
> 
> # run the executable file 'foo' using the qmpirun script
> mpirun /usr/global/gromacs/i686-pc-linux-gnu/bin/mdrun -v -s 
> full.tpr -o full.trr -c after_em.gro -np 2 -g after_md.log
> 
> 2) I Grompp it for two nodes to prepare the input tpr file 
> using the following command
> 
> grompp -v -f full -o full -c after_em -p speptide -np 2
> 
> 3) The error message i have been receving consistently is as follows
> 
> Reading file full.tpr, VERSION 3.2.1 (single precision)
> Reading file full.tpr, VERSION 3.2.1 (single precision)
> Fatal error: run input file full.tpr was made for 2 nodes,
>              while mdrun expected it to be for 1 nodes.
> Fatal error: run input file full.tpr was made for 2 nodes,
>              while mdrun expected it to be for 1 nodes.
> Fatal error: run input file full.tpr was made for 2 nodes,
>              while mdrun expected it to be for 1 nodes.
> Fatal error: run input file full.tpr was made for 2 nodes,
>              while mdrun expected it to be for 1 nodes.
> /var/spool/pbs/mom_priv/jobs/610948.lion.SC: full.trr: 
> command not found
> 
> 
> Can anyone please help me with the mistake i have been doing? 
> The cluster has a MPIGM kind of network
> 
> I shall be very thankful for any kind of suggestions.
> 
> Sincerely
> Regards
> Rama
> 
> 
> 
> 
> 
> 
> The important thing is not to stop questioning. Curiosity has 
> its own reason for existing... -Einstein 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org 
> http://www.gromacs.org/mailman/listinfo/gmx-> users
> Please 
> don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 
> ---
> Incoming mail is certified Virus Free.
> Checked by AVG anti-virus system (http://www.grisoft.com).
> Version: 6.0.859 / Virus Database: 585 - Release Date: 2/14/2005
>  
> 

---
Outgoing mail is certified Virus Free.
Checked by AVG anti-virus system (http://www.grisoft.com).
Version: 6.0.859 / Virus Database: 585 - Release Date: 2/14/2005