[gmx-users] using tpbconv for continuing parallel jobs

[David van der Spoel]

On Tue, 2005-03-08 at 23:45 -0500, Hwankyu Lee wrote:
> Dear gmx-users,
> 
> I've run parallel simulations, and quit those jobs and tried to 
> continue them by using tpbconv.
> When I didn't do parallel simulations, I've always used tpbconv to 
> continue jobs without any problem.
> But, when I use tpbconv to continue parallel jobs, it didn't work.
> Here, I used grompp  with shuffle option. And, my pbs-script file looks 
> like below.
> After I quit my job, I used "tpbconv  -f **.trr  -s **.tpr  -o **.tpr  
> -time **  -until **  (or with -n deshuf.ndx).
> And then, I submitted the job with pbs-script file, which is shown 
> below. but, it didn't work.
> Could you tell me how to continue parallel jobs by using tpbconv?
> Thanks for  your help in advance.

You can only continue a job if it is the same number of processors. In
addition you want to add the -e flag BUT NOT THE -n flag!


> ----------------------------------------
> #PBS -S /bin/sh
> #PBS -l nodes=1,walltime=200:00:00
> #PBS -q route
> #PBS -N spbmut1
> #PBS -j oe
> #PBS -M leehk at umich.edu
> #PBS -m abe
> 
> #
> echo "I ran on `hostname`"
> cat $PBS_NODEFILE
> #
> cd /home/leehk/work/spbmut1
> #
> lamboot $PBS_NODEFILE
> #
> mpirun -c 2 -c2c -ssi rpi sysv 
> /home/leehk/local/gromacs/powerpc-apple-darwin7.\
> 6.0/bin/mdrun -s spbmut1-md01.tpr -deffnm spbmut1-md01 -c 
> spbmut1-30ns.gro -np \
> 2
> #
> lamhalt
> -----------------------------
> 
> 
> best,
> Hwankyu.
> 
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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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