I generally build a tpr for the whole simulation then submit one job using a command such as:

mpirun -n ${NUM_PROCESSORS} mdrun -deffnm ${NAME} -maxh ${WALL_TIME_IN_HOURS}

copy all the files back at the end of the script if necessary then:

then resubmit it (sending out all the files again if necessary) this time using the command

mpirun -n ${NUM_PROCESSORS} mdrun -deffnm ${NAME} -maxh ${WALL_TIME_IN_HOURS} -cpi

you can then keep resubmitting with that line till the job is finished.

In my case I have a maximum wall clock of 24hrs on some machines so this gets used a lot

I also think that 1.6ns/day which is what you seem to be getting is very low performance and you might want to consider using more processors. Check the log file as the profiling information at the end will indicate whether this might be beneficial.

Richard


On 25/04/13 13:58, Francesco wrote:
You can split the simulation in different part (for example 5 ns each),
every time you'll finish one you will extend it adding more time.
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend

My cluster uses a different "script system" than yours so I can't help
with it, but basically you have to submit more than 1 job with different
command to execute:

1) first production
mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8
2) modify the tpr file
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
3) next X ns
mpirun -n 8 mdrun -s next.tpr -cpi previous.cpt
4) modify the tpr file
5) production md
and so on

with qsub you can submit a depending job (-hold_jid) that will run only
when the previous step will finish, in your case there should be a
similar way to do it.

cheers

Fra

On Thu, 25 Apr 2013, at 12:28 PM, Sainitin Donakonda wrote:
Hey all,

I recently ran 20ns simulation of protein ligand complex on cluster i
used
following script to run simulation

grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
md_test.tpr

mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8

*I saved this as MD.sh And then submited to cluster using following
script*

#!/bin/bash
#BSUB -J testgromacs             # the job's name/array job
#BSUB -W 120:00                       # max. wall clock time in hh:mm
#BSUB -n 8,8                          # number of processors Min,Max
#BSUB -o test/output_%J.log             # output file
#BSUB -e test/errors_%J.log             # error file
#BSUB -M 8192     #Memory limit in MB

echo "Started at `date`"
echo

cd test

echo "Running gromacs test in `pwd`"

./MD.sh

echo "Finished at `date`"


It gave result but when checked files .xtc and created RMSD plots in that
x-axis of this plot i see only 8ns ...but in MD.MDP file i specified
20ns..

Cluster Output says that "TERM_RUNLIMIT: job killed after reaching LSF
run
time limit.
Exited with exit code 140". i gave maximum cluster time 120 hours..still
it
is not sufficient ..

Can any body tell me  how do it split script i such  that i will get all
20ns simulation


Thanks in advance ,

Sainitin
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