[gmx-users] setting working directory

[Efrat Exlrod]

Hi There!



Is it possible to run mdrun from a shared directory and set the working 
directory to a local directory on the computer on which it runs, in order to 
decrease NFS load?



Thanks, Efrat
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Re: [gmx-users] setting working directory

[Mark Abraham]

On 1/11/2011 6:33 PM, Efrat Exlrod wrote:


Hi There!

Is it possible to run mdrun from a shared directory and set the 
working directory to a local directory on the computer on which it 
runs, in order to decrease NFS load?





/path/to/shared/mdrun -deffnm /path/to/local/my_simulation

Mark
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Re: [gmx-users] setting working directory

[lina]

On Tue, Nov 1, 2011 at 3:33 PM, Efrat Exlrod efrat.exl...@biu.ac.il wrote:
 Hi There!



 Is it possible to run mdrun from a shared directory and set the working
 directory to a local directory on the computer on which it runs, in order to
 decrease NFS load?

Yes. I attached a generic script, you can modify from it if you want.

##project set up by the user
GENERICNAME=Your_project_name

## input data folder
INPUTDATAFOLDER=${HOME}/data


## cluster environment
 shared scratch folder
SCRATCH=${HOME}/globalscracth

 node local scratch folder
LOCALSCRATCH=${LOCALSCRATCH:-/scratch}/${USER}

## set up a unique tag suffix
JOBSUFFIX=$(date +%Y_%m_%d-%H_%M_%S-%N)-$$

## job name
JOBNAME=${GENERICNAME}-${JOBSUFFIX}


## share job working directory
JOBFOLDER=${SCRATCH}/${JOBNAME}
mkdir -p ${JOBFOLDER}

## local job working directory
LOCALJOBFOLDER=${LOCALSCRATCH}/${JOBNAME}
mkdir -p ${LOCALJOBFOLDER}

## let work on the local computer
cd ${LOCALJOBFOLDER}

## let transfert input data
cp -p ${INPUTDATAFOLDER}/*.data .

## let begin the job


## let transfert output data
mv outputdata.data ${JOBFOLDER}

## clean up the local scratch
cd ..
rm -rf ${JOBNAME}

## go home
cd

## exit
exit 0

##
## eos





 Thanks, Efrat

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