I am using slurm to send file to make calculation on a server at my university.
The time limit for these calculation is 5 days but sometimes it is not enough. For this reason I need a clean up function that before the calculation ends copy the unfinished calculation file ( in order to restart them later). I trapped this function with a SIGUSR2 signal and I used the command --signal=SIGUSR2@600 to launch the signal 10 minutes before the end of the calculation but it doesn't seems to work. You will find following the code:
this is the command:
Code:
FILE=0
InPath="${inputdir}/*.gjf"
for FILE in $InPath ; do
if [ -s ${FILE} ]
then
FILENAME=${FILE##*/}
FILENAME=${FILENAME%.*}
JOB=${FILENAME:0:5}
echo ${FILE} was submitted as ${JOB}
mv "${inputdir}/${FILENAME}".* "${submitdir}/"
outputpath="${outputdir}/${FILENAME}.out"
# Launch the executable
SubFile="${submitdir}/${FILENAME}.gjf"
sbatch -A jgu-heinze-oshell -p ${QUEUE} -J ${JOB} -o ${outputpath} -n ${PROCS} -t ${RUN} --mem-per-cpu=2000 --signal=SIGUSR2@600 ./orca.sh ${SubFile}
FILENAME=""
fi
done
This is the orca.sh file
Code:
# Store working directory to be safe
SAVEDPWD=$(pwd)
# We define a bash function to do the cleaning when the signal is caught
cleanup(){
for FILE3 in "${rundir}"/*.gjf ; do
if [ -s ${FILE3} ]
then
FILENAME=${FILE3##*/}
FILENAME=${FILENAME%.*}
rm /localscratch/${SLURM_JOB_ID}/*.tmp
cp /localscratch/${SLURM_JOB_ID}/* "${outputdir}"/
mv "${rundir}"/${FILENAME}.* "${findir}"/
exit 0
fi
done
}
# Register the cleanup function when SIGUSR2 is sent,
# ten minutes before the job gets killed
trap 'cleanup' SIGUSR2
# Copy input file
#SubFile="${submitdir}/*.gjf"
# echo ${SubFile}
for FILE2 in ${SubFile} ; do
if [ -s ${FILE2} ]
then
FILENAME=${FILE2##*/}
FILENAME=${FILENAME%.*}
# ls /localscratch/
cp "${submitdir}/${FILENAME}".* /localscratch/${SLURM_JOB_ID}
mv "${submitdir}/${FILENAME}".* "${rundir}/"
# Go to jobdir and start the program
cd /localscratch/${SLURM_JOB_ID}
set OMPI_MCA_btl=self,sm
/cluster/Apps/orca/3.0.2/orca ${FILENAME}.gjf
# Call the cleanup function when everything went fine
cleanup
FILENAME=""
fi
done
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LEARN ABOUT DEBIAN
gnunet-namestore
GNUNET-NAMESTORE(1) General Commands Manual GNUNET-NAMESTORE(1)NAME
gnunet-namestore - manipulate GNUnet zones
SYNOPSIS
gnunet-namestore [options]-zZONEFILE
DESCRIPTION
gnunet-namestore can be used to create and manipulate a GNS zone.
OPTIONS -a, --add
Desired operation is adding a record
-c FILENAME, --config=FILENAME
Use the configuration file FILENAME.
-d, --delete
Desired operation is deleting a record
-D, --display
Desired operation is listing of matching records
-e TIME, --expiration=TIME
Specifies expiration time of record to add; format is relative time, i.e "1 h" or "7 d 30 m". Supported units are "ms", "s", "min"
or "minutes", "h" (hours), "d" (days) and "a" (years).
-h, --help
Print short help on options.
-L LOGLEVEL, --loglevel=LOGLEVEL
Use LOGLEVEL for logging. Valid values are DEBUG, INFO, WARNING and ERROR.
-n NAME, --name=NAME
Name of the record to add/delete/display
-t TYPE, --type=TYPE
Type of the record to add/delete/display (i.e. "A", "AAAA", "NS", "PKEY", "MX" etc.)
-v, --version
Print GNUnet version number.
-V VALUE, --value=VALUE
Value to store or remove from the GNS zone. Specific format depends on the record type. A records expect a dotted decimal IPv4
address, AAAA records an IPv6 address, PKEY a public key in GNUnet's printable format, and CNAME and NS records should be a domain
name.
-z FILENAME, --zonekey=FILENAME
Specifies the filename with the private key for the zone (mandatory option)
BUGS
Report bugs by using Mantis <https://gnunet.org/bugs/> or by sending electronic mail to <gnunet-developers@gnu.org>
SEE ALSO gnunet-gns(1)GNUnet Mar 5, 2012 GNUNET-NAMESTORE(1)
08-17-2017
