Mod:Hunt Research Group/pimpQSUB
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How to... speed up your job queing
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
vi ~/bin/gf
and copy and paste this:
#!/bin/bash
#########################################################################################
# Default Variables #
#########################################################################################
DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
WLOGf="$HOME/bin/.wulog"
CUE="pqph"
CORE=12
MEM=47988
WALLT="119:59:00"
QUIET=1
FRC=0
CORRECTION=1
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0
#########################################################################################
# Debugging Function #
#########################################################################################
debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}
#########################################################################################
# Help output #
#########################################################################################
usage(){
echo -e "gaussian function v1.2
${RED}NAME${NC}
gfunc
${RED}SYNOPSIS${NC}
gf [jobfilename.com]
${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC} [select]
select =
all
work ID (e.g. '7197851')
prints the log of the jobs sent
${BLUE}-h${NC}
help
${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}
bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;
eval $__resultvar="'$MBYTES'"
}
#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################
if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi
if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh
# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name
# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=12:mem=48000MB:tmpspace=400gb
#PBS -j oe
#PBS -q pqph
#PBS -m ae
# load modules
#
module load gaussian/g09-d01
# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi
if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;12;48000MB;119:59:00;d01;400GB' > "${PFILE}"
fi
#########################################################################################
# Retriving inputted options #
#########################################################################################
while getopts fhnsc:d:g:l:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi
case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-99] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};
if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-9"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
f)
FRC=1;
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
if [[ ${OPTARG} == 'all' ]]
then
cat $WLOG;
else
sed -n "/${OPTARG}/p" $WLOG;
fi
;;
?)
usage;
exit;
;;
esac
done
if [[ $# -eq 0 ]]
then
usage
exit
fi
shift $OPT
if [[ ! -f $GAUSS && -f "${GAUSS}.com" ]]
then
$GAUSS="${GAUSS}.com"
fi
#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}MB/" ${SFILE}
else
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${SFILE}
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${SFILE}
if [ "$CUE" != "PUBLIC" ]
then
grep -q "#PBS -q .*" ${SFILE} && sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" "${SFILE}" || sed -i "14s/^/#PBS -q ${CUE}\n/" ${SFILE}
else
grep -q "#PBS -q .*" ${SFILE} && sed -i "/#PBS -q .*/d" ${SFILE}
fi
if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian\/g09-.*/module load gaussian\/g09-${GAUSS}/" ${SFILE}
fi
#########################################################################################
# Pushing the job to the HPC #
#########################################################################################
while [ $# -gt 0 ]
do
if [[ ! -f ${1} && -f "${1}.com" ]]
then
set -- "${1}.com"
fi
NMFL=${1%.com}
if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi
if [[ $CORRECTION -eq 1 ]]
then
CD=$(pwd)
CD=${CD//\//\\\/}'\/'
GMEM=$((${MEM} * 15 / 20))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=./" ${1})
echo $gmem $gpshar $gchk
grep -q "%mem=" ${1} && sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1} || sed -i "1s/^/%mem=${GMEM}MB\n/" ${1}
grep -q "%nprocshared=" ${1} && sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1} || sed -i "1s/^/%nprocshared=${CORE}\n/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
# sed -i "s/%chk=.*chk/%chk=$CD${1%com}chk/" ${1}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}MB/" ${1}
fi
fi
if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N ${NMFL:0:15} -v in=${1} ~/bin/.rng"
echo "Cores: $CORE; Memory: $MEM; Cue: $CUE; Walltime: $WALLT; Gaussian-version: $GAUSS; Maxdisk: $MAXDISK"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi
if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
if [[ $FRC=1 ]]
then
out=$(qsub -p 100 -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng);
else
out=$(qsub -N "${NMFL:0:15}" -v in="${1%.com}" ~/bin/.rng);
fi
cp="$(pwd)"
if [[ -n $out ]]
then
echo "$(date -u +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/gd2613/jobs/}" >> $WLOG
echo "$(date -u +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/gd2613/jobs/}" >> $WLOGf
fi
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi
shift
done
write and quit
:wq
and then set the file as executable file
chmod +x gf
I've reduced the function name to gf, more similar to gv and shorter. A complete guide to the function is printed writing gf or gf ? or gf help in the terminal. The old rng file are no more need.
I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-" alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-" alias loadbh="source ~/.bashrc"
bhrc and gfunc have become my favorite commands quite soon!! And bhrc.old is my panic button, a perfect backup plan if you mess up something in the bashrc file.
Using The Script
To submit a job using the default parameters of the script simply type
gf jobname.com
where jobname.com is the name of the Gaussian input file. Note it is possible to use wildcards with this script, for example to simultaneously submit all input files in your current directory type
gf *.com
You can also submit jobs using different parameters (e.g to use a different number of processors) by using a .presets file. This file will be created in ~/bin the first time you run a job. An example of a .presets file is
## Here is where to list the preset for gaussian calculations ## Each line is a preset and it is written in this way : ## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK] ## e.g pqph;8;14400MB;119:59:00;d01;800GB ## ## ##----------------------------------------------------------------------------- ## ## presets starts from next line pqph;4;7500MB;119:59:00;d01;400GB pqph;16;64000MB;119:59:00;d01;400GB pqph;20;128000MB;119:59:00;d01;400GB
The uncommented lines contain adjustable parametes. For example the first uncommented line tell the script to submit to the pqph queue using 4 processors, 7500MB memory, 120 hours walltime, Gaussian version d01 and 400GB temporary space. To use one these presets type one of the following commands
gf -p0 jobname.com gf -p1 jobname.com gf -p2 jobname.com
Where jobname.com is the name of your input file. For the example .presets file; p0 uses the 4 core/7500MB parameters (the first uncommented line), p1 uses the 16 core/64000MB parameters (2nd uncommented line) and p2 uses the 20 core/128000MB parameters (3rd uncommented line).