From 34b247b9552a1080e1b5c223a1ab6fa087edbc32 Mon Sep 17 00:00:00 2001
From: Anne Philipp <anne.philipp@univie.ac.at>
Date: Fri, 12 Oct 2018 12:56:04 +0200
Subject: [PATCH] new installation
---
run/jobscripts/compilejob.ksh | 68 +++++++++++++++++++++++++++
run/jobscripts/job.ksh | 87 ++++++++++++++++++-----------------
run/run.sh | 8 ++--
setup.sh | 4 +-
templates/compilejob.template | 8 ++--
templates/job.temp | 76 ++++++++++++++++++++++++++++++
6 files changed, 200 insertions(+), 51 deletions(-)
create mode 100644 run/jobscripts/compilejob.ksh
create mode 100644 templates/job.temp
diff --git a/run/jobscripts/compilejob.ksh b/run/jobscripts/compilejob.ksh
new file mode 100644
index 0000000..566f03c
--- /dev/null
+++ b/run/jobscripts/compilejob.ksh
@@ -0,0 +1,68 @@
+#!/bin/ksh
+
+# ON ECGB:
+# start with ecaccess-job-submit -queueName ecgb NAME_OF_THIS_FILE on gateway server
+# start with sbatch NAME_OF_THIS_FILE directly on machine
+
+#SBATCH --workdir=/scratch/ms/at/km4a
+#SBATCH --qos=normal
+#SBATCH --job-name=flex_ecmwf
+#SBATCH --output=flex_ecmwf.%j.out
+#SBATCH --error=flex_ecmwf.%j.out
+#SBATCH --mail-type=FAIL
+#SBATCH --time=12:00:00
+
+## CRAY specific batch requests
+##PBS -N flex_ecmwf
+##PBS -q ns
+##PBS -S /usr/bin/ksh
+##PBS -o /scratch/ms/at/km4a/flex_ecmwf.${Jobname}.${Job_ID}.out
+# job output is in .ecaccess_DO_NOT_REMOVE
+##PBS -j oe
+##PBS -V
+##PBS -l EC_threads_per_task=1
+##PBS -l EC_memory_per_task=3200MB
+
+set -x
+export VERSION=7.1
+case ${HOST} in
+ *ecg*)
+# module load python
+# module unload grib_api
+ module unload emos
+# module load grib_api/1.14.5
+ module load emos/437-r64
+ export FLEXPART_ROOT_SCRIPTS=${HOME}
+ export MAKEFILE=Makefile.gfortran
+ ;;
+ *cca*)
+ module switch PrgEnv-cray PrgEnv-intel
+ module load grib_api
+ module load emos
+ module load python
+ echo ${GROUP}
+ echo ${HOME}
+ echo ${HOME} | awk -F / '{print $1, $2, $3, $4}'
+ export GROUP=`echo ${HOME} | awk -F / '{print $4}'`
+ export SCRATCH=/scratch/ms/${GROUP}/${USER}
+ export FLEXPART_ROOT_SCRIPTS=${HOME}
+ export MAKEFILE=Makefile.gfortran
+ ;;
+esac
+
+mkdir -p ${FLEXPART_ROOT_SCRIPTS}/flex_extract_v${VERSION}
+cd ${FLEXPART_ROOT_SCRIPTS}/flex_extract_v${VERSION} # if FLEXPART_ROOT is not set this means cd to the home directory
+tar -xvf ${HOME}/flex_extract_v${VERSION}.tar
+cd source/fortran
+\rm *.o *.mod CONVERT2
+make -f ${MAKEFILE} >flexcompile 2>flexcompile
+
+ls -l CONVERT2 >>flexcompile
+if [ $? -eq 0 ]; then
+ echo 'SUCCESS!' >>flexcompile
+ mail -s flexcompile.${HOST}.$$ ${USER} <flexcompile
+else
+ echo Environment: >>flexcompile
+ env >> flexcompile
+ mail -s "ERROR! flexcompile.${HOST}.$$" ${USER} <flexcompile
+fi
diff --git a/run/jobscripts/job.ksh b/run/jobscripts/job.ksh
index 7a7b1e4..dbe90c8 100644
--- a/run/jobscripts/job.ksh
+++ b/run/jobscripts/job.ksh
@@ -16,7 +16,7 @@
##PBS -N flex_ecmwf
##PBS -q np
##PBS -S /usr/bin/ksh
-## -o /scratch/ms/spatlh00/lh0/flex_ecmwf.$PBS_JOBID.out
+## -o /scratch/ms/at/km4a/flex_ecmwf.${PBS_JOBID}.out
## job output is in .ecaccess_DO_NOT_REMOVE
##PBS -j oe
##PBS -V
@@ -25,7 +25,7 @@
set -x
export VERSION=7.1
-case $HOST in
+case ${HOST} in
*ecg*)
module load python
module unload grib_api
@@ -39,95 +39,100 @@ case $HOST in
module load grib_api
module load emos
module load python
- export SCRATCH=$TMPDIR
+ export SCRATCH=${TMPDIR}
export PATH=${PATH}:${HOME}/flex_extract_v7.1/source/python
;;
esac
-cd $SCRATCH
+cd ${SCRATCH}
mkdir -p python$$
cd python$$
export CONTROL=CONTROL
-cat >$CONTROL<<EOF
-accuracy 16
+cat >${CONTROL}<<EOF
+accmaxstep 12
+acctime 06/18
+acctype FC
+accuracy 24
addpar 186 187 188 235 139 39
area
basetime None
-controlfile CONTROL.temp
+controlfile CONTROL_EA5.testgrid
cwc 0
+dataset None
date_chunk 3
debug 1
destination annep@genericSftp
dpdeta 1
-dtime 3
+dtime 1
ecfsdir ectmp:/${USER}/econdemand/
ecgid at
ecstorage 0
ectrans 1
ecuid km4a
-end_date 20120908
-eta 0
+end_date 20180108
+eta 1
etadiff 0
etapar 77
expver 1
format GRIB1
gateway srvx8.img.univie.ac.at
-gauss 1
+gauss 0
+gaussian
grib2flexpart 0
-grid 5000
-inputdir ../../run/workspace/test
+grid 1000
+inputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace
install_target None
job_template job.temp
-left -15000
-level 60
-levelist 40/to/60
-logicals gauss omega omegadiff eta etadiff dpdeta cwc wrf grib2flexpart ecstorage ectrans debug request
-lower 30000
+left -5000
+level 137
+levelist 100/to/137
+logicals gauss omega omegadiff eta etadiff dpdeta cwc wrf grib2flexpart ecstorage ectrans debug request public
+lower 10000
mailfail ${USER}
mailops ${USER}
makefile Makefile.gfortran
-marsclass EI
-maxstep 11
+marsclass EA
+maxstep 0
number OFF
omega 0
omegadiff 0
-outputdir ../../run/workspace/test
-ppid 41511
-prefix EI
-queue local
-request 1
-resol 63
-right 45000
+outputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace
+prefix EA
+public 0
+queue ecgate
+request 2
+resol 159
+right 5000
smooth 0
-start_date 20120908
-step 00 01 02 03 04 05 00 07 08 09 10 11 00 01 02 03 04 05 00 07 08 09 10 11
+start_date 20180108
+step 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
stream OPER
-time 00 00 00 00 00 00 06 00 00 00 00 00 12 12 12 12 12 12 18 12 12 12 12 12
-type AN FC FC FC FC FC AN FC FC FC FC FC AN FC FC FC FC FC AN FC FC FC FC FC
-upper 75000
+time 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23
+type AN AN AN AN AN AN AN AN AN AN AN AN AN AN AN AN AN AN AN AN AN AN AN AN
+upper 20000
wrf 0
EOF
-submit.py --controlfile=$CONTROL --inputdir=./work --outputdir=./work 1> prot 2>&1
+submit.py --controlfile=${CONTROL} --inputdir=./work --outputdir=./work 1> prot 2>&1
if [ $? -eq 0 ] ; then
l=0
- for muser in `grep -i MAILOPS $CONTROL`; do
- if [ $l -gt 0 ] ; then
- mail -s flex.${HOST}.$$ $muser <prot
+ for muser in `grep -i MAILOPS ${CONTROL}`; do
+ if [ ${l} -gt 0 ] ; then
+ mail -s flex.${HOST}.$$ ${muser} <prot
fi
- l=$(($l+1))
+ l=$((${l}+1))
done
else
l=0
- for muser in `grep -i MAILFAIL $CONTROL`; do
- if [ $l -gt 0 ] ; then
- mail -s "ERROR! flex.${HOST}.$$" $muser <prot
+ for muser in `grep -i MAILFAIL ${CONTROL}`; do
+ if [ ${l} -gt 0 ] ; then
+ mail -s "ERROR! flex.${HOST}.$$" ${muser} <prot
fi
- l=$(($l+1))
+ l=$((${l}+1))
done
fi
diff --git a/run/run.sh b/run/run.sh
index 65acf26..045b343 100755
--- a/run/run.sh
+++ b/run/run.sh
@@ -14,20 +14,20 @@
# THE USER HAS TO SPECIFY THESE PARAMETER
#
-QUEUE=None
-START_DATE='20120908'
+QUEUE='ecgate'
+START_DATE='20180108'
END_DATE=None
DATE_CHUNK=None
BASETIME=None
STEP=None
LEVELIST=None
AREA=None
-INPUTDIR='/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace/test3'
+INPUTDIR=''
OUTPUTDIR=None
FLEXPART_ROOT_SCRIPTS=None
PP_ID=None
JOB_TEMPLATE='job.temp'
-CONTROLFILE='CONTROL_EA5'
+CONTROLFILE='CONTROL_EA5.testgrid'
DEBUG=1
REQUEST=2
PUBLIC=0
diff --git a/setup.sh b/setup.sh
index 18d3395..013ece4 100755
--- a/setup.sh
+++ b/setup.sh
@@ -19,8 +19,8 @@ ECGID='at'
GATEWAY='srvx8.img.univie.ac.at'
DESTINATION='annep@genericSftp'
FLEXPART_ROOT_SCRIPTS=""
-JOB_TEMPLATE="job.temp.o"
-CONTROLFILE="CONTROL.test"
+JOB_TEMPLATE="job.template"
+CONTROLFILE="CONTROL_EA5.testgrid"
# -----------------------------------------------------------------
#
# AFTER THIS LINE THE USER DOES NOT HAVE TO CHANGE ANYTHING !!!
diff --git a/templates/compilejob.template b/templates/compilejob.template
index e75a9aa..927633a 100644
--- a/templates/compilejob.template
+++ b/templates/compilejob.template
@@ -27,10 +27,10 @@ set -x
export VERSION=$version_number
case $${HOST} in
*ecg*)
- module load python
- module unload grib_api
+# module load python
+# module unload grib_api
module unload emos
- module load grib_api/1.14.5
+# module load grib_api/1.14.5
module load emos/437-r64
export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
export MAKEFILE=$makefile
@@ -53,7 +53,7 @@ esac
mkdir -p $${FLEXPART_ROOT_SCRIPTS}/flex_extract_v$${VERSION}
cd $${FLEXPART_ROOT_SCRIPTS}/flex_extract_v$${VERSION} # if FLEXPART_ROOT is not set this means cd to the home directory
tar -xvf $${HOME}/flex_extract_v$${VERSION}.tar
-cd src
+cd source/fortran
\rm *.o *.mod $fortran_program
make -f $${MAKEFILE} >flexcompile 2>flexcompile
diff --git a/templates/job.temp b/templates/job.temp
new file mode 100644
index 0000000..ae3ac9a
--- /dev/null
+++ b/templates/job.temp
@@ -0,0 +1,76 @@
+#!/bin/ksh
+
+# ON ECGB:
+# start with ecaccess-job-submit -queueName ecgb NAME_OF_THIS_FILE on gateway server
+# start with sbatch NAME_OF_THIS_FILE directly on machine
+
+#SBATCH --workdir=/scratch/ms/at/km4a
+#SBATCH --qos=normal
+#SBATCH --job-name=flex_ecmwf
+#SBATCH --output=flex_ecmwf.%j.out
+#SBATCH --error=flex_ecmwf.%j.out
+#SBATCH --mail-type=FAIL
+#SBATCH --time=12:00:00
+
+## CRAY specific batch requests
+##PBS -N flex_ecmwf
+##PBS -q np
+##PBS -S /usr/bin/ksh
+## -o /scratch/ms/at/km4a/flex_ecmwf.${PBS_JOBID}.out
+## job output is in .ecaccess_DO_NOT_REMOVE
+##PBS -j oe
+##PBS -V
+##PBS -l EC_threads_per_task=24
+##PBS -l EC_memory_per_task=32000MB
+
+set -x
+export VERSION=7.1
+case ${HOST} in
+ *ecg*)
+ module load python
+ module unload grib_api
+ module unload emos
+ module load grib_api/1.14.5
+ module load emos/437-r64
+ export PATH=${PATH}:${HOME}/flex_extract_v7.1/source/python
+ ;;
+ *cca*)
+ module switch PrgEnv-cray PrgEnv-intel
+ module load grib_api
+ module load emos
+ module load python
+ export SCRATCH=${TMPDIR}
+ export PATH=${PATH}:${HOME}/flex_extract_v7.1/source/python
+ ;;
+esac
+
+cd ${SCRATCH}
+mkdir -p python$$
+cd python$$
+
+export CONTROL=CONTROL
+
+cat >${CONTROL}<<EOF
+EOF
+
+
+submit.py --controlfile=${CONTROL} --inputdir=./work --outputdir=./work 1> prot 2>&1
+
+if [ $? -eq 0 ] ; then
+ l=0
+ for muser in `grep -i MAILOPS ${CONTROL}`; do
+ if [ ${l} -gt 0 ] ; then
+ mail -s flex.${HOST}.$$ ${muser} <prot
+ fi
+ l=$((${l}+1))
+ done
+else
+ l=0
+ for muser in `grep -i MAILFAIL ${CONTROL}`; do
+ if [ ${l} -gt 0 ] ; then
+ mail -s "ERROR! flex.${HOST}.$$" ${muser} <prot
+ fi
+ l=$((${l}+1))
+ done
+fi
+
--
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