From c5074d295840f29091c45f8333ce650ad2a25ccd Mon Sep 17 00:00:00 2001
From: Anne Philipp <anne.philipp@univie.ac.at>
Date: Tue, 9 Oct 2018 22:42:16 +0200
Subject: [PATCH] added making of namelist file and jobscript via genshi
templates
---
run/jobscripts/compilejob.ksh | 78 -------------------
source/python/_config.py | 3 +-
source/python/classes/EcFlexpart.py | 54 +++++++------
source/python/install.py | 77 ++++++------------
source/python/mods/prepare_flexpart.py | 2 +-
source/pythontest/TestData/CONTROL.temp | 2 +-
source/pythontest/TestData/compilejob.test | 24 +++---
source/pythontest/TestData/convert.nl.test | 19 +++++
.../pythontest/TestData/job.temp.test | 34 ++++----
source/pythontest/TestEcFlexpart.py | 35 +++++++--
source/pythontest/TestInstall.py | 26 ++++++-
templates/compilejob.temp | 77 ------------------
templates/compilejob.template | 30 +++----
templates/convert.nl | 19 +++++
templates/{job.temp.o => job.template} | 41 +++++-----
15 files changed, 216 insertions(+), 305 deletions(-)
delete mode 100644 run/jobscripts/compilejob.ksh
create mode 100644 source/pythontest/TestData/convert.nl.test
rename templates/job.temp => source/pythontest/TestData/job.temp.test (57%)
delete mode 100644 templates/compilejob.temp
create mode 100644 templates/convert.nl
rename templates/{job.temp.o => job.template} (55%)
diff --git a/run/jobscripts/compilejob.ksh b/run/jobscripts/compilejob.ksh
deleted file mode 100644
index 027c087..0000000
--- a/run/jobscripts/compilejob.ksh
+++ /dev/null
@@ -1,78 +0,0 @@
-#!/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
-# -o /scratch/ms/no/sbc/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 src
-\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/source/python/_config.py b/source/python/_config.py
index 3ce4c73..05f1ecc 100644
--- a/source/python/_config.py
+++ b/source/python/_config.py
@@ -37,10 +37,11 @@ TEMPFILE_USER_ENVVARS = 'ECMWF_ENV.template'
FILE_USER_ENVVARS = 'ECMWF_ENV'
TEMPFILE_INSTALL_COMPILEJOB = 'compilejob.template'
FILE_INSTALL_COMPILEJOB = 'compilejob.ksh'
-TEMPFILE_INSTALL_JOB = 'job.temp.o'
+TEMPFILE_INSTALL_JOB = 'job.template'
TEMPFILE_JOB = 'job.temp'
FILE_JOB_OD = 'job.ksh'
FILE_JOB_OP = 'jopoper.ksh'
+TEMPFILE_NAMELIST = 'convert.nl'
FILE_NAMELIST = 'fort.4'
FILE_GRIB_INDEX = 'date_time_stepRange.idx'
FILE_GRIBTABLE = 'ecmwf_grib1_table_128'
diff --git a/source/python/classes/EcFlexpart.py b/source/python/classes/EcFlexpart.py
index eece37d..b90c8ec 100644
--- a/source/python/classes/EcFlexpart.py
+++ b/source/python/classes/EcFlexpart.py
@@ -657,7 +657,7 @@ class EcFlexpart(object):
return
- def write_namelist(self, c, filename):
+ def write_namelist(self, c):
'''
@Description:
Creates a namelist file in the temporary directory and writes
@@ -682,6 +682,13 @@ class EcFlexpart(object):
<nothing>
'''
+ from genshi.template.text import NewTextTemplate
+ from genshi.template import TemplateLoader
+
+ loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False)
+ compile_template = loader.load(_config.TEMPFILE_NAMELIST,
+ cls=NewTextTemplate)
+
self.inputdir = c.inputdir
area = np.asarray(self.area.split('/')).astype(float)
grid = np.asarray(self.grid.split('/')).astype(float)
@@ -691,27 +698,30 @@ class EcFlexpart(object):
maxl = int((area[3] - area[1]) / grid[1]) + 1
maxb = int((area[0] - area[2]) / grid[0]) + 1
- with open(self.inputdir + '/' + filename, 'w') as f:
- f.write('&NAMGEN\n')
- f.write(',\n '.join(['maxl = ' + str(maxl), 'maxb = ' + str(maxb),
- 'mlevel = ' + str(self.level),
- 'mlevelist = ' + '"' + str(self.levelist)
- + '"',
- 'mnauf = ' + str(self.resol),
- 'metapar = ' + '77',
- 'rlo0 = ' + str(area[1]),
- 'rlo1 = ' + str(area[3]),
- 'rla0 = ' + str(area[2]),
- 'rla1 = ' + str(area[0]),
- 'momega = ' + str(c.omega),
- 'momegadiff = ' + str(c.omegadiff),
- 'mgauss = ' + str(c.gauss),
- 'msmooth = ' + str(c.smooth),
- 'meta = ' + str(c.eta),
- 'metadiff = ' + str(c.etadiff),
- 'mdpdeta = ' + str(c.dpdeta)]))
-
- f.write('\n/\n')
+ stream = compile_template.generate(
+ maxl = str(maxl),
+ maxb = str(maxb),
+ mlevel = str(self.level),
+ mlevelist = str(self.levelist),
+ mnauf = str(self.resol),
+ metapar = '77',
+ rlo0 = str(area[1]),
+ rlo1 = str(area[3]),
+ rla0 = str(area[2]),
+ rla1 = str(area[0]),
+ momega = str(c.omega),
+ momegadiff = str(c.omegadiff),
+ mgauss = str(c.gauss),
+ msmooth = str(c.smooth),
+ meta = str(c.eta),
+ metadiff = str(c.etadiff),
+ mdpdeta = str(c.dpdeta)
+ )
+
+ namelistfile = os.path.join(self.inputdir, _config.FILE_NAMELIST)
+
+ with open(namelistfile, 'w') as f:
+ f.write(stream.render('text'))
return
diff --git a/source/python/install.py b/source/python/install.py
index b624592..cbef571 100755
--- a/source/python/install.py
+++ b/source/python/install.py
@@ -395,8 +395,8 @@ def mk_compilejob(makefile, target, ecuid, ecgid, fp_root):
fp_root = '$HOME'
stream = compile_template.generate(
- username = ecuid,
usergroup = ecgid,
+ username = ecuid,
version_number = _config._VERSION_STR,
fp_root_scripts = fp_root,
makefile = makefile,
@@ -409,36 +409,6 @@ def mk_compilejob(makefile, target, ecuid, ecgid, fp_root):
with open(compilejob, 'w') as f:
f.write(stream.render('text'))
-
- # template = os.path.join(_config.PATH_REL_TEMPLATES,
- # _config.TEMPFILE_INSTALL_COMPILEJOB)
- # with open(template) as f:
- # fdata = f.read().split('\n')
-
-
- # with open(compilejob, 'w') as fo:
- # for data in fdata:
- # if 'MAKEFILE=' in data:
- # data = 'export MAKEFILE=' + makefile
- # elif 'FLEXPART_ROOT_SCRIPTS=' in data:
- # if fp_root != '../':
- # data = 'export FLEXPART_ROOT_SCRIPTS=' + fp_root
- # else:
- # data = 'export FLEXPART_ROOT_SCRIPTS=$HOME'
- # elif target.lower() != 'local':
- # if '--workdir' in data:
- # data = '#SBATCH --workdir=/scratch/ms/' + \
- # ecgid + '/' + ecuid
- # elif '##PBS -o' in data:
- # data = '##PBS -o /scratch/ms/' + ecgid + '/' + ecuid + \
- # 'flex_ecmwf.$Jobname.$Job_ID.out'
- # elif 'FLEXPART_ROOT_SCRIPTS=' in data:
- # if fp_root != '../':
- # data = 'export FLEXPART_ROOT_SCRIPTS=' + fp_root
- # else:
- # data = 'export FLEXPART_ROOT_SCRIPTS=$HOME'
- # fo.write(data + '\n')
-
return
def mk_job_template(ecuid, ecgid, gateway, destination, fp_root):
@@ -469,27 +439,30 @@ def mk_job_template(ecuid, ecgid, gateway, destination, fp_root):
@Return:
<nothing>
'''
- fp_root_path_to_python = os.path.join(fp_root, _config.FLEXEXTRACT_DIRNAME,
- _config.PATH_REL_PYTHON)
-
- template = os.path.join(_config.PATH_REL_TEMPLATES,
- _config.TEMPFILE_INSTALL_JOB)
- with open(template) as f:
- fdata = f.read().split('\n')
-
- jobfile_temp = os.path.join(_config.PATH_REL_TEMPLATES,
- _config.TEMPFILE_JOB)
- with open(jobfile_temp, 'w') as fo:
- for data in fdata:
- if '--workdir' in data:
- data = '#SBATCH --workdir=/scratch/ms/' + ecgid + '/' + ecuid
- elif '##PBS -o' in data:
- data = '##PBS -o /scratch/ms/' + ecgid + '/' + \
- ecuid + 'flex_ecmwf.$Jobname.$Job_ID.out'
- elif 'export PATH=${PATH}:' in data:
- data += fp_root_path_to_python
-
- fo.write(data + '\n')
+ from genshi.template.text import NewTextTemplate
+ from genshi.template import TemplateLoader
+
+ loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False)
+ compile_template = loader.load(_config.TEMPFILE_INSTALL_JOB,
+ cls=NewTextTemplate)
+
+ fp_root_path_to_python = os.path.join(fp_root,
+ _config.FLEXEXTRACT_DIRNAME,
+ _config.PATH_REL_PYTHON)
+
+ stream = compile_template.generate(
+ usergroup = ecgid,
+ username = ecuid,
+ version_number = _config._VERSION_STR,
+ fp_root_path = fp_root_path_to_python,
+ )
+
+ tempjobfile = os.path.join(_config.PATH_TEMPLATES,
+ _config.TEMPFILE_JOB)
+
+ with open(tempjobfile, 'w') as f:
+ f.write(stream.render('text'))
+
return
def delete_convert_build(src_path):
diff --git a/source/python/mods/prepare_flexpart.py b/source/python/mods/prepare_flexpart.py
index a3ca22b..c45c32f 100755
--- a/source/python/mods/prepare_flexpart.py
+++ b/source/python/mods/prepare_flexpart.py
@@ -159,7 +159,7 @@ def prepare_flexpart(ppid, c):
# deaccumulate the flux data
flexpart = EcFlexpart(c, fluxes=True)
- flexpart.write_namelist(c, _config.FILE_NAMELIST)
+ flexpart.write_namelist(c)
flexpart.deacc_fluxes(inputfiles, c)
# get a list of all files from the root inputdir
diff --git a/source/pythontest/TestData/CONTROL.temp b/source/pythontest/TestData/CONTROL.temp
index c3d0974..d5f4137 100644
--- a/source/pythontest/TestData/CONTROL.temp
+++ b/source/pythontest/TestData/CONTROL.temp
@@ -8,7 +8,7 @@ CLASS EI
STREAM OPER
NUMBER OFF
EXPVER 1
-GRID 5000
+GRID 1000
LEFT -15000
LOWER 30000
UPPER 75000
diff --git a/source/pythontest/TestData/compilejob.test b/source/pythontest/TestData/compilejob.test
index 8ae61bf..9f9a5a1 100644
--- a/source/pythontest/TestData/compilejob.test
+++ b/source/pythontest/TestData/compilejob.test
@@ -16,7 +16,7 @@
##PBS -N flex_ecmwf
##PBS -q ns
##PBS -S /usr/bin/ksh
-##PBS -o /scratch/ms/testgroup/testuser/flex_ecmwf.$Jobname.$Job_ID.out
+##PBS -o /scratch/ms/testgroup/testuser/flex_ecmwf.${Jobname}.${Job_ID}.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
@@ -42,27 +42,27 @@ case $HOST in
module load python
echo ${GROUP}
echo ${HOME}
- echo $HOME | awk -F / '{print $1, $2, $3, $4}'
- export GROUP=`echo $HOME | awk -F / '{print $4}'`
+ 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=p_root_test_path
+ export FLEXPART_ROOT_SCRIPTS=fp_root_test_path
export MAKEFILE=Makefile.TEST
;;
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
+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
\rm *.o *.mod CONVERT2
-make -f $MAKEFILE >flexcompile 2>flexcompile
+make -f ${MAKEFILE} >flexcompile 2>flexcompile
ls -l CONVERT2 >>flexcompile
if [ $? -eq 0 ]; then
echo 'SUCCESS!' >>flexcompile
- mail -s flexcompile.$HOST.$$ $USER <flexcompile
+ mail -s flexcompile.${HOST}.$$ ${USER} <flexcompile
else
echo Environment: >>flexcompile
env >> flexcompile
- mail -s "ERROR! flexcompile.$HOST.$$" $USER <flexcompile
-fi
\ No newline at end of file
+ mail -s "ERROR! flexcompile.${HOST}.$$" ${USER} <flexcompile
+fi
diff --git a/source/pythontest/TestData/convert.nl.test b/source/pythontest/TestData/convert.nl.test
new file mode 100644
index 0000000..6134989
--- /dev/null
+++ b/source/pythontest/TestData/convert.nl.test
@@ -0,0 +1,19 @@
+&NAMGEN
+ maxl = 61,
+ maxb = 46,
+ mlevel = 60,
+ mlevelist = "55/to/60",
+ mnauf = 63,
+ metapar = 77,
+ rlo0 = -15.0,
+ rlo1 = 45.0,
+ rla0 = 30.0,
+ rla1 = 75.0,
+ momega = 0,
+ momegadiff = 0,
+ mgauss = 1,
+ msmooth = 0,
+ meta = 0,
+ metadiff = 0,
+ mdpdeta = 1
+/
diff --git a/templates/job.temp b/source/pythontest/TestData/job.temp.test
similarity index 57%
rename from templates/job.temp
rename to source/pythontest/TestData/job.temp.test
index 43becc4..4103775 100644
--- a/templates/job.temp
+++ b/source/pythontest/TestData/job.temp.test
@@ -4,7 +4,7 @@
# start with ecaccess-job-submit -queueName ecgb NAME_OF_THIS_FILE on gateway server
# start with sbatch NAME_OF_THIS_FILE directly on machine
-#SBATCH --workdir=/scratch/ms/at/km4a
+#SBATCH --workdir=/scratch/ms/testgroup/testuser
#SBATCH --qos=normal
#SBATCH --job-name=flex_ecmwf
#SBATCH --output=flex_ecmwf.%j.out
@@ -16,7 +16,7 @@
##PBS -N flex_ecmwf
##PBS -q np
##PBS -S /usr/bin/ksh
-## -o /scratch/ms/spatlh00/lh0/flex_ecmwf.$PBS_JOBID.out
+## -o /scratch/ms/testgroup/testuser/flex_ecmwf.${PBS_JOBID}.out
## job output is in .ecaccess_DO_NOT_REMOVE
##PBS -j oe
##PBS -V
@@ -25,52 +25,52 @@
set -x
export VERSION=7.1
-case $HOST in
+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}:${HOME}/flex_extract_v7.1/source/python
+ export PATH=${PATH}:fp_root_test_path/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}:${HOME}/flex_extract_v7.1/source/python
+ export SCRATCH=${TMPDIR}
+ export PATH=${PATH}:fp_root_test_path/flex_extract_v7.1/source/python
;;
esac
-cd $SCRATCH
+cd ${SCRATCH}
mkdir -p python$$
cd python$$
export CONTROL=CONTROL
-cat >$CONTROL<<EOF
+cat >${CONTROL}<<EOF
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/source/pythontest/TestEcFlexpart.py b/source/pythontest/TestEcFlexpart.py
index e1b7a9c..49f5161 100644
--- a/source/pythontest/TestEcFlexpart.py
+++ b/source/pythontest/TestEcFlexpart.py
@@ -3,23 +3,44 @@
import sys
+import os
+import inspect
import pytest
sys.path.append('../python')
+import _config
from classes.EcFlexpart import EcFlexpart
+from classes.ControlFile import ControlFile
+from mods.tools import silent_remove
class TestEcFlexpart():
'''
'''
- def test_init(self):
- # create an instance of EcFlexpart and get a dictionary of the
- # class attributes, compare this dict with an expected dict!
- assert True == True
-
def test_write_namelist(self):
- # simple
- assert True == True
+ import filecmp
+
+ control_file = os.path.join(_config.PATH_TEST_DIR,
+ 'TestData',
+ 'CONTROL.temp')
+ c = ControlFile(control_file)
+ flexpart = EcFlexpart(c)
+
+ c.inputdir = 'TestData'
+
+ # comparison file
+ testfile = os.path.join(_config.PATH_TEST_DIR,
+ 'TestData',
+ 'convert.nl.test')
+
+ # create
+ flexpart.write_namelist(c)
+
+ finalfile = os.path.join(c.inputdir, _config.FILE_NAMELIST)
+ assert filecmp.cmp(testfile, finalfile, shallow=False)
+
+ # delete test file
+ silent_remove(finalfile)
def test_retrieve(self):
# not sure how to check
diff --git a/source/pythontest/TestInstall.py b/source/pythontest/TestInstall.py
index ddb3b2d..c6995d2 100644
--- a/source/pythontest/TestInstall.py
+++ b/source/pythontest/TestInstall.py
@@ -24,8 +24,8 @@ class TestTools():
#! - mk_tarball
#! - un_tarball
#! - mk_env_vars
- # - mk_compilejob
- # - mk_job_template
+ #! - mk_compilejob
+ #! - mk_job_template
# - delete_convert_build
# - make_convert_build
@@ -154,3 +154,25 @@ class TestTools():
# delete test file
silent_remove(finalfile)
+
+ def test_mk_job_template(self):
+ import filecmp
+
+ # comparison file
+ testfile = os.path.join(_config.PATH_TEST_DIR,
+ 'TestData',
+ 'job.temp.test')
+
+ # create
+ install.mk_job_template('testuser',
+ 'testgroup',
+ 'gateway.test.ac.at',
+ 'dest@generic',
+ 'fp_root_test_path')
+
+ finalfile = os.path.join(_config.PATH_TEMPLATES,
+ _config.TEMPFILE_JOB)
+ assert filecmp.cmp(testfile, finalfile, shallow=False)
+
+ # delete test file
+ silent_remove(finalfile)
\ No newline at end of file
diff --git a/templates/compilejob.temp b/templates/compilejob.temp
deleted file mode 100644
index 715308b..0000000
--- a/templates/compilejob.temp
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/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/spatlh00/lh0
-#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
-# -o /scratch/ms/no/sbc/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=
- 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=
- export MAKEFILE=Makefile.CRAY
- ;;
-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
-\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.$$ $USER <flexcompile
-else
- echo Environment: >>flexcompile
- env >> flexcompile
- mail -s "ERROR! flexcompile.$HOST.$$" $USER <flexcompile
-fi
-
-
-
-
-
-
-
-
-
diff --git a/templates/compilejob.template b/templates/compilejob.template
index bb1348e..e75a9aa 100644
--- a/templates/compilejob.template
+++ b/templates/compilejob.template
@@ -16,7 +16,7 @@
##PBS -N flex_ecmwf
##PBS -q ns
##PBS -S /usr/bin/ksh
-##PBS -o /scratch/ms/$usergroup/$username/flex_ecmwf.$Jobname.$Job_ID.out
+##PBS -o /scratch/ms/$usergroup/$username/flex_ecmwf.$${Jobname}.$${Job_ID}.out
# job output is in .ecaccess_DO_NOT_REMOVE
##PBS -j oe
##PBS -V
@@ -25,7 +25,7 @@
set -x
export VERSION=$version_number
-case $HOST in
+case $${HOST} in
*ecg*)
module load python
module unload grib_api
@@ -40,29 +40,29 @@ case $HOST in
module load grib_api
module load emos
module load python
- echo ${GROUP}
- echo ${HOME}
- echo $HOME | awk -F / '{print $1, $2, $3, $4}'
- export GROUP=`echo $HOME | awk -F / '{print $4}'`
- export SCRATCH=/scratch/ms/${GROUP}/${USER}
+ echo $${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}/$${USER}
export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
export MAKEFILE=$makefile
;;
esac
-mkdir -p $FLEXPART_ROOT_SCRIPTS/flex_extract_v$VERSION
-cd $FLEXPART_ROOT_SCRIPTS/flex_extract_v$VERSION # if FLEXPART_ROOT is not set this means cd to the home directory
-tar -xvf $HOME/flex_extract_v$VERSION.tar
+mkdir -p $${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$${VERSION}.tar
cd src
\rm *.o *.mod $fortran_program
-make -f $MAKEFILE >flexcompile 2>flexcompile
+make -f $${MAKEFILE} >flexcompile 2>flexcompile
ls -l $fortran_program >>flexcompile
-if [ $? -eq 0 ]; then
+if [ $$? -eq 0 ]; then
echo 'SUCCESS!' >>flexcompile
- mail -s flexcompile.$HOST.$$ $USER <flexcompile
+ mail -s flexcompile.$${HOST}.$$$$ $${USER} <flexcompile
else
echo Environment: >>flexcompile
env >> flexcompile
- mail -s "ERROR! flexcompile.$HOST.$$" $USER <flexcompile
-fi
\ No newline at end of file
+ mail -s "ERROR! flexcompile.$${HOST}.$$$$" $${USER} <flexcompile
+fi
diff --git a/templates/convert.nl b/templates/convert.nl
new file mode 100644
index 0000000..c0c8fa4
--- /dev/null
+++ b/templates/convert.nl
@@ -0,0 +1,19 @@
+&NAMGEN
+ maxl = $maxl,
+ maxb = $maxb,
+ mlevel = $mlevel,
+ mlevelist = "$mlevelist",
+ mnauf = $mnauf,
+ metapar = $metapar,
+ rlo0 = $rlo0,
+ rlo1 = $rlo1,
+ rla0 = $rla0,
+ rla1 = $rla1,
+ momega = $momega,
+ momegadiff = $momegadiff,
+ mgauss = $mgauss,
+ msmooth = $msmooth,
+ meta = $meta,
+ metadiff = $metadiff,
+ mdpdeta = $mdpdeta
+/
diff --git a/templates/job.temp.o b/templates/job.template
similarity index 55%
rename from templates/job.temp.o
rename to templates/job.template
index fbdbd81..16e016e 100644
--- a/templates/job.temp.o
+++ b/templates/job.template
@@ -4,7 +4,7 @@
# start with ecaccess-job-submit -queueName ecgb NAME_OF_THIS_FILE on gateway server
# start with sbatch NAME_OF_THIS_FILE directly on machine
-#SBATCH --workdir=/scratch/ms/spatlh00/lh0
+#SBATCH --workdir=/scratch/ms/$usergroup/$username
#SBATCH --qos=normal
#SBATCH --job-name=flex_ecmwf
#SBATCH --output=flex_ecmwf.%j.out
@@ -16,7 +16,7 @@
##PBS -N flex_ecmwf
##PBS -q np
##PBS -S /usr/bin/ksh
-## -o /scratch/ms/spatlh00/lh0/flex_ecmwf.$PBS_JOBID.out
+## -o /scratch/ms/$usergroup/$username/flex_ecmwf.$${PBS_JOBID}.out
## job output is in .ecaccess_DO_NOT_REMOVE
##PBS -j oe
##PBS -V
@@ -24,52 +24,53 @@
##PBS -l EC_memory_per_task=32000MB
set -x
-export VERSION=7.1
-case $HOST in
+export VERSION=$version_number
+case $${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}:
+ export PATH=$${PATH}:$fp_root_path
;;
*cca*)
module switch PrgEnv-cray PrgEnv-intel
module load grib_api
module load emos
module load python
- export SCRATCH=$TMPDIR
- export PATH=${PATH}:
+ export SCRATCH=$${TMPDIR}
+ export PATH=$${PATH}:$fp_root_path
;;
esac
-cd $SCRATCH
-mkdir -p python$$
-cd python$$
+cd $${SCRATCH}
+mkdir -p python$$$$
+cd python$$$$
export CONTROL=CONTROL
-cat >$CONTROL<<EOF
+cat >$${CONTROL}<<EOF
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
+
--
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