Fix for spack

blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/main

+#!/bin/bash -l
+#SBATCH --partition=alcc1,epyc
+#SBATCH -o __runDir__/__mainJobName__.%j.%N.out
+#SBATCH -D __runDir__
+#SBATCH -J __mainJobName__
+#SBATCH --nodes=3
+#SBATCH --ntasks-per-node=28
+#SBATCH --mem-per-cpu=2000
+#SBATCH --mail-type=FAIL
+#SBATCH --mail-user=christoph.knote@med.uni-augsburg.de
+#SBATCH --time=18:00:00

blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/post

+#!/bin/bash -l
+#SBATCH --partition=alcc1
+#SBATCH -o __runDir__/__postJobName__.%j.%N.out
+#SBATCH -D __runDir__
+#SBATCH -J __postJobName__
+#SBATCH --ntasks=1
+#SBATCH --mem=5G
+#SBATCH --mail-type=FAIL
+#SBATCH --mail-user=christoph.knote@med.uni-augsburg.de
+#SBATCH --time=02:00:00

blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/pre

+#!/bin/bash -l
+#SBATCH --partition=alcc1
+#SBATCH -o __runDir__/__preJobName__.%j.%N.out
+#SBATCH -D __runDir__
+#SBATCH -J __preJobName__
+#SBATCH --ntasks=1
+#SBATCH --mem=10G
+#SBATCH --mail-type=FAIL
+#SBATCH --mail-user=christoph.knote@med.uni-augsburg.de
+#SBATCH --time=03:00:00

blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/spinup

+#!/bin/bash -l
+#SBATCH --partition=alcc1,epyc
+#SBATCH -o __runDir__/__spinupJobName__.%j.%N.out
+#SBATCH -D __runDir__
+#SBATCH -J __spinupJobName__
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=28
+#SBATCH --mem-per-cpu=2000
+#SBATCH --mail-type=FAIL
+#SBATCH --mail-user=christoph.knote@med.uni-augsburg.de
+#SBATCH --time=01:00:00

blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/staging

+#!/bin/bash -l
+#SBATCH --partition=alcc1
+#SBATCH -o __runDir__/__stagingJobName__.%j.%N.out
+#SBATCH -D __runDir__
+#SBATCH -J __stagingJobName__
+#SBATCH --ntasks=1
+#SBATCH --mem=5G
+#SBATCH --mail-type=FAIL
+#SBATCH --mail-user=christoph.knote@med.uni-augsburg.de
+#SBATCH --time=01:00:00

blueprints/operational_chemistry/machine_specific/alcc_spack/config.bash

+#!/bin/bash
+# ------------------------------------------------------------------------------
+# WRFOTRON v 2.0b
+# Christoph Knote (LMU Munich, Germany)
+# 06/2016
+# christoph.knote@lmu.de
+# ------------------------------------------------------------------------------
+
+# path to the WRFotron installation
+chainDir=${HOME}/wrfotron
+
+# --- Executable locations ---
+
+# WPS installation directory
+WPSDir=${WPS_SRC_PATH}
+# WRF installation directory
+WRFDir=${WRF_SRC_PATH}
+
+# --- Input data settings ---
+
+# path to geogrid input data
+geogDir=/alcc/gpfs2/home/mbees/data/geog/
+
+# meteo input
+# Vtable for the chosen meteo input
+metVtableFile=${WPS_SRC_PATH}/ungrib/Variable_Tables/Vtable.GFS
+# time increment in hours
+metInc=1
+# full path to a met input file - you can use any "%<>" abbreviations known
+# to the "date" command
+metFilePattern="/alcc/gpfs2/home/mbees/data/meteo/GFS/GF%Y%m%d%H"
+# example:
+# "/glade/p/rda/data/ds083.2/grib2/%Y/%Y.%m/fnl_%Y%m%d_%H_00.grib2"
+
+# --- Pre/Postprocessing settings ---
+
+# prepararation script
+preScriptPath=NONEXISTENT.bash
+
+# postprocessing scripts (arbitrary)
+postScriptPath=NONEXISTENT.bash
+# postprocessing scripts (actions for each wrfout file)
+postPerFileScriptPath=NONEXISTENT.bash
+
+# --- Working directories ---
+
+# where the WRF will be run (some fast, large disk like "scratch" or similar)
+workDir=${SCRATCH}/WRF/work/
+
+# where the unprocessed WRF output will be stored
+stagingRootDir=${SCRATCH}/WRF/staging/
+# where the WRF output will be stored
+archiveRootDir=${SCRATCH}/archive/WRF/
+# where the WRF restart files will be stored
+restartRootDir=${SCRATCH}/WRF/restart/
+
+# remove run directory after run is finished?
+removeRunDir=false
+
+# --- MPI settings ---
+
+mpiCommandPre="mpirun /usr/bin/time -v"
+mpiCommandMain="mpirun /usr/bin/time -v"
+mpiCommandReal=${mpiCommandPre}
+
+# --- Batch system ---
+
+# argument to submit a job in a held state
+batchHoldArgument="--hold"
+# command to release a held job
+batchReleaseCommand="scontrol release"
+# command to submit jobs to the queueing system
+batchSubmitCommand=sbatch
+# dependency argument for chaining runs upon submission
+batchDepArgument="--dependency=afterok:__id__"
+# sed command ("used as s/__command/\1/") to retrieve job run PID upon
+# submission with $batchSubmitCommand
+batchPidSedCommand="Submitted batch job \(.*\)"
+
+# --- Chemistry ---
+
+withChemistry=true
+
+# WRF-Chem installation directory
+WRFChemDir=${WRF_CHEM_SRC_PATH}
+
+# path to utility executables
+meganBioEmissBin=megan_bio_emiss
+mozbcBin=mozbc
+weselyBin=wesely
+exo_coldensBin=exo_coldens
+anthro_emisBin=anthro_emis
+fire_emisBin=fire_emis
+
+# path to MEGAN input data
+MEGANdir=/alcc/gpfs2/home/mbees/data/emissions/biogenic/MEGAN
+
+# use anthro_emiss or predefined files?
+emissUseAnthroEmiss=false
+# raw emission input - the files you read in with anthro_emiss
+emissDir=/alcc/gpfs2/home/mbees/data/emissions/anthropogenic/EDGARv5/MOZART_MOSAIC
+# emission conversion script for anthro_emis - must match emissions in emissDir
+emissInpFile=emis_edgarv5_mozmos.inp
+# year the emissions are valid for (for offset calculation)
+emissYear=2015
+
+# FINN fires
+fireFilePattern="/alcc/gpfs2/home/mbees/data/emissions/fires/FINN/GLOB_MOZ4_%Y%j.txt"
+fireInpFile=finn_fires.inp
+
+# boundary condition input
+chembcFilePattern="/alcc/gpfs2/home/mbees/data/chembc/WACCM/WACCM%Y%m%d"
+chembcInpFile=waccm.inp
+
+# TUV photolysis option 4 data file
+TUVDataPath="/alcc/gpfs2/home/mbees/data/tuv/TUV.phot.bz2"

jobs/pre/20_chem_recreate_megan.bash

@@ -20,8 +20,7 @@ fi
 if [ ! -f ${workDir}/${experiment}/wrfbiochemi_d01 ]
 then
   echo "MEGAN input files do not not exist - recreating from scratch. Grab a coffee..."
-  ln -s ${WRFMEGANdir}/megan_bio_emiss .
-  ./megan_bio_emiss < megan_bio_emiss.inp > megan_bio_emiss.out
+  ${meganBioEmissBin} < megan_bio_emiss.inp > megan_bio_emiss.out
   for domain in $(seq -f "0%g" 1 ${max_dom})
   do
     meganDataFile=${workDir}/${experiment}/wrfbiochemi_d${domain}

jobs/pre/30_chem_wes_coldens.bash

@@ -2,8 +2,6 @@
 # Wesely, Exo_coldens
 # -----------------------------------------------------------------------------
 
-ln -s ${WRFmztoolsdir}/* .
+${weselyBin} < wesely.inp > wesely.out
 
-./wesely < wesely.inp > wesely.out
-
-./exo_coldens < exo_coldens.inp > exo_coldens.out
+${exo_coldensBin} < exo_coldens.inp > exo_coldens.out

jobs/pre/50_chem_anthro_emiss.bash

@@ -6,13 +6,11 @@ if [ "$emissUseAnthroEmiss" = "true" ]
 then
   if [ -f anthro_emis.inp ]
   then
-    # using anthro_emiss
-    ln -s ${WRFanthrodir}/anthro_emis .
     # difference in years for emission offset
     emissYearOffset=0
     let "emissYearOffset = __startYear__ - emissYear"
     sed -e "s/__emissYearOffset__/${emissYearOffset}/g" -i anthro_emis.inp
-    ./anthro_emis < anthro_emis.inp > anthro_emis.out
+    ${anthro_emisBin} < anthro_emis.inp > anthro_emis.out
   fi
 else
 if [ -f anthro_emis.inp ]
@@ -28,13 +26,11 @@ if [ -f anthro_emis.inp ]
 
     if [ ! -f ${workDir}/${experiment}/wrfchemi_d01 ]
     then
-        # using anthro_emiss
-        ln -s ${WRFanthrodir}/anthro_emis .
         # difference in years for emission offset
         emissYearOffset=0
         let "emissYearOffset = __startYear__ - emissYear"
         sed -e "s/__emissYearOffset__/${emissYearOffset}/g" -i anthro_emis.inp
-        ./anthro_emis < anthro_emis.inp > anthro_emis.out
+        ${anthro_emisBin} < anthro_emis.inp > anthro_emis.out
 
         for domain in $(seq -f "0%g" 1 ${max_dom})
         do

jobs/pre/60_chem_fire_emiss.bash

@@ -6,7 +6,6 @@
 # using fire_emis:
 if [ -f fire_emis.inp ]
 then
-  ln -s ${WRFfiredir}/fire_emis .
   
   ln -s $(dirname ${fireFilePattern})/*nc .
   
@@ -58,5 +57,5 @@ EOF
   fi
 
   /bin/sed -s "s/__domain__/${max_dom}/" -i fire_emis.inp
-  ./fire_emis < fire_emis.inp > fire_emis.out
+  ${fire_emisBin} < fire_emis.inp > fire_emis.out
 fi

jobs/pre/70_chem_mozbc.bash

@@ -4,7 +4,6 @@
 
 if [ -f mozbc_outer.inp ]
 then
-ln -s $WRFMOZARTdir/mozbc .
 
 let totDays="((spinupTime+fcstTime)/24)+2"
 i=0
@@ -24,11 +23,11 @@ do
 done
 
 # first domain, always
-./mozbc < mozbc_outer.inp > mozbc.log
+${mozbcBin} < mozbc_outer.inp > mozbc.log
 
 for domain in $(seq 2 ${max_dom})
 do
   /bin/sed -s "s/__domain__/${domain}/" < mozbc_inner.inp > mozbc_inner_d${domain}.inp
-  ./mozbc < mozbc_inner_d${domain}.inp >> mozbc.log
+  ${mozbcBin} < mozbc_inner_d${domain}.inp >> mozbc.log
 done
 fi

machine_profiles/alcc_spack

+module load wrf wps anthro_emis fire_emis megan_bio_emiss mozbc wesely-exo_coldens
+
+ulimit -s unlimited