Make batch config global

blueprints/.gitignore

-*/config.bash
-*/batch_preambles
 **/.DS_Store

blueprints/operational_chemistry/VERSION

-21
\ No newline at end of file
+22
\ No newline at end of file

blueprints/operational_chemistry/machine_specific/alcc_spack/config.bash → blueprints/operational_chemistry/config.bash

@@ -57,26 +57,6 @@ restartRootDir=${SCRATCH}/WRF/restart/
 # remove run directory after run is finished?
 removeRunDir=false
 
-# --- MPI settings ---
-
-mpiCommandPre="mpirun /usr/bin/time -v"
-mpiCommandMain="mpirun -mca pml ucx -mca coll ^hcoll -x UCX_TLS=tcp,shm -x UCX_NET_DEVICES=eth5 /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

blueprints/operational_chemistry/machine_specific/alcc_gnu/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=2
-#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=12:00:00
-
-#
-# variable $MACHINEFILE just holds the filename where acquired
-# nodes/cores names are written. e.g.
-#
-MACHINEFILE=__runDir__/slurm.hosts
-
-#
-# Generate Machinefile for openmpi such that hosts are in the same
-# order as if run via srun
-#
-srun hostname -s | sort -n > $MACHINEFILE

blueprints/operational_chemistry/machine_specific/alcc_gnu/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
-
-#
-# variable $MACHINEFILE just holds the filename where acquired
-# nodes/cores names are written. e.g.
-#
-MACHINEFILE=__runDir__/slurm.hosts
-
-#
-# Generate Machinefile for openmpi such that hosts are in the same
-# order as if run via srun
-#
-srun hostname -s | sort -n > $MACHINEFILE

blueprints/operational_chemistry/machine_specific/alcc_gnu/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
-
-#
-# variable $MACHINEFILE just holds the filename where acquired
-# nodes/cores names are written. e.g.
-#
-MACHINEFILE=__runDir__/slurm.hosts
-
-#
-# Generate Machinefile for openmpi such that hosts are in the same
-# order as if run via srun
-#
-srun hostname -s | sort -n > $MACHINEFILE

blueprints/operational_chemistry/machine_specific/alcc_gnu/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
-
-#
-# variable $MACHINEFILE just holds the filename where acquired
-# nodes/cores names are written. e.g.
-#
-MACHINEFILE=__runDir__/slurm.hosts
-
-#
-# Generate Machinefile for openmpi such that hosts are in the same
-# order as if run via srun
-#
-srun hostname -s | sort -n > $MACHINEFILE

blueprints/operational_chemistry/machine_specific/alcc_gnu/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
-
-#
-# variable $MACHINEFILE just holds the filename where acquired
-# nodes/cores names are written. e.g.
-#
-MACHINEFILE=__runDir__/slurm.hosts
-
-#
-# Generate Machinefile for openmpi such that hosts are in the same
-# order as if run via srun
-#
-srun hostname -s | sort -n > $MACHINEFILE

blueprints/operational_chemistry/machine_specific/alcc_gnu/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=${WRF_SRC_PATH}
-
-# --- Input data settings ---
-
-# path to geogrid input data
-geogDir=${WRF_GEOG_PATH}
-
-# meteo input
-# Vtable for the chosen meteo input
-metVtableFile=${WPS_SRC_PATH}/ungrib/Variable_Tables/Vtable.GFS
-# time increment in hours
-metInc=1
-# full path to a met input file - you can use any "%<>" abbreviations known
-# to the "date" command
-metFilePattern="${WRF_GFS_METEO_PATH}/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 ---
-
-# mental note for GNU:
-#mpirun  -mca pml ucx -x UCX_TLS=rc,shm  -N $SLURM_NTASKS_PER_NODE -hostfile $MACHINEFILE 
-mpiCommandPre="mpirun -mca pml ucx -x UCX_TLS=rc,shm -hostfile $MACHINEFILE /usr/bin/time -v"
-mpiCommandMain="mpirun -mca pml ucx -x UCX_TLS=rc,shm -N $SLURM_NTASKS_PER_NODE -hostfile $MACHINEFILE /usr/bin/time -v"
-mpiCommandReal=${mpiCommandPre}
-
-# mental note for INTEL:
-#mpiCommandPre="srun /usr/bin/time -v"
-#mpiCommandMain="srun /usr/bin/time -v"
-#mpiCommandReal="srun /usr/bin/time -v"
-
-# --- 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=afterany:__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=${WRF_CHEM_SRC_PATH}
-
-# megan_bio_emiss installation directory
-WRFMEGANdir=${WRF_CHEM_MEGAN_BIO_EMISS_PATH}
-# mozbc installation directory
-WRFMOZARTdir=${WRF_CHEM_MOZBC_PATH}
-# wesley/exocoldens installation directory
-WRFmztoolsdir=${WRF_CHEM_WES_COLDENS_PATH}
-# anthro_emiss installation directory
-WRFanthrodir=${WRF_CHEM_ANTHRO_EMIS_PATH}
-# fire_emis installation directory
-WRFfiredir=${WRF_CHEM_FIRE_EMIS_PATH}
-
-# 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/EDGAR-HTAP/MOZART_MOSAIC
-# emission conversion script for anthro_emis - must match emissions in emissDir
-emissInpFile=emis_edgarhtap_mozmos.inp
-# year the emissions are valid for (for offset calculation)
-emissYear=2010
-
-# 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"

blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/main

-#!/bin/bash -l
-#SBATCH --partition=alcc1
-#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_intel/batch_preambles/spinup

-#!/bin/bash -l
-#SBATCH --partition=alcc1
-#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_intel/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=${WRF_SRC_PATH}
-
-# --- Input data settings ---
-
-# path to geogrid input data
-geogDir=${WRF_GEOG_PATH}
-
-# meteo input
-# Vtable for the chosen meteo input
-metVtableFile=${WPS_SRC_PATH}/ungrib/Variable_Tables/Vtable.GFS
-# time increment in hours
-metInc=1
-# full path to a met input file - you can use any "%<>" abbreviations known
-# to the "date" command
-metFilePattern="${WRF_GFS_METEO_PATH}/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=${WRF_CHEM_SRC_PATH}
-
-# megan_bio_emiss installation directory
-WRFMEGANdir=${WRF_CHEM_MEGAN_BIO_EMISS_PATH}
-# mozbc installation directory
-WRFMOZARTdir=${WRF_CHEM_MOZBC_PATH}
-# wesley/exocoldens installation directory
-WRFmztoolsdir=${WRF_CHEM_WES_COLDENS_PATH}
-# anthro_emiss installation directory
-WRFanthrodir=${WRF_CHEM_ANTHRO_EMIS_PATH}
-# fire_emis installation directory
-WRFfiredir=${WRF_CHEM_FIRE_EMIS_PATH}
-
-# 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"

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/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