diff --git a/blueprints/.gitignore b/blueprints/.gitignore index bef82e3b337b19a30c73e022e852a480a1e3163c..79b5594df7fa295b000b84210837761e854c61ee 100644 --- a/blueprints/.gitignore +++ b/blueprints/.gitignore @@ -1,3 +1 @@ -*/config.bash -*/batch_preambles **/.DS_Store diff --git a/blueprints/operational_chemistry/VERSION b/blueprints/operational_chemistry/VERSION index b5045cc4046dbc1d7cafa4c603fd3cdf35dc5dde..8fdd954df9831dfd29ceec0d74829b02f3f5d8c3 100644 --- a/blueprints/operational_chemistry/VERSION +++ b/blueprints/operational_chemistry/VERSION @@ -1 +1 @@ -21 \ No newline at end of file +22 \ No newline at end of file diff --git a/blueprints/operational_chemistry/machine_specific/alcc_spack/config.bash b/blueprints/operational_chemistry/config.bash similarity index 80% rename from blueprints/operational_chemistry/machine_specific/alcc_spack/config.bash rename to blueprints/operational_chemistry/config.bash index 8febf3bf9c3bdf5dd7a7ba6bae5a443b60e4b7f0..7dd12edb2fe58da685375b08069b418d9e3d16f4 100644 --- a/blueprints/operational_chemistry/machine_specific/alcc_spack/config.bash +++ b/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 diff --git a/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/main b/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/main deleted file mode 100644 index 7cea60269ce19abca900b055770ae9dd65cf478d..0000000000000000000000000000000000000000 --- a/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/main +++ /dev/null @@ -1,23 +0,0 @@ -#!/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 diff --git a/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/post b/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/post deleted file mode 100644 index e7ed998f3c7a3bcf8f63cde38d0d4614c2d07c49..0000000000000000000000000000000000000000 --- a/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/post +++ /dev/null @@ -1,22 +0,0 @@ -#!/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 diff --git a/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/pre b/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/pre deleted file mode 100644 index a82c3dd0cc529e1bac55cf6a6de9f7de6196a4f8..0000000000000000000000000000000000000000 --- a/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/pre +++ /dev/null @@ -1,22 +0,0 @@ -#!/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 diff --git a/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/spinup b/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/spinup deleted file mode 100644 index d5ed322e8d9eaa2c81a89e88ce1b7da9e76da9d5..0000000000000000000000000000000000000000 --- a/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/spinup +++ /dev/null @@ -1,23 +0,0 @@ -#!/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 diff --git a/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/staging b/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/staging deleted file mode 100644 index 7e33cdb7f332dd774d56b135bdf0489df2607733..0000000000000000000000000000000000000000 --- a/blueprints/operational_chemistry/machine_specific/alcc_gnu/batch_preambles/staging +++ /dev/null @@ -1,22 +0,0 @@ -#!/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 > $MACHINEFILE diff --git a/blueprints/operational_chemistry/machine_specific/alcc_gnu/config.bash b/blueprints/operational_chemistry/machine_specific/alcc_gnu/config.bash deleted file mode 100644 index aeabc0a45d252641793526fee3ff7d6d6919d862..0000000000000000000000000000000000000000 --- a/blueprints/operational_chemistry/machine_specific/alcc_gnu/config.bash +++ /dev/null @@ -1,126 +0,0 @@ -#!/bin/bash -# ------------------------------------------------------------------------------ -# WRFOTRON v 2.0b -# Christoph Knote (LMU Munich, Germany) -# 06/2016 -# christoph.knote@lmu.de -# ------------------------------------------------------------------------------ - -# path to the WRFotron installation -chainDir=${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" diff --git a/blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/main b/blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/main deleted file mode 100644 index 818ee826f0ca4cee57d994d9e0bc2b2ef87c0355..0000000000000000000000000000000000000000 --- a/blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/main +++ /dev/null @@ -1,11 +0,0 @@ -#!/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 diff --git a/blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/spinup b/blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/spinup deleted file mode 100644 index 0879749e80c120d9e7563ff6338076ea06786be2..0000000000000000000000000000000000000000 --- a/blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/spinup +++ /dev/null @@ -1,11 +0,0 @@ -#!/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 diff --git a/blueprints/operational_chemistry/machine_specific/alcc_intel/config.bash b/blueprints/operational_chemistry/machine_specific/alcc_intel/config.bash deleted file mode 100644 index 0b89a4c008bde0dd0d1bcfdee0057ba18a2b09ca..0000000000000000000000000000000000000000 --- a/blueprints/operational_chemistry/machine_specific/alcc_intel/config.bash +++ /dev/null @@ -1,119 +0,0 @@ -#!/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" diff --git a/blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/post b/blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/post deleted file mode 100644 index 9cecb891d441d841608a66d6cc6bd2c874488598..0000000000000000000000000000000000000000 --- a/blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/post +++ /dev/null @@ -1,10 +0,0 @@ -#!/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 diff --git a/blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/pre b/blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/pre deleted file mode 100644 index 2bb27db5fd1bfd8c733b1f17bd49b1e301a0c4b2..0000000000000000000000000000000000000000 --- a/blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/pre +++ /dev/null @@ -1,10 +0,0 @@ -#!/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 diff --git a/blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/staging b/blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/staging deleted file mode 100644 index 66b09ee6b48048058b626d7a6642151323cdc194..0000000000000000000000000000000000000000 --- a/blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/staging +++ /dev/null @@ -1,10 +0,0 @@ -#!/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 diff --git a/machine_profiles/alcc_gnu b/machine_profiles/OLD/alcc_gnu similarity index 100% rename from machine_profiles/alcc_gnu rename to machine_profiles/OLD/alcc_gnu diff --git a/machine_profiles/alcc_intel b/machine_profiles/OLD/alcc_intel similarity index 100% rename from machine_profiles/alcc_intel rename to machine_profiles/OLD/alcc_intel diff --git a/machine_profiles/cheyenne b/machine_profiles/OLD/cheyenne similarity index 100% rename from machine_profiles/cheyenne rename to machine_profiles/OLD/cheyenne diff --git a/machine_profiles/lrzcluster b/machine_profiles/OLD/lrzcluster similarity index 100% rename from machine_profiles/lrzcluster rename to machine_profiles/OLD/lrzcluster diff --git a/machine_profiles/mim b/machine_profiles/OLD/mim similarity index 100% rename from machine_profiles/mim rename to machine_profiles/OLD/mim diff --git a/machine_profiles/alcc_spack b/machine_profiles/alcc_spack deleted file mode 100644 index 39d138d1f903c6b3183fdef3f65ad1e0429a4162..0000000000000000000000000000000000000000 --- a/machine_profiles/alcc_spack +++ /dev/null @@ -1,3 +0,0 @@ -module load wrf wrf-chem wps nco netcdf-c netcdf-fortran anthro_emis fire_emis megan_bio_emiss mozbc wesely-exo_coldens python gdal py-requests py-cdsapi py-cartopy py-matplotlib py-netcdf4 py-numpy py-pyproj py-rasterio py-scipy py-shapely py-simplekml py-xarray py-pyshp py-pandas - -ulimit -s unlimited diff --git a/blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/main b/machine_profiles/alcc_spack/batch_preambles/main similarity index 100% rename from blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/main rename to machine_profiles/alcc_spack/batch_preambles/main diff --git a/blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/post b/machine_profiles/alcc_spack/batch_preambles/post similarity index 100% rename from blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/post rename to machine_profiles/alcc_spack/batch_preambles/post diff --git a/blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/pre b/machine_profiles/alcc_spack/batch_preambles/pre similarity index 100% rename from blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/pre rename to machine_profiles/alcc_spack/batch_preambles/pre diff --git a/blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/spinup b/machine_profiles/alcc_spack/batch_preambles/spinup similarity index 100% rename from blueprints/operational_chemistry/machine_specific/alcc_spack/batch_preambles/spinup rename to machine_profiles/alcc_spack/batch_preambles/spinup diff --git a/blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/staging b/machine_profiles/alcc_spack/batch_preambles/staging similarity index 100% rename from blueprints/operational_chemistry/machine_specific/alcc_intel/batch_preambles/staging rename to machine_profiles/alcc_spack/batch_preambles/staging diff --git a/master.bash b/master.bash index fa38aced6d5dc7b521517bf29b7f3cdbc15911d0..bb541392adda014ec86a1949373fc3320f552338 100755 --- a/master.bash +++ b/master.bash @@ -1,7 +1,8 @@ #!/bin/bash -l # ------------------------------------------------------------------------------ -# WRFOTRON v 2.1 +# WRFOTRON v 2.2 # Christoph Knote (MBEES, University Augsburg) +# 09/2022 v 2.2 # 04/2022 v 2.1 # 09/2019 v 2.0 # 02/2016 v 1.0 @@ -29,7 +30,7 @@ # * in case of met-only simulations, there's only one (nudged) run # from startDate to endDate -WRFOTRON_VERSION=21 +WRFOTRON_VERSION=22 # ----------------------------------------------------------------------------- # 1) read command line parameters @@ -38,12 +39,10 @@ WRFOTRON_VERSION=21 OPTIND=1 dryRun=false -useBatchSystem=true -while getopts "db" opt +while getopts "d" opt do case $opt in d) dryRun=true ;; - b) useBatchSystem=false ;; esac done @@ -60,7 +59,6 @@ then echo " * needs to be a multiple of meteoInc." echo "" echo " -d dry run, prepare only, do not submit or run" - echo " -b do not use batch system, execute directly in shell" echo "" [[ "$0" != "$BASH_SOURCE" ]] && return 1 || exit 1 fi @@ -389,7 +387,7 @@ nmlChemPatchPath=${experimentDir}/namelist_timecontrol_chem_patch.wrf for job in pre main spinup staging post do # add batch settings - cat ${experimentDir}/batch_preambles/${job} > ${job}.bash + cat ${chainDir}/batch_preambles/${job} > ${job}.bash # add general preamble cat ${chainDir}/jobs/preamble.bash >> ${job}.bash # add jobs @@ -495,49 +493,33 @@ then [[ "$0" != "$BASH_SOURCE" ]] && return 1 || exit 1 fi -if [ "$useBatchSystem" = "true" ] +if [ "$isDependent" = "true" ] then - if [ "$isDependent" = "true" ] - then - pretxt=$(${batchSubmitCommand} ${batchDepArgument/__id__/${depjobnr}} < pre.bash) - else - pretxt=$(${batchSubmitCommand} ${batchHoldArgument} < pre.bash) - fi - prejobnr=$(echo $pretxt | sed -n "s/${batchPidSedCommand}/\1/p") - - spinuptxt=$(${batchSubmitCommand} ${batchDepArgument/__id__/${prejobnr}} < spinup.bash) - spinupjobnr=$(echo $spinuptxt | sed -n "s/${batchPidSedCommand}/\1/p") - - maintxt=$(${batchSubmitCommand} ${batchDepArgument/__id__/${spinupjobnr}} < main.bash) - mainjobnr=$(echo $maintxt | sed -n "s/${batchPidSedCommand}/\1/p") - - stagingtxt=$(${batchSubmitCommand} ${batchDepArgument/__id__/${mainjobnr}} < staging.bash) - stagingjobnr=$(echo $stagingtxt | sed -n "s/${batchPidSedCommand}/\1/p") + pretxt=$(${batchSubmitCommand} ${batchDepArgument/__id__/${depjobnr}} < pre.bash) +else + pretxt=$(${batchSubmitCommand} ${batchHoldArgument} < pre.bash) +fi +prejobnr=$(echo $pretxt | sed -n "s/${batchPidSedCommand}/\1/p") - posttxt=$(${batchSubmitCommand} ${batchDepArgument/__id__/${stagingjobnr}} < post.bash) - postjobnr=$(echo $posttxt | sed -n "s/${batchPidSedCommand}/\1/p") +spinuptxt=$(${batchSubmitCommand} ${batchDepArgument/__id__/${prejobnr}} < spinup.bash) +spinupjobnr=$(echo $spinuptxt | sed -n "s/${batchPidSedCommand}/\1/p") - if [ ! "$isDependent" = "true" ] - then - ${batchReleaseCommand} ${prejobnr} - fi +maintxt=$(${batchSubmitCommand} ${batchDepArgument/__id__/${spinupjobnr}} < main.bash) +mainjobnr=$(echo $maintxt | sed -n "s/${batchPidSedCommand}/\1/p") - echo $mainjobnr -else +stagingtxt=$(${batchSubmitCommand} ${batchDepArgument/__id__/${mainjobnr}} < staging.bash) +stagingjobnr=$(echo $stagingtxt | sed -n "s/${batchPidSedCommand}/\1/p") -cat >> config.bash << EOF -mpiCommandPre="" -mpiCommandMain="" -mpiCommandReal="" -EOF +posttxt=$(${batchSubmitCommand} ${batchDepArgument/__id__/${stagingjobnr}} < post.bash) +postjobnr=$(echo $posttxt | sed -n "s/${batchPidSedCommand}/\1/p") - . ./pre.bash - . ./spinup.bash - . ./main.bash - . ./staging.bash - . ./post.bash +if [ ! "$isDependent" = "true" ] +then + ${batchReleaseCommand} ${prejobnr} fi +echo $mainjobnr + # ----------------------------------------------------------------------------- # 10) cleanup # -----------------------------------------------------------------------------