From 1fdb205daf6300b1a1bbf447a1d4fdd7ea9d1427 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Oriol=20Tint=C3=B3?= <oriol.tinto@lmu.de>
Date: Fri, 19 May 2023 13:53:25 +0200
Subject: [PATCH] Adding real-from-idea+psp case.
---
.gitlab-ci.yml | 23 +++++
examples/01_real-from-ideal+psp.sh | 154 +++++++++++++++++++++++++++++
2 files changed, 177 insertions(+)
create mode 100755 examples/01_real-from-ideal+psp.sh
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8764819..fb778d8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -20,6 +20,29 @@ real-from-ideal:
artifacts:
name: real-from-ideal-logs
when: always
+ paths:
+ - ./autosubmit/**/tmp
+ expire_in: 7 days
+
+real-from-ideal-psp:
+ stage: everything
+ script:
+ # Build
+ - ./examples/01_real-from-ideal+psp.sh 0
+ # Run Ideal
+ - ./examples/01_real-from-ideal+psp.sh 1
+ # Run Real
+ - ./examples/01_real-from-ideal+psp.sh 2
+ # Post-process and clean
+ - ./examples/01_real-from-ideal+psp.sh 3
+ tags:
+ - slurm.meteo.physik.lmu.de
+ variables:
+ SRUN_OPTIONS: "--time 04:00:00 --mem 18G -n 4 -c 2"
+
+ artifacts:
+ name: real-from-ideal+psp-logs
+ when: always
paths:
- ./autosubmit/**/tmp
expire_in: 7 days
\ No newline at end of file
diff --git a/examples/01_real-from-ideal+psp.sh b/examples/01_real-from-ideal+psp.sh
new file mode 100755
index 0000000..07e6121
--- /dev/null
+++ b/examples/01_real-from-ideal+psp.sh
@@ -0,0 +1,154 @@
+#!/bin/bash
+set -euo pipefail
+
+STAGE=${1:-}
+
+function help() {
+ echo "Need to provide a integer for the stage we want to run."
+ echo " e.g."
+ echo " - 0: Build Icon and python environemnts"
+ echo " - 1: Run the ideal case used to initialize a real run from"
+ echo " - 2: Run the real case"
+ echo " - 3: postprocess outputs"
+}
+
+if [ -z "$STAGE" ]; then
+ help
+ exit 1
+fi
+
+if [[ "$STAGE" -lt 0 ]] || [[ "$STAGE" -gt 3 ]]; then
+ echo "invalid stage id: $STAGE"
+ help
+ exit 2
+fi
+
+
+AUTOSUBMIT_VERSION="4.0.76"
+
+SCRIPTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+PROJECT_ROOT=$(readlink -f $SCRIPTDIR/../)
+
+OUTPUTDIR=$PROJECT_ROOT/output
+mkdir -p $OUTPUTDIR
+
+WORKDIR=$SCRATCH/autosubmit_rundir
+PROJECTNAME='ls-mayer'
+mkdir -p $WORKDIR/$PROJECTNAME/$(whoami)
+
+virtualenv -p python3 pyenv
+. pyenv/bin/activate
+
+cat > requirements.txt <<EOF
+autosubmit==$AUTOSUBMIT_VERSION
+EOF
+pip install -r requirements.txt
+
+if [ ! -e ./.autosubmitrc ] || [ ! -e autosubmit ] ; then
+ # Note that we create autosubmit here with --local to create the .autosubmitrc not in the home dir
+ # This requires to run all autosubmit calls from within this root dir.
+ autosubmit configure --local -db $(pwd)/autosubmit -dbf autosubmit.db -lr $(pwd)/autosubmit
+fi
+
+if [ ! -e autosubmit/autosubmit.db ]; then
+ autosubmit install
+fi
+
+PROJECT_ORIGIN="https://gitlab.physik.uni-muenchen.de/w2w/autoicon.git"
+PROJECT_BRANCH="master"
+EXPID=rfi001
+
+if [ ! -e autosubmit/$EXPID/ ]; then
+ mkdir -p autosubmit/$EXPID/
+ autosubmit expid -min -H lmu -d myiconsim -repo $PROJECT_ORIGIN -b $PROJECT_BRANCH &> >(tee autosubmit/$EXPID/log.autosubmit.expid)
+ AUTOID=$(grep Experiment autosubmit/$EXPID/log.autosubmit.expid | awk '{print $2}')
+ mv -v autosubmit/$AUTOID/* autosubmit/$EXPID
+ rmdir -v autosubmit/$AUTOID
+fi
+
+cat > autosubmit/$EXPID/conf/minimal.yml <<EOF
+ICON_CASE: "real-from-ideal"
+
+CONFIG:
+ AUTOSUBMIT_VERSION: "$AUTOSUBMIT_VERSION"
+ TOTALJOBS: 20
+ MAXWAITINGJOBS: 20
+ RETRIALS: 0
+DEFAULT:
+ EXPID: "$EXPID"
+ HPCARCH: "LOCAL" # use LMU to run on cluster
+ CUSTOM_CONFIG:
+ PRE:
+ - "%PROJDIR%/conf/common"
+ - "%PROJDIR%/conf/%ICON_CASE%"
+
+PROJECT:
+ PROJECT_TYPE: "git"
+ PROJECT_DESTINATION: "autoicon"
+GIT:
+ PROJECT_ORIGIN: "$PROJECT_ORIGIN"
+ PROJECT_BRANCH: "$PROJECT_BRANCH"
+ PROJECT_COMMIT: ""
+ PROJECT_SUBMODULES: ""
+ FETCH_SINGLE_BRANCH: True
+EOF
+
+cat > autosubmit/${EXPID}/conf/myconf.yml <<EOF
+spack:
+ init: "" # command to load spack environment, e.g. module load spack, use spack/setup-env.sh if empty
+ url: https://github.com/spack/spack.git # url to download spack if necessary
+ branch: develop # if downloaded, branch name to use
+ compiler: "gcc@11.3.0" # desired compiler for spack
+ root: "$SCRATCH/autoicon-spack" # path to a spack install, will be downloaded to if not present
+ externals: "slurm"
+ user_cache_path: "$SCRATCH/autoicon-spackcache" # spack puts data here when bootstrapping, leave empty to use home folder
+ user_config_path: "$SCRATCH/autoicon-spackconfig" # spack puts data here when bootstrapping, leave empty to use home folder
+ disable_local_config: false # if true, spack installs into spack source dir
+ upstreams: "/software/opt/focal/x86_64/spack/2023.02"
+
+icon:
+ #build_cmd: "icon-nwp@%ICON.VERSION%% %SPACK.COMPILER%+debug+petsc target=x86_64_v2 ^openmpi+pmi+legacylaunchers schedulers=slurm fabrics=ucx ucx+dc+dm+ib_hw_tm+mlx5_dv+rc+rdmacm+thread_multiple+ud+verbs"
+ build_cmd: "icon-nwp@%ICON.VERSION%% %SPACK.COMPILER%+debug target=x86_64_v2 source=dkrz_https"
+ version: 2.6.5-nwp0
+
+data_management:
+ # Where do we put the output files afterwards?
+ local_destination_folder: $OUTPUTDIR/
+
+EOF
+
+if [ "$STAGE" -eq 0 ]; then
+ echo "Running Stage 0"
+ autosubmit create ${EXPID} -np
+ autosubmit refresh ${EXPID}
+ autosubmit setstatus ${EXPID} -ft PREPARE_EXPERIMENT -t SUSPENDED -s -np
+ autosubmit run ${EXPID}
+ # Check if there are failed jobs
+ [ -s autosubmit/${EXPID}/tmp/ASLOGS/jobs_failed_status.log ] && exit 1
+fi
+
+if [ "$STAGE" -eq 1 ]; then
+ echo "Running Stage 1"
+ autosubmit setstatus ${EXPID} -fs SUSPENDED -t WAITING -s -np
+ autosubmit setstatus ${EXPID} -ft "EXTPAR_FROM_IDEALIZED FG_ANA_FROM_IDEALIZED" -t SUSPENDED -s -np
+ autosubmit run ${EXPID}
+ # Check if there are failed jobs
+ [ -s autosubmit/${EXPID}/tmp/ASLOGS/jobs_failed_status.log ] && exit 1
+fi
+
+if [ "$STAGE" -eq 2 ]; then
+ echo "Running Stage 2"
+ autosubmit setstatus ${EXPID} -fs SUSPENDED -t WAITING -s -np
+ autosubmit setstatus ${EXPID} -ft TRANSFER -t SUSPENDED -s -np
+ autosubmit run ${EXPID}
+ # Check if there are failed jobs
+ [ -s autosubmit/${EXPID}/tmp/ASLOGS/jobs_failed_status.log ] && exit 1
+fi
+
+if [ "$STAGE" -eq 3 ]; then
+ echo "Running Stage 3"
+ autosubmit setstatus ${EXPID} -fs SUSPENDED -t WAITING -s -np
+ autosubmit run ${EXPID}
+ # Check if there are failed jobs
+ [ -s autosubmit/${EXPID}/tmp/ASLOGS/jobs_failed_status.log ] && exit 1
+fi
--
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