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Feature: perfect restart and n-cores CI #589

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Feature: perfect restart and n-cores CI

Feature: perfect restart and n-cores CI #589

Workflow file for this run

.github/workflows/test-pr.yml at b3833f0
name: build
on:
push:
branches: [ main ]
pull_request:
branches: [ main ]
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
inputs:
pr:
description: "PR to test"
required: true
jobs:
Model_Testing:
strategy:
fail-fast: false
matrix:
configuration: [nwm_ana, nwm_long_range, gridded, reach, reach_lakes]
runs-on: ubuntu-latest
env:
MPI_HOME: /usr/share/miniconda
NETCDF: /usr/share/miniconda
NETCDF_INCLUDES: /usr/share/miniconda/include
NETCDF_LIBRARIES: /usr/share/miniconda/lib
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: Checkout candidate (pull request / push)
if: ${{ github.event_name == 'pull_request' || github.event_name == 'push' }}
uses: actions/checkout@v4
with:
path: candidate
- name: Checkout candidate (manual)
if: ${{ github.event_name == 'workflow_dispatch' }}
env:
GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
run: gh repo clone ${{ github.repository }} candidate && cd candidate && gh pr checkout -R ${{ github.repository }} ${{ github.event.inputs.pr }}
- name: Checkout reference (pull request)
if: ${{ github.event_name == 'pull_request' }}
uses: actions/checkout@v4
with:
ref: ${{ github.event.pull_request.base.ref }}
path: reference
- name: Checkout reference (push)
if: ${{ github.event_name == 'push' }}
uses: actions/checkout@v4
with:
ref: ${{ github.event.before }}
path: reference
- name: Checkout reference (manual)
if: ${{ github.event_name == 'workflow_dispatch' }}
env:
GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
run: gh repo clone ${{ github.repository }} reference && cd reference && git checkout origin/$(gh pr view ${{ github.event.inputs.pr }} --json baseRefName --jq '.baseRefName')
- name: Install dependencies with apt-get
run: |
sudo apt-get update \
&& sudo apt-get install -yq --no-install-recommends \
wget \
curl \
bzip2 \
ca-certificates \
libhdf5-dev \
gfortran \
g++ \
m4 \
make \
libswitch-perl \
git \
bc \
openmpi-bin openmpi-common libopenmpi-dev \
libxml2-dev \
libnetcdf-dev \
libnetcdff-dev
- name: Install dependencies with pip
run: |
python3 -m pip install matplotlib numpy xarray dask netCDF4 pygithub
- name: Compile reference
run: |
cd $GITHUB_WORKSPACE/reference
cmake -B build
make -C build -j
- name: Compile candidate
run: |
cd $GITHUB_WORKSPACE/candidate
cmake -B build
make -C build -j
- name: Run reference model
run: |
cd $GITHUB_WORKSPACE/reference/build/Run
make run-croton-${{ matrix.configuration }}
- name: Run candidate model
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
make run-croton-${{ matrix.configuration }}
- name: Compare HYDRO_RST.* output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
for file in output_${{ matrix.configuration }}/HYDRO_RST.*; do\
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
done
- name: Compare RESTART.* output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
for file in output_${{ matrix.configuration }}/RESTART.*; do\
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
done
- name: Compare last *.CHANOBS_DOMAIN1 output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
file=$(ls -t output_${{ matrix.configuration }}/*.CHANOBS_DOMAIN1 | head -n 1)
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
- name: Compare last *.CHRTOUT_DOMAIN1 output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
file=$(ls -t output_${{ matrix.configuration }}/*.CHRTOUT_DOMAIN1 | head -n 1)
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
- name: Compare last *.LSMOUT_DOMAIN1 output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
file=$(ls -t output_${{ matrix.configuration }}/*.LSMOUT_DOMAIN1 | head -n 1)
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
- name: Compare last *.RTOUT_DOMAIN1 output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
file=$(ls -t output_${{ matrix.configuration }}/*.RTOUT_DOMAIN1 | head -n 1)
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
- name: Compare output with compare_output
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
mkdir output_diff
python -c \
"import sys; \
sys.path.append('${GITHUB_WORKSPACE}/candidate/tests/utils'); \
import compare_output; \
from pathlib import Path; \
compare_output.plot_diffs('${GITHUB_WORKSPACE}/candidate/build/Run/output_diff', \
'${GITHUB_WORKSPACE}/candidate/build/Run/output_${{ matrix.configuration }}/', \
'${GITHUB_WORKSPACE}/reference/build/Run/output_${{ matrix.configuration }}/', \
'${{ matrix.configuration }}')"
- name: Copy test results from container
if: ${{ always() }}
run: |
mkdir -p $GITHUB_WORKSPACE/test_report
cp -r $GITHUB_WORKSPACE/candidate/build/Run/output_diff/diff_plots/* $GITHUB_WORKSPACE/test_report/
- name: Attach diff plots to PR
if: ${{ failure() }}
shell: bash
run: |
cd $GITHUB_WORKSPACE/candidate/tests/local/utils
bash attach_all_plots.bash $(jq --raw-output .pull_request.number "$GITHUB_EVENT_PATH") ${{ matrix.configuration }}
- name: Archive test results to GitHub
if: ${{ failure() }}
uses: actions/upload-artifact@v4
with:
name: test-reports
path: |
${{ github.workspace }}/test_report/*
# n-cores test
- name: Run parallel candidate model
run: |
rm -r $GITHUB_WORKSPACE/test_report/
cd $GITHUB_WORKSPACE/candidate/build/Run
make clean
make run-croton-${{ matrix.configuration }}-parallel
- name: n-cores: Compare HYDRO_RST.* output with xrcmp

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if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
for file in output_${{ matrix.configuration }}/HYDRO_RST.*; do\
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
done
- name: n-cores: Compare RESTART.* output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
for file in output_${{ matrix.configuration }}/RESTART.*; do\
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
done
- name: n-cores: Compare last *.CHANOBS_DOMAIN1 output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
file=$(ls -t output_${{ matrix.configuration }}/*.CHANOBS_DOMAIN1 | head -n 1)
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
- name: n-cores: Compare last *.CHRTOUT_DOMAIN1 output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
file=$(ls -t output_${{ matrix.configuration }}/*.CHRTOUT_DOMAIN1 | head -n 1)
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
- name: n-cores: Compare last *.LSMOUT_DOMAIN1 output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
file=$(ls -t output_${{ matrix.configuration }}/*.LSMOUT_DOMAIN1 | head -n 1)
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
- name: n-cores: Compare last *.RTOUT_DOMAIN1 output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
file=$(ls -t output_${{ matrix.configuration }}/*.RTOUT_DOMAIN1 | head -n 1)
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
- name: n-cores: Compare output with compare_output
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
rm -rf output_diff
mkdir output_diff
python -c \
"import sys; \
sys.path.append('${GITHUB_WORKSPACE}/candidate/tests/utils'); \
import compare_output; \
from pathlib import Path; \
compare_output.plot_diffs('${GITHUB_WORKSPACE}/candidate/build/Run/output_diff', \
'${GITHUB_WORKSPACE}/candidate/build/Run/output_${{ matrix.configuration }}/', \
'${GITHUB_WORKSPACE}/reference/build/Run/output_${{ matrix.configuration }}/', \
'${{ matrix.configuration }}')"
- name: n-cores: Copy test results from container
if: ${{ always() }}
run: |
mkdir -p $GITHUB_WORKSPACE/test_report
cp -r $GITHUB_WORKSPACE/candidate/build/Run/output_diff/diff_plots/* $GITHUB_WORKSPACE/test_report/
- name: n-cores: Attach diff plots to PR
if: ${{ failure() }}
shell: bash
run: |
cd $GITHUB_WORKSPACE/candidate/tests/local/utils
bash attach_all_plots.bash $(jq --raw-output .pull_request.number "$GITHUB_EVENT_PATH") ${{ matrix.configuration }}
- name: n-cores: Archive test results to GitHub
if: ${{ failure() }}
uses: actions/upload-artifact@v4
with:
name: test-reports
path: |
${{ github.workspace }}/test_report/*
# Testing perfect restart, not cleaning candidate model output
- name: Setup and run candidate model perfect restart startup
run: |
rm -r $GITHUB_WORKSPACE/test_report/
cd $GITHUB_WORKSPACE/candidate/build/Run
sed -i 's|RESTART_FILENAME_REQUESTED = "RESTART/RESTART.2011082600_DOMAIN1"|RESTART_FILENAME_REQUESTED = "./RESTART.2011090100_DOMAIN1"|' namelist.hrldas
sed -i 's/KDAY = 7/KDAY = 1/' namelist.hrldas
rm output_${{ matrix.configuration }}/RESTART.2011090200_DOMAIN1
rm output_${{ matrix.configuration }}/HYDRO_RST.2011-09-02_00:00_DOMAIN1
make run-croton-${{ matrix.configuration }}-parallel
- name: restart: Compare HYDRO_RST.* output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
for file in output_${{ matrix.configuration }}/HYDRO_RST.2011-09-02_00:00_DOMAIN1; do\
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
done
- name: restart: Compare RESTART.* output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
for file in output_${{ matrix.configuration }}/RESTART.2011090200_DOMAIN1; do\
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
done
- name: restart: Compare last *.CHANOBS_DOMAIN1 output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
file=$(ls -t output_${{ matrix.configuration }}/*.CHANOBS_DOMAIN1 | head -n 1)
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
- name: restart: Compare last *.CHRTOUT_DOMAIN1 output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
file=$(ls -t output_${{ matrix.configuration }}/*.CHRTOUT_DOMAIN1 | head -n 1)
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
- name: restart: Compare last *.LSMOUT_DOMAIN1 output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
file=$(ls -t output_${{ matrix.configuration }}/*.LSMOUT_DOMAIN1 | head -n 1)
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
- name: restart: Compare last *.RTOUT_DOMAIN1 output with xrcmp
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
file=$(ls -t output_${{ matrix.configuration }}/*.RTOUT_DOMAIN1 | head -n 1)
python ${GITHUB_WORKSPACE}/candidate/tests/utils/xrcmp.py \
--candidate $file \
--reference $GITHUB_WORKSPACE/reference/build/Run/$file \
--log_file $file_diff.txt \
--n_cores 1; \
- name: restart: Compare output with compare_output
if: ${{ always() }}
run: |
cd $GITHUB_WORKSPACE/candidate/build/Run
rm -rf output_diff
mkdir output_diff
python -c \
"import sys; \
sys.path.append('${GITHUB_WORKSPACE}/candidate/tests/utils'); \
import compare_output; \
from pathlib import Path; \
compare_output.plot_diffs('${GITHUB_WORKSPACE}/candidate/build/Run/output_diff', \
'${GITHUB_WORKSPACE}/candidate/build/Run/output_${{ matrix.configuration }}/', \
'${GITHUB_WORKSPACE}/reference/build/Run/output_${{ matrix.configuration }}/', \
'${{ matrix.configuration }}')"
- name: restart: Copy test results from container
if: ${{ always() }}
run: |
mkdir -p $GITHUB_WORKSPACE/test_report
cp -r $GITHUB_WORKSPACE/candidate/build/Run/output_diff/diff_plots/* $GITHUB_WORKSPACE/test_report/
- name: restart: Attach diff plots to PR
if: ${{ failure() }}
shell: bash
run: |
cd $GITHUB_WORKSPACE/candidate/tests/local/utils
bash attach_all_plots.bash $(jq --raw-output .pull_request.number "$GITHUB_EVENT_PATH") ${{ matrix.configuration }}
- name: restart: Archive test results to GitHub
if: ${{ failure() }}
uses: actions/upload-artifact@v4
with:
name: test-reports
path: |
${{ github.workspace }}/test_report/*