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improved coverage test result of secondarystructure/ParabetaRMSD.cpp #3175

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improved coverage test result of secondarystructure/ParabetaRMSD.cpp

improved coverage test result of secondarystructure/ParabetaRMSD.cpp #3175

Workflow file for this run

.github/workflows/ci.yml at 1ae73b0
name: CI
on:
push:
pull_request:
env:
# on CI, better dump stack trace in case there is an error
PLUMED_STACK_TRACE: yes
# use two threads for openMP tests
PLUMED_NUM_THREADS: 2
# these are used to build required packages
CC: gcc
CXX: g++
jobs:
linux:
runs-on: ubuntu-22.04
strategy:
fail-fast: false
matrix:
variant:
- -doc-mpi-
- -mpi-
- -coverage-mpi-
- -debug-
- -debug-mpi-
# temporarily commented out
# see https://github.com/plumed/plumed2/issues/976
# - -intel-
steps:
- uses: actions/checkout@v4
- uses: actions/cache@v4
with:
path: ~/.ccache
key: ccache-reset1-linux${{ matrix.variant }}hash-${{ github.sha }}
restore-keys: ccache-reset1-linux${{ matrix.variant }}hash-
- name: Removed unused stuff
run: |
df -h
sudo rm -rf /usr/share/dotnet
sudo rm -rf /usr/local/lib/android
sudo rm -rf /opt/ghc
df -h
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.9
- name: Set paths
run: |
echo "$HOME/opt/bin" >> $GITHUB_PATH
# path required for pytest:
echo "$HOME/.local/bin" >> $GITHUB_PATH
echo "CPATH=$HOME/opt/include:$CPATH" >> $GITHUB_ENV
echo "INCLUDE=$HOME/opt/include:$INCLUDE" >> $GITHUB_ENV
echo "LIBRARY_PATH=$HOME/opt/lib:$LIBRARY_PATH" >> $GITHUB_ENV
echo "LD_LIBRARY_PATH=$HOME/opt/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
echo "PYTHONPATH=$HOME/opt/lib/plumed/python:$PYTHONPATH" >> $GITHUB_ENV
# this is to avoid errors on ubuntu 22. this is overridden in intel build
echo "FC=gfortran -fallow-argument-mismatch" >> $GITHUB_ENV
- name: Install generic packages
run: |
sudo apt-get update -qq
sudo apt-get install -y libatlas-base-dev
sudo apt-get install -y libfftw3-dev
sudo apt-get install -y gsl-bin
sudo apt-get install -y libgsl0-dev
sudo apt-get install -y ccache
- name: Install system boost
if: ${{ ! contains( matrix.variant, '-debug-' ) }}
run: |
sudo apt-get install -y libboost-serialization-dev
- name: Install boost with debug flags
if: contains( matrix.variant, '-debug-' )
run: |
.ci/install.boost
- name: Install python packages needed for tests
run: |
python -m pip install --upgrade pip
pip install --user Cython
pip install --user numpy
pip install --user pytest
pip install --user six ;
pip install --user pandas ;
pip install --user mdtraj ;
pip install --user MDAnalysis ;
python -c "import MDAnalysis" ;
python -c "import mdtraj" ;
- name: Install Libtorch
if: ${{ ! contains( matrix.variant, '-debug-' ) }} # libtorch is not compiled with GLIBCXX_DEBUG
run: |
# added by luigibonati
mkdir -p $HOME/opt/
cd $HOME/opt/ # GB: install in $HOME/opt/libtorch
wget --no-check-certificate https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.13.1%2Bcpu.zip ;
unzip libtorch-cxx11-abi-shared-with-deps-1.13.1+cpu.zip ;
echo "LIBRARY_PATH=$PWD/libtorch/lib:$LIBRARY_PATH" >> $GITHUB_ENV
echo "LD_LIBRARY_PATH=$PWD/libtorch/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
echo "CPATH=$PWD/libtorch/include/torch/csrc/api/include/:$PWD/libtorch/include/:$PWD/libtorch/include/torch:$CPATH" >> $GITHUB_ENV
echo "INCLUDE=$PWD/libtorch/include/torch/csrc/api/include/:$PWD/libtorch/include/:$PWD/libtorch/include/torch:$INCLUDE" >> $GITHUB_ENV
echo "PLUMED_CONFIG=$PLUMED_CONFIG --enable-libtorch" >> $GITHUB_ENV
- name: Install Doxygen
if: contains( matrix.variant, '-doc-' )
run: |
sudo apt-get install -y graphviz
sudo apt-get install -y doxygen-latex
.ci/install.doxygen Release_1_8_17
echo "PLUMED_CONFIG=$PLUMED_CONFIG --enable-pdfdoc" >> $GITHUB_ENV
# make sure all tests are run
echo "PLUMED_ALL_TESTS=yes" >> $GITHUB_ENV
- name: Install lcov
if: contains( matrix.variant, '-coverage-' )
run: |
.ci/install.lcov v1.16
echo "PLUMED_CONFIG=$PLUMED_CONFIG --disable-external-lapack --disable-external-blas --enable-gcov CXXFLAGS=-O" >> $GITHUB_ENV
# make sure all tests are run
echo "PLUMED_ALL_TESTS=yes" >> $GITHUB_ENV
- name: Setup debug flags
if: contains( matrix.variant, '-debug-' )
run: |
echo "PLUMED_CONFIG=$PLUMED_CONFIG --enable-debug --enable-debug-glibcxx" >> $GITHUB_ENV
- name: Install INTEL compiler
# install INTEL at last since it modifies CC and CXX
if: contains( matrix.variant, '-intel-' )
run: |
wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
sudo apt-get update
sudo apt-get install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-mkl intel-oneapi-mkl-devel intel-oneapi-compiler-fortran
source /opt/intel/oneapi/setvars.sh
printenv >> $GITHUB_ENV
echo "CXX=icpc" >> $GITHUB_ENV
echo "CC=icc" >> $GITHUB_ENV
echo "FC=ifort" >> $GITHUB_ENV
- name: Install MPI
# install MPI at last since it modifies CC and CXX
if: contains( matrix.variant, '-mpi-' )
run: |
sudo apt-get install -y libopenmpi-dev openmpi-bin
echo "CC=mpicc" >> $GITHUB_ENV
echo "CXX=mpic++" >> $GITHUB_ENV
echo "OMPI_MCA_btl_base_warn_component_unused=0" >> $GITHUB_ENV
echo "OMPI_MCA_btl_base_verbose=0" >> $GITHUB_ENV
echo "OMPI_MCA_plm=isolated" >> $GITHUB_ENV
echo "OMPI_MCA_btl_vader_single_copy_mechanism=none" >> $GITHUB_ENV
echo "OMPI_MCA_rmaps_base_oversubscribe=yes" >> $GITHUB_ENV
pip install --user mpi4py
python -c "import mpi4py"
- name: Build PLUMED
run: |
ccache -s -M 100M
./configure CXX="ccache $CXX" --enable-boost_serialization --disable-dependency-tracking --enable-modules=all LDFLAGS=-Wl,-rpath,$LD_LIBRARY_PATH $PLUMED_CONFIG --prefix="$HOME/opt"
make -j 4
make install
# check for global symbols, see https://github.com/plumed/plumed2/issues/549
make nmcheck
ccache -s -M 100M
- name: Run tests
if: ${{ ! contains( matrix.variant, '-doc-mpi-' ) }}
run: |
(while true; do # see https://github.com/actions/virtual-environments/issues/1860
df -h
sleep 15
done) &
make --no-print-directory -C regtest testclean
# these can fail for numerical reasons
make -C regtest checkfail
- name: Run python tests
run: |
cd python
pytest -v
- name: Build doc
env:
GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }}
if: contains( matrix.variant, '-doc-' )
run: |
make doc >/dev/null
- name: Coverage
env:
GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }}
if: contains( matrix.variant, '-coverage-' )
run: |
make -C developer-doc coverage
.ci/push coverage
# this is hanging for some reason now (2024-04-03) - GB
#bash <(curl -s https://codecov.io/bash) > /dev/null
- name: Push doc
if: contains( matrix.variant, '-doc-' )
env:
GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }}
run: |
.ci/push doc
codecheck:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v4
- name: Set path
run: |
echo "$HOME/opt/bin" >> $GITHUB_PATH
- name: Install requirements
run: |
.ci/install.cppcheck 2.10.3
# it is important that this is the same version used to generate the actual ./configure
.ci/install.autoconf 2.69
- name: Build astyle
run: |
make -j 4 -C astyle
- name: Checking code
run: |
# this is required so as to have all the include files in place
# notice that this is done automatically in build
# first make sure that dirslinks are generated for all modules
./configure --enable-modules=all
# then generate the links
make -C src/lib/ dirslinks
make codecheck
# We test on fedora37 to make sure we have compatibility with newer compilers (gcc 12)
fedora37:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v4
- name: Build and run tests
run: |
make -C docker fedora37
# We test on rockylinux8 as well
rocky8:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v3
- name: Build and run tests
run: |
make -C docker rocky8
macports:
runs-on: macos-12
strategy:
fail-fast: false
matrix:
variant: [ "" , "+allmodules" ]
# see https://github.community/t/how-to-conditionally-include-exclude-items-in-matrix-eg-based-on-branch/16853/6 for possible exclusions
env:
PYVERS: "py39 py310"
steps:
- uses: actions/checkout@v4
- uses: actions/cache@v4
with:
path: ~/.macports-ci-ccache
key: ccache-macports-${{ matrix.variant }}-${{ github.sha }}
restore-keys: ccache-macports-${{ matrix.variant }}-
- name: Install MacPorts
run: |
wget https://raw.githubusercontent.com/GiovanniBussi/macports-ci/master/macports-ci
source ./macports-ci install
source ./macports-ci ccache
- name: Build local Portfile
run: |
make macports
source ./macports-ci localports macports
- name: Build PLUMED
run: |
sudo port -N -k install plumed ${{ matrix.variant }}
plumed config show
for p in $PYVERS ; do
sudo port -N install $p-plumed
done
source ./macports-ci ccache --save
- name: Run tests
run: |
sudo port -N -d test plumed ${{ matrix.variant }}
- name: Run python tests
run: |
for p in $PYVERS ; do
sudo port test $p-plumed
done
macsimple:
runs-on: macos-12
steps:
- uses: actions/checkout@v4
- name: Set paths
run: |
echo "$HOME/opt/bin" >> $GITHUB_PATH
echo "CPATH=$HOME/opt/include:$CPATH" >> $GITHUB_ENV
echo "INCLUDE=$HOME/opt/include:$INCLUDE" >> $GITHUB_ENV
echo "LIBRARY_PATH=$HOME/opt/lib:$LIBRARY_PATH" >> $GITHUB_ENV
echo "LD_LIBRARY_PATH=$HOME/opt/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
- name: Build PLUMED
run: |
# it seems brew update is screwing up something
# GB on Mar 8, 2024
#brew update > /dev/null
brew install gawk
./configure --disable-dependency-tracking --prefix="$HOME/opt"
make -j 4
make install
- name: Run tests
run: |
make --no-print-directory -C regtest
# these can fail for numerical reasons
make -C regtest checkfail
conda:
strategy:
fail-fast: false
matrix:
os: [ubuntu-20.04 , macos-12, macos-14 ]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
- name: Install conda
run: |
curl -LO https://raw.githubusercontent.com/GiovanniBussi/conda-ci/master/conda-ci
source ./conda-ci install
source ./conda-ci install-conda-build
- name: Build PLUMED
run: |
source activate base
export VERSION=none
if [[ $GITHUB_REF == "refs/tags/"* ]]; then
VERSION=${GITHUB_REF#refs/tags/}
VERSION=${VERSION//-/_}
VERSION=${VERSION#v}
fi
make -C conda
- name: Deploy
env:
CONDA_UPLOAD_TOKEN: ${{ secrets.CONDA_UPLOAD_TOKEN }}
if: ${{ startsWith( github.ref , 'refs/tags/' ) }}
run: |
source activate base
export CONDA_LABEL=tag
make -C conda upload