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deps update and energy file bugfix. #66

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merged 1 commit into from
Aug 4, 2024
Merged

deps update and energy file bugfix. #66

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205 changes: 105 additions & 100 deletions .github/workflows/supercell-cicd.yml
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Original file line number Diff line number Diff line change
@@ -1,174 +1,179 @@
name: Build jobs
run-name:
run-name:
on:
push:
paths:
- 'src/**'
- 'lib/**'
- '3rd_party/**'
pull_request:
branches:
branches:
- master
release:
types: [published]

jobs:
build-develop-linux:
strategy:
fail-fast: false
matrix:
os: [ubuntu-20.04, ubuntu-22.04]
compiler: [gcc-9, gcc-10, clang-11, clang-12, clang-13]
os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04]
compiler: [gcc, gcc-9, gcc-10, gcc-11, gcc-12, gcc-13, clang]
include:
- os: ubuntu-latest
compiler: gcc
- os: ubuntu-latest
compiler: clang
- os: ubuntu-20.04
compiler: clang-11
- os: ubuntu-22.04
compiler: clang-13
- os: ubuntu-24.04
compiler: gcc-14
exclude:
- os: ubuntu-20.04
compiler: gcc-12
- os: ubuntu-20.04
compiler: gcc-13
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: true
- name: Setup C++
uses: aminya/setup-cpp@v0.21.0
uses: aminya/setup-cpp@v0.37.0
with:
compiler: ${{ matrix.compiler }}
cmake: true
make: true
- name: "Install dependencies"
run: "sudo apt update && sudo apt install -y
cmake build-essential libboost-test-dev libtinfo5 libtbb-dev
libarchive-dev libboost-program-options-dev libboost-filesystem-dev
libboost-system-dev libeigen3-dev liblzma-dev libbz2-dev zlib1g-dev zip"
run: |
sudo apt update && sudo apt install -y \
cmake build-essential libboost-test-dev libtbb-dev \
libarchive-dev libboost-program-options-dev libboost-filesystem-dev \
libboost-system-dev libeigen3-dev liblzma-dev libbz2-dev zlib1g-dev zip
- name: "Compile supercell."
run: cmake . -DCMAKE_BUILD_TYPE=Release && make supercell -j 2
run: cmake . -DCMAKE_BUILD_TYPE=Release && make supercell -j 4
- name: "Check supercell"
run: 'src/sc_cli/supercell -d -i ./data/examples/Ca2Al2SiO7/Ca2Al2SiO7.cif | grep -q "The total number of combinations is 6"'
deploy-build-macos:
strategy:
fail-fast: false
runs-on: macos-latest
runs-on: macos-13
steps:
- name: Set up Homebrew
id: set-up-homebrew
uses: Homebrew/actions/setup-homebrew@master
uses: Homebrew/actions/setup-homebrew@master
- name: "Install brew dependencies"
run: |
brew install boost eigen libarchive zlib
- name: "Get TBB"
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
repository: oneapi-src/oneTBB
ref: v2021.7.0
ref: v2021.13.0
path: ./tbb
submodules: true
- name: "Compile and install tbb"
working-directory: ./tbb
run: |
cmake . -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=OFF -DTBB_TEST=OFF
make -j 2
make -j 4
sudo make install
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
path: ./supercell
submodules: true
- name: "Compile supercell."
working-directory: ./supercell
run: |
run: |
export PKG_CONFIG_PATH="/usr/local/opt/libarchive/lib/pkgconfig"
cmake . -DCMAKE_BUILD_TYPE=Release -DLINK_STATIC_LIBS=ON -DLibArchive_INCLUDE_DIR=/usr/local/opt/libarchive/include && make supercell -j 2
cmake . -DCMAKE_BUILD_TYPE=Release -DLINK_STATIC_LIBS=ON -DLibArchive_INCLUDE_DIR=/usr/local/opt/libarchive/include && make supercell -j 4
- name: "Check supercell"
working-directory: ./supercell
run: 'src/sc_cli/supercell -d -i ./data/examples/Ca2Al2SiO7/Ca2Al2SiO7.cif | grep -q "The total number of combinations is 6"'
- name: "Check supercell dynamic libs."
working-directory: ./supercell
run: 'otool -l src/sc_cli/supercell'
- name: Upload Supercell
uses: actions/upload-artifact@v3.1.1
uses: actions/upload-artifact@v4
with:
name: macos-bin
path: ./supercell/src/sc_cli/supercell
path: ./supercell/src/sc_cli/supercell
deploy-build-linux:
strategy:
fail-fast: false
runs-on: ubuntu-latest
container: ubuntu:18.04
runs-on: ubuntu-20.04
steps:
- name: "Install dependencies"
run: |
apt-get update && apt-get full-upgrade -y
apt-get install -y software-properties-common wget tar cmake build-essential \
ccache libboost-program-options-dev libboost-filesystem-dev libboost-test-dev \
libarchive-dev liblzma-dev libbz2-dev zlib1g-dev zip libboost-system-dev
add-apt-repository ppa:git-core/ppa
add-apt-repository ppa:ubuntu-toolchain-r/test
apt-get update
apt-get install -y git gcc-9 g++-9
- name: Cache
uses: pat-s/[email protected]
with:
path: /github/home/.ccache
key: linux-deploy-cache-${{ github.run_id }} # Can use time based key as well
restore-keys: |
linux-deploy-cache-
- name: "Compile and install dependencies"
run: |
ccache -s
export CC=gcc-9
export CXX=g++-9
export PATH="/usr/lib/ccache:$PATH"
export BASE_DIR=${PWD}
mkdir eigen && cd eigen
wget -nv https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz -O - | tar -zxf -
mkdir build && cd build
cmake ../eigen-3.4.0
make install
cd $BASE_DIR
git clone https://github.com/oneapi-src/oneTBB.git
cd oneTBB && git checkout v2021.7.0
mkdir cmake-build && cd cmake-build
cmake ../ -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=OFF -DTBB_TEST=OFF
make -j 2 && make install
cd $BASE_DIR
wget -nv https://github.com/libarchive/libarchive/releases/download/v3.6.1/libarchive-3.6.1.tar.gz -O - | tar -zxf -
cd libarchive-3.6.1
./configure --without-openssl --without-libb2 --without-xml2 --without-expat --disable-bsdtar
sed -ir '/^.*#define HAVE_LZMA_STREAM_ENCODER_MT 1.*$/d' config.h
make -j 2
make install
cd $BASE_DIR
- name: "Clone supercell"
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
path: ./supercell
submodules: true
- name: "Compile and install supercell"
run: |
export CC=gcc-9
export CXX=g++-9
export PATH="/usr/lib/ccache:$PATH"
cd supercell
cmake . -DCMAKE_BUILD_TYPE=Release -DLINK_STATIC_LIBS=ON && make supercell -j 2
ccache -s
- name: "Test supercell"
run: |
supercell/src/sc_cli/supercell -d -i supercell/data/examples/Ca2Al2SiO7/Ca2Al2SiO7.cif | grep -q "The total number of combinations is 6"
- name: Upload Supercell
uses: actions/[email protected]
- name: "Clone oneTBB"
uses: actions/checkout@v4
with:
repository: oneapi-src/oneTBB
ref: v2021.13.0
path: ./oneTBB
submodules: true
- name: "Compile supercell with deps"
uses: addnab/docker-run-action@v3
with:
image: ubuntu:18.04
options: -v ${{ github.workspace }}:/work
run: |
apt-get update && apt-get full-upgrade -y
apt-get install -y software-properties-common wget tar cmake build-essential \
libboost-program-options-dev libboost-filesystem-dev libboost-test-dev \
libarchive-dev liblzma-dev libbz2-dev zlib1g-dev zip libboost-system-dev
add-apt-repository ppa:git-core/ppa
add-apt-repository ppa:ubuntu-toolchain-r/test
apt-get update
apt-get install -y git gcc-9 g++-9
export CC=gcc-9
export CXX=g++-9
export BASE_DIR="/work"
mkdir ${BASE_DIR}/eigen && cd ${BASE_DIR}/eigen
wget -nv https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz -O - | tar -zxf -
mkdir build && cd build
cmake ../eigen-3.4.0
make install
cd $BASE_DIR/oneTBB
mkdir cmake-build && cd cmake-build
cmake ../ -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=OFF -DTBB_TEST=OFF
make -j 4 && make install
wget -nv https://github.com/libarchive/libarchive/releases/download/v3.7.4/libarchive-3.7.4.tar.gz -O - | tar -zxf -
cd libarchive-3.7.4
./configure --without-openssl --without-libb2 --without-xml2 --without-expat --disable-bsdtar
sed -ir '/^.*#define HAVE_LZMA_STREAM_ENCODER_MT 1.*$/d' config.h
make -j 4
make install
cd $BASE_DIR/supercell
cmake . -DCMAKE_BUILD_TYPE=Release -DLINK_STATIC_LIBS=ON && make supercell -j 4
$BASE_DIR/supercell/src/sc_cli/supercell -d -i $BASE_DIR/supercell/data/examples/Ca2Al2SiO7/Ca2Al2SiO7.cif | grep -q "The total number of combinations is 6"
- name: Upload Supercell
uses: actions/upload-artifact@v4
with:
name: linux-bin
path: ./supercell/src/sc_cli/supercell
deploy-build-windows:
runs-on: ubuntu-20.04
runs-on: ubuntu-22.04
steps:
- name: "Install dependencies"
run: |
sudo apt update && sudo apt -y full-upgrade
sudo apt install -y gcc cmake build-essential wine-stable autopoint gperf intltool libtool libtool-bin lzip p7zip-full python3 python3-mako
- name: "Download MXE"
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
repository: mxe/mxe
path: ./mxe
submodules: true
- name: Cache
uses: pat-s/always-upload-cache@v3.0.11
uses: actions/cache@v4
with:
save-always: true
path: ./mxe/.ccache
key: win-cache-${{ github.run_id }} # Can use time based key as well
restore-keys: |
Expand All @@ -177,14 +182,14 @@ jobs:
working-directory: ./mxe
run: |
sed -i -r 's/ nettle / /g' src/libarchive.mk && sed -i -r 's/with-nettle/without-nettle --without-openssl --without-iconv /g' src/libarchive.mk
make MXE_TARGETS=x86_64-w64-mingw32.static MXE_PLUGIN_DIRS=plugins/gcc10 ccache
make MXE_TARGETS=x86_64-w64-mingw32.static MXE_PLUGIN_DIRS=plugins/gcc13 ccache
echo 'max_size = 15.0G' > .ccache/ccache/ccache.conf
.ccache/bin/ccache -s
make MXE_TARGETS=x86_64-w64-mingw32.static MXE_PLUGIN_DIRS=plugins/gcc10 ccache cc cmake intel-tbb boost eigen libarchive --jobs=4 JOBS=2
.ccache/bin/ccache -s
make MXE_TARGETS=x86_64-w64-mingw32.static MXE_PLUGIN_DIRS=plugins/gcc13 ccache cc cmake intel-tbb boost eigen libarchive --jobs=4 JOBS=4
.ccache/bin/ccache -s
echo "${PWD}/usr/bin" >> $GITHUB_PATH
- name: "Clone supercell"
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
path: ./supercell
submodules: true
Expand All @@ -196,34 +201,34 @@ jobs:
- name: "Run supercell"
working-directory: ./supercell
run: 'wine64 src/sc_cli/supercell.exe -d -i ./data/examples/Ca2Al2SiO7/Ca2Al2SiO7.cif | grep -q "The total number of combinations is 6"'
- name: Upload Supercell
uses: actions/upload-artifact@v3.1.1
- name: Upload Supercell
uses: actions/upload-artifact@v4
with:
name: windows-bin
path: ./supercell/src/sc_cli/supercell.exe

deploy-to-site:
if: github.event_name == 'release'
needs: [deploy-build-linux, deploy-build-macos, deploy-build-windows]
needs: [ deploy-build-linux, deploy-build-macos, deploy-build-windows ]
runs-on: ubuntu-latest
steps:
- name: "Install dependencies"
run: |
sudo apt-get update && sudo apt-get full-upgrade -y
sudo apt-get update
sudo apt-get install -y git wget tar openssh-client zip
- uses: actions/download-artifact@v3
- uses: actions/download-artifact@v4
with:
name: linux-bin
path: ./art/linux
- uses: actions/download-artifact@v3
- uses: actions/download-artifact@v4
with:
name: windows-bin
path: ./art/windows
- uses: actions/download-artifact@v3
- uses: actions/download-artifact@v4
with:
name: macos-bin
path: ./art/osx
path: ./art/osx
- name: "Deploy to file"
env:
SITE_REPO_KEY: ${{ secrets.DEPLOY_KEY }}
Expand All @@ -234,11 +239,11 @@ jobs:
DEPLOY_REPO="[email protected]:orex/orex.github.io.git"
DEPLOY_BRANCH="master"
DEPLOY_DIR="supercell/external"
#
#
mkdir ~/.ssh
eval `ssh-agent -s`
echo "${SITE_REPO_KEY}" | ssh-add -
ssh-keyscan -t rsa github.com > ~/.ssh/known_hosts
ssh-keyscan -t rsa github.com > ~/.ssh/known_hosts
# Clone the existing gh-pages for this repo into out/
# Create a new empty branch if gh-pages doesn't exist yet (should only happen on first deply)
git clone --recurse-submodules "${DEPLOY_REPO}" --branch "${DEPLOY_BRANCH}" out && cd out
Expand All @@ -249,7 +254,7 @@ jobs:
#Main code
mkdir -p "${REPO_PATH}/${DEPLOY_DIR}/exe/."
cd `mktemp -d -t XXXXXX`
wget -nv https://github.com/orex/supercell/raw/deploy/README -O README
wget -nv https://github.com/orex/supercell/raw/deploy/README -O README
for i in ${ART_DIR}/*
do
cp -a "${i}"/* .
Expand All @@ -274,4 +279,4 @@ jobs:
git status
git commit -m "Deploy to GitHub Pages: ${GITHUB_SHA}"
# Now that we're all set up, we can push.
git push $DEPLOY_REPO $DEPLOY_BRANCH
git push $DEPLOY_REPO $DEPLOY_BRANCH
2 changes: 1 addition & 1 deletion 3rd_party/gemmi
Open in desktop
Submodule gemmi updated 515 files
2 changes: 1 addition & 1 deletion 3rd_party/xxHash
Open in desktop
Submodule xxHash updated 58 files
+7 −0 .github/dependabot.yml
+243 −52 .github/workflows/ci.yml
+5 −0 .gitignore
+24 −0 CHANGELOG
+9 −4 Doxyfile
+63 −0 Doxyfile-internal
+1 −1 LICENSE
+114 −20 Makefile
+35 −18 README.md
+13 −0 SECURITY.md
+3 −0 cli/.tipi/deps
+0 −0 cli/.tipi/opts
+24 −8 cli/xsum_arch.h
+13 −1 cli/xsum_bench.c
+30 −4 cli/xsum_os_specific.c
+1 −1 cli/xsum_os_specific.h
+2 −1 cli/xsum_output.c
+1 −1 cli/xsum_output.h
+30 −28 cli/xsum_sanity_check.c
+1 −1 cli/xsum_sanity_check.h
+31 −17 cli/xxhsum.1
+33 −27 cli/xxhsum.1.md
+229 −22 cli/xxhsum.c
+49 −11 cmake_unofficial/CMakeLists.txt
+23 −0 cmake_unofficial/JoinPaths.cmake
+1 −0 cmake_unofficial/README.md
+474 −5 doc/xxhash_spec.md
+3 −3 libxxhash.pc.in
+25 −2 tests/Makefile
+1 −1 tests/bench/Makefile
+3 −1 tests/bench/benchHash.c
+1 −1 tests/bench/benchHash.h
+2 −1 tests/bench/benchfn.c
+1 −1 tests/bench/benchfn.h
+1 −1 tests/bench/bhDisplay.c
+1 −1 tests/bench/bhDisplay.h
+1 −1 tests/bench/hashes.h
+1 −1 tests/bench/main.c
+1 −1 tests/bench/timefn.c
+1 −1 tests/bench/timefn.h
+32 −0 tests/cli-comment-line.sh
+51 −0 tests/cli-ignore-missing.sh
+1 −1 tests/collisions/Makefile
+1 −1 tests/collisions/hashes.h
+2 −2 tests/collisions/main.c
+1 −1 tests/collisions/pool.c
+1 −1 tests/collisions/pool.h
+1 −1 tests/collisions/sort.cc
+1 −1 tests/collisions/sort.hh
+21 −0 tests/filename-escape.sh
+763 −0 tests/sanity_test.c
+45,832 −0 tests/sanity_test_vectors.h
+464 −0 tests/sanity_test_vectors_generator.c
+1 −1 xxh3.h
+145 −70 xxh_x86dispatch.c
+9 −10 xxh_x86dispatch.h
+1 −1 xxhash.c
+2,108 −915 xxhash.h
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