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Delay null file handle closure until after post-processing #522

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Delay null file handle closure until after post-processing

Delay null file handle closure until after post-processing #522

Workflow file for this run

.github/workflows/CI.yaml at cd9b9aa
name: CI
on:
push:
branches:
- main
pull_request:
branches:
- main
schedule:
- cron: "0 0 * * 0"
# Download links for the Intel MKL library & Fortran compiler from:
# https://www.intel.com/content/www/us/en/developer/articles/tool/oneapi-standalone-components.html
# (while MKL is available through several package managers, the compiler is not and we are grouping these dependencies for simplicity)
env:
IFORT_LINUX_URL: https://registrationcenter-download.intel.com/akdlm/IRC_NAS/0d65c8d4-f245-4756-80c4-6712b43cf835/l_fortran-compiler_p_2023.2.1.8_offline.sh
MKL_LINUX_URL: https://registrationcenter-download.intel.com/akdlm/IRC_NAS/adb8a02c-4ee7-4882-97d6-a524150da358/l_onemkl_p_2023.2.0.49497_offline.sh
IFORT_MAC_URL: https://registrationcenter-download.intel.com/akdlm/IRC_NAS/2fbce033-15f4-4e13-8d14-f5a2016541ce/m_fortran-compiler-classic_p_2023.2.0.49001_offline.dmg
MKL_MAC_URL: https://registrationcenter-download.intel.com/akdlm/IRC_NAS/9399bece-76fb-4b1c-b15c-8ac295448513/m_onemkl_p_2023.2.0.49501_offline.dmg
IFORT_WINDOWS_URL: https://registrationcenter-download.intel.com/akdlm/IRC_NAS/1720594b-b12c-4aca-b7fb-a7d317bac5cb/w_fortran-compiler_p_2023.2.1.7_offline.exe
MKL_WINDOWS_URL: https://registrationcenter-download.intel.com/akdlm/IRC_NAS/2b9cdf66-5291-418e-a7e8-f90515cc9098/w_onemkl_p_2023.2.0.49500_offline.exe
IFORT_WINDOWS_VERSION: 2023.2.1
MKL_WINDOWS_VERSION: 2023.2.0
jobs:
linux-static:
runs-on: ubuntu-latest
timeout-minutes: 30
steps:
- name: Check number of cores
run: |
lscpu
lscpu | grep "CPU(s): " | awk '{print $2}' > num_cores
echo "NUM_CORES=$(cat num_cores)" >> $GITHUB_ENV
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.x'
- name: Install dependencies with PyPI
run: pip install numpy
- name: Configure MOPAC with CMake
run: |
cmake -B build \
-DCMAKE_BUILD_TYPE=Debug \
-DTHREADS_KEYWORD=OFF \
-DSTATIC_BUILD=ON
- name: Build MOPAC with Make
run: |
cmake --build build -- -j$NUM_CORES
# - name: Run Valgrind on MOPAC API tester
# run: |
# sudo apt update && sudo apt install -y valgrind
# cd build/tests
# valgrind -s --track-origins=yes --leak-check=yes ./mopac-api-test
- name: Test MOPAC with CTest
run: |
cd build
ctest -V -j $NUM_CORES
- name: Save test results as an artifact (on failure)
if: ${{ failure() }}
uses: actions/upload-artifact@v4
with:
name: static-test-output
path: build/tests
code-coverage:
runs-on: ubuntu-latest
timeout-minutes: 30
steps:
- name: Check number of cores
run: |
lscpu
lscpu | grep "CPU(s): " | awk '{print $2}' > num_cores
echo "NUM_CORES=$(cat num_cores)" >> $GITHUB_ENV
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.x'
- name: Install lcov with Ubuntu package manager
run: sudo apt-get install lcov
- name: Install dependencies with PyPI
run: pip install numpy
- name: Configure MOPAC with CMake
run: |
cmake -B build \
-DCMAKE_BUILD_TYPE=Debug \
-DTHREADS_KEYWORD=OFF \
-DENABLE_COVERAGE=ON
- name: Build MOPAC with Make
run: |
cmake --build build -- -j$NUM_CORES
# - name: Run Valgrind on MOPAC API tester
# run: |
# sudo apt update && sudo apt install -y valgrind
# cd build/tests
# valgrind -s --track-origins=yes --leak-check=yes ./mopac-api-test
- name: Test MOPAC with CTest
run: |
cd build
ctest -V -j $NUM_CORES
- name: Save test results as an artifact (on failure)
if: ${{ failure() }}
uses: actions/upload-artifact@v4
with:
name: coverage-test-output
path: build/tests
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v4
with:
directory: build
files: coverage.info
token: ${{ secrets.CODECOV_TOKEN }}
linux-build:
# Ubuntu 22+ switched to newer glibc (2.34) that breaks the compatibility library right now
runs-on: ubuntu-20.04
timeout-minutes: 30
steps:
- name: Check number of cores
run: |
lscpu
lscpu | grep "CPU(s): " | awk '{print $2}' > num_cores
echo "NUM_CORES=$(cat num_cores)" >> $GITHUB_ENV
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.x'
# Set up the QT installer framework
- uses: jmarrec/setup-qtifw@v1
with:
qtifw-version: '4.6.x'
- name: Cache Intel dependencies
id: cache-intel
uses: actions/cache@v4
with:
path: /opt/intel
key: cache-${{ env.IFORT_LINUX_URL }}-${{ env.MKL_LINUX_URL }}
- name: Download & install Intel dependencies
if: steps.cache-intel.outputs.cache-hit != 'true'
run: |
curl $IFORT_LINUX_URL --output ifort_download.sh
sudo sh ifort_download.sh -a --silent --eula accept
curl $MKL_LINUX_URL --output mkl_download.sh
sudo sh mkl_download.sh -a --silent --eula accept
- name: Clone glibc compatibility library
uses: actions/checkout@v4
with:
repository: wheybags/glibc_version_header
path: glibc
- name: Install dependencies with PyPI
run: pip install numpy
- name: Configure MOPAC with CMake
run: |
source /opt/intel/oneapi/setvars.sh
cmake -B build \
-DCMAKE_Fortran_COMPILER=ifort \
-DCMAKE_Fortran_FLAGS="-static-intel" \
-DCMAKE_C_COMPILER=gcc \
-DCMAKE_C_FLAGS="-include $GITHUB_WORKSPACE/glibc/version_headers/x64/force_link_glibc_2.17.h" \
-DAUTO_BLAS=OFF \
-DMOPAC_LINK="-Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -liomp5 -lpthread -lm -ldl"
- name: Build MOPAC with Make
run: |
source /opt/intel/oneapi/setvars.sh
cmake --build build -- -j$NUM_CORES
ldd -v build/mopac
- name: Test MOPAC with CTest
run: |
source /opt/intel/oneapi/setvars.sh
cd build
ctest -V -j $NUM_CORES
- name: Save test results as an artifact (on failure)
if: ${{ failure() }}
uses: actions/upload-artifact@v4
with:
name: linux-test-output
path: build/tests
- name: Package MOPAC with CPack
run: |
source /opt/intel/oneapi/setvars.sh
cd build
cpack -G IFW
ls -l
- name: Local installation test & minimal packaging
run: |
cd build
sudo make install
sudo cpack -G TGZ
- name: Save executable as an artifact
uses: actions/upload-artifact@v4
with:
name: linux-dist
path: build/mopac-*-linux.*
mac-build:
# macos-latest is now ARM-based, MOPAC is being distributed for Intel-based Macs right now, so using latest free Intel-based standard runner
runs-on: macos-13
timeout-minutes: 30
steps:
- name: Check number of cores
run: |
system_profiler SPHardwareDataType
system_profiler SPHardwareDataType | grep "Total Number of Cores" | awk '{print $5}' > num_cores
echo "NUM_CORES=$(cat num_cores)" >> $GITHUB_ENV
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.x'
# Set up the QT installer framework
- uses: jmarrec/setup-qtifw@v1
with:
qtifw-version: '4.6.x'
- name: Fix permissions for cache restore
run: |
sudo mkdir -p /opt/intel
sudo chown $USER /opt/intel
- name: Cache Intel Fortran compiler
id: cache-intel
uses: actions/cache@v4
with:
path: /opt/intel
key: cache-${{ env.IFORT_MAC_URL }}-${{ env.MKL_MAC_URL }}-macos-13
- name: Download & install Intel Fortran compiler
if: steps.cache-intel.outputs.cache-hit != 'true'
run: |
curl $MKL_MAC_URL --output mkl_download.dmg
hdiutil attach mkl_download.dmg
sudo /Volumes/m_onemkl*/bootstrapper.app/Contents/MacOS/install.sh --silent --eula accept
curl $IFORT_MAC_URL --output ifort_download.dmg
hdiutil attach ifort_download.dmg
sudo /Volumes/m_fortran-compiler*/bootstrapper.app/Contents/MacOS/install.sh --silent --eula accept
- name: Install dependencies with PyPI
run: pip3 install numpy
# AUTO_BLAS=OFF because find_package(BLAS) has a bug with static BLAS libraries on Mac
- name: Configure MOPAC with CMake
run: |
source /opt/intel/oneapi/setvars.sh
cmake -B build \
-DCMAKE_OSX_DEPLOYMENT_TARGET=10.8 \
-DCMAKE_Fortran_COMPILER=ifort \
-DCMAKE_Fortran_FLAGS="-static-intel" \
-DCMAKE_C_COMPILER=gcc \
-DAUTO_BLAS=OFF \
-DCMAKE_SHARED_LINKER_FLAGS="-Wl,-ld_classic" \
-DCMAKE_EXE_LINKER_FLAGS="-Wl,-ld_classic" \
-DMOPAC_LINK="${MKLROOT}/lib/libmkl_intel_lp64.a ${MKLROOT}/lib/libmkl_intel_thread.a ${MKLROOT}/lib/libmkl_core.a -liomp5 -lpthread -lm -ldl"
# an Intel-suggested hack is temporarily circumventing excessively slow calls to xcodebuild hidden in ifort, taken from:
# https://community.intel.com/t5/Intel-oneAPI-HPC-Toolkit/slow-execution-of-ifort-icpc-on-MacOSX-catalina/m-p/1203190
- name: Build MOPAC with Make
run: |
source /opt/intel/oneapi/setvars.sh
mkdir xcode_hack
echo -ne '#!/bin/bash\ncase "$4" in\n "")\n echo $INTEL_OSXSDK_VER;;\n *)\n echo $INTEL_OSXSDK_PATH;;\nesac\n' > xcode_hack/xcodebuild
chmod 755 xcode_hack/xcodebuild
export INTEL_OSXSDK_VER=`xcodebuild -sdk macosx -version | grep SDKVersion`
export INTEL_OSXSDK_PATH=`xcodebuild -sdk macosx -version Path`
export PATH=$GITHUB_WORKSPACE/xcode_hack:${PATH}
cmake --build build -- -j$NUM_CORES
- name: Test MOPAC with CTest
run: |
source /opt/intel/oneapi/setvars.sh
cd build
ctest -V -j $NUM_CORES
- name: Save test results as an artifact (on failure)
if: ${{ failure() }}
uses: actions/upload-artifact@v4
with:
name: mac-test-output
path: build/tests
- name: Local installation test
run: |
cd build
make install
- name: Package MOPAC with CPack
run: |
source /opt/intel/oneapi/setvars.sh
cd build
cpack -G IFW
ls -l
- name: Local installation test & minimal packaging
run: |
cd build
sudo make install
sudo cpack -G ZIP
- name: Save executable as an artifact
uses: actions/upload-artifact@v4
with:
name: mac-dist
path: build/mopac-*-mac.*
windows-build:
# NOTE: windows-latest has been switched to Visual Studio 2022, which is not yet supported by Intel development tools
runs-on: windows-2019
timeout-minutes: 30
steps:
- name: Check number of cores
shell: bash
run: |
WMIC CPU Get -Format:List
WMIC CPU Get NumberOfLogicalProcessors | head -2 | tail -1 > num_cores
echo "NUM_CORES=$(cat num_cores)" >> $GITHUB_ENV
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.x'
# Set up the QT installer framework
- uses: jmarrec/setup-qtifw@v1
with:
qtifw-version: '4.6.x'
- name: Cache Intel Fortran compiler
id: cache-intel
uses: actions/cache@v4
with:
path: C:\Program Files (x86)\Intel
key: cache-${{ env.IFORT_WINDOWS_URL }}-${{ env.MKL_WINDOWS_URL }}
- name: Download & install Intel Fortran compiler
if: steps.cache-intel.outputs.cache-hit != 'true'
shell: cmd
run: |
curl ${{ env.IFORT_WINDOWS_URL }} --output ifort_download.exe
ifort_download -s -x -f ifort_unpack
ifort_unpack\bootstrapper --silent --eula accept -p=NEED_VS2019_INTEGRATION=0
curl ${{ env.MKL_WINDOWS_URL }} --output mkl_download.exe
mkl_download -s -x -f mkl_unpack
mkl_unpack\bootstrapper --silent --eula accept -p=NEED_VS2019_INTEGRATION=0
- name: Install dependencies with PyPI
run: pip3 install numpy
# The main Intel\oneAPI\setvars.bat script is not setting up the correct version of ifort, so using component-level scripts
- name: Configure MOPAC with CMake
shell: cmd
run: |
call "C:\Program Files (x86)\Intel\oneAPI\compiler\${{ env.IFORT_WINDOWS_VERSION }}\env\vars.bat"
call "C:\Program Files (x86)\Intel\oneAPI\mkl\${{ env.MKL_WINDOWS_VERSION }}\env\vars.bat"
echo %PATH%
cmake -Bbuild ^
-GNinja ^
-DBUILD_BZ=ON ^
-DCMAKE_Fortran_COMPILER=ifort ^
-DCMAKE_Fortran_FLAGS="/libs:static" ^
-DBLA_STATIC=ON ^
-DBLA_VENDOR=Intel10_64lp
- name: Build MOPAC with Ninja
shell: cmd
run: |
call "C:\Program Files (x86)\Intel\oneAPI\compiler\${{ env.IFORT_WINDOWS_VERSION }}\env\vars.bat"
call "C:\Program Files (x86)\Intel\oneAPI\mkl\${{ env.MKL_WINDOWS_VERSION }}\env\vars.bat"
cmake --build build -- -v
- name: Test MOPAC with CTest
shell: cmd
run: |
call "C:\Program Files (x86)\Intel\oneAPI\compiler\${{ env.IFORT_WINDOWS_VERSION }}\env\vars.bat"
call "C:\Program Files (x86)\Intel\oneAPI\mkl\${{ env.MKL_WINDOWS_VERSION }}\env\vars.bat"
cd build
ctest -V -j %NUM_CORES%
- name: Save test results as an artifact (on failure)
if: ${{ failure() }}
uses: actions/upload-artifact@v4
with:
name: windows-test-output
path: build/tests
- name: Local installation test
shell: cmd
run: |
cd build
cmake --install .
- name: Package MOPAC with CPack (in development)
shell: cmd
run: |
call "C:\Program Files (x86)\Intel\oneAPI\compiler\${{ env.IFORT_WINDOWS_VERSION }}\env\vars.bat"
call "C:\Program Files (x86)\Intel\oneAPI\mkl\${{ env.MKL_WINDOWS_VERSION }}\env\vars.bat"
cd build
cpack -G IFW
dir
- name: Local installation test & minimal packaging
shell: cmd
run: |
call "C:\Program Files (x86)\Intel\oneAPI\compiler\${{ env.IFORT_WINDOWS_VERSION }}\env\vars.bat"
call "C:\Program Files (x86)\Intel\oneAPI\mkl\${{ env.MKL_WINDOWS_VERSION }}\env\vars.bat"
cd build
make install
cpack -G ZIP
- name: Save executable as an artifact
uses: actions/upload-artifact@v4
with:
name: windows-dist
path: build/mopac-*-win.*