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Add 'rescut' and 'bondoffset' keywords to 'prepareforleap' #469

Add 'rescut' and 'bondoffset' keywords to 'prepareforleap'

Add 'rescut' and 'bondoffset' keywords to 'prepareforleap' #469

Workflow file for this run

name: Cpptraj Tests
on:
push:
branches: [master]
pull_request:
branches: [master]
jobs:
linux_build:
runs-on: ubuntu-latest
name: Build ${{ matrix.compiler }} with CMake ${{ matrix.use_cmake }}
strategy:
fail-fast: false
matrix:
compiler: ["gnu", "clang"]
use_cmake: ["0", "1"]
use_openmp: ["no"]
use_mpi: ["no"]
include:
- use_openmp: "yes"
compiler: "gnu"
use_mpi: "no"
use_cmake: "0"
- use_openmp: "no"
compiler: "gnu"
use_mpi: "yes"
use_cmake: "0"
- use_openmp: "yes"
compiler: "gnu"
use_mpi: "yes"
use_cmake: "0"
- use_openmp: "no"
compiler: "gnu"
use_mpi: "yes"
use_cmake: "1"
env:
COMPILER: ${{ matrix.compiler }}
USE_CMAKE: ${{ matrix.use_cmake }}
BUILD_TYPE: "install"
TEST_TYPE: "test.showerrors"
USE_MPI: ${{ matrix.use_mpi }}
USE_OPENMP: ${{ matrix.use_openmp }}
steps:
- name: Install prerequisite packages
run: |
sudo apt-get install gfortran
sudo apt-get install libbz2-dev
sudo apt-get install libblas-dev liblapack-dev
sudo apt-get install libfftw3-dev
sudo apt-get install clang
sudo apt-get install cmake-data cmake
- name: Checkout source code
uses: actions/checkout@v4
- name: Compile and test cpptraj
shell: bash -lex {0}
run: |
curl -OL https://anaconda.org/AmberMD/amber_phenix/0.9.6/download/linux-64/amber_phenix-0.9.6-0.tar.bz2
tar jxf amber_phenix-0.9.6-0.tar.bz2 lib/libsander.so AmberTools/src/sander/sander.h
mkdir -p include && mv AmberTools/src/sander/sander.h include
mv lib include $HOME
if [ $USE_OPENMP = "yes" ]; then
export OPT="openmp"
export OMP_NUM_THREADS=4
if [ "$USE_CMAKE" = "1" ]; then
export BUILD_FLAGS="-DOPENMP=TRUE"
else
export BUILD_FLAGS="-openmp"
fi
fi
if [ $USE_MPI = "yes" ]; then
curl -OL http://www.mpich.org/static/downloads/3.4.2/mpich-3.4.2.tar.gz
tar -zxf mpich-3.4.2.tar.gz
cd mpich-3.4.2
export FFLAGS=-fallow-argument-mismatch
./configure --with-device=ch3 --prefix=$HOME
make -j2
make install
cd ..
export PATH=$HOME/bin:$PATH
export LD_LIBRARY_PATH=$HOME/lib:$LD_LIBRARY_PATH
export DO_PARALLEL="mpirun -n 2"
if [ $USE_OPENMP = "yes" ]; then
export OMP_NUM_THREADS=1
fi
if [ "$USE_CMAKE" = "1" ]; then
export BUILD_FLAGS="-DMPI=TRUE ${BUILD_FLAGS}"
else
export BUILD_FLAGS="-mpi ${BUILD_FLAGS}"
fi
fi
if [ "$USE_CMAKE" = "1" ]; then
curl -OL https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.2.tar.gz
tar -zxf v4.9.2.tar.gz
cd netcdf-c-4.9.2
./configure --disable-byterange --disable-libxml2 --disable-netcdf-4 --disable-dap --disable-doxygen --prefix=$HOME
make -j2
make install
cd ..
export PATH=$HOME/bin:$PATH
export LD_LIBRARY_PATH=$HOME/lib:${LD_LIBRARY_PATH}
mkdir build install
installdir=$(pwd)
cd build
cmake .. $BUILD_FLAGS -DCOMPILER=${COMPILER^^} -DINSTALL_HEADERS=FALSE \
-DCMAKE_INSTALL_PREFIX=$installdir -DCMAKE_LIBRARY_PATH=$HOME/lib \
-DPRINT_PACKAGING_REPORT=TRUE -DNetCDF_LIBRARIES_C=$HOME/lib/libnetcdf.so \
-DNetCDF_INCLUDES=$HOME/include
make -j2 install
cd ..
export PATH=$installdir/bin:$PATH
else
export LD_LIBRARY_PATH=$HOME/lib:${LD_LIBRARY_PATH}
./configure --buildlibs ${BUILD_FLAGS} ${COMPILER}
source cpptraj.sh
make -j2 install
fi
cd test && make $TEST_TYPE
build-pytraj:
runs-on: ubuntu-latest
strategy:
max-parallel: 5
steps:
- name: Install prerequisite packages
run: |
sudo apt-get install gfortran
sudo apt-get install libbz2-dev
sudo apt-get install libblas-dev liblapack-dev
sudo apt-get install libfftw3-dev
sudo apt-get install clang
sudo apt-get install cmake-data cmake
- uses: actions/checkout@v4
- name: Set up Python 3.10
uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: Add conda to system path
run: |
# $CONDA is an environment variable pointing to the root of the miniconda directory
echo $CONDA/bin >> $GITHUB_PATH
- name: Install conda packages
run: |
which conda
conda install conda=23.11.0 python=3.10
conda --version
conda env update --file devtools/ci/environment.yml --name base
- name: Install cpptraj
run: |
export PATH=$HOME/bin:${PATH}
export LD_LIBRARY_PATH=$HOME/lib:${LD_LIBRARY_PATH}
export MAKE_COMMAND="make -j2"
./configure --buildlibs -openmp -shared gnu
source cpptraj.sh
make -j2 libcpptraj
- name: Install pytraj
run: |
git clone https://github.com/Amber-MD/pytraj.git
source cpptraj.sh
cd pytraj
python setup.py install
cd ..
- name: Test with pytest
run: |
source cpptraj.sh && cd pytraj/tests && pytest -vs --ignore=test_parallel_pmap