# these are the different stages for our pipelines # jobs in the same stage run in parallel # next stage doesn't start until previous stage finishes with 'OK' # by now we only do build and test, we could add another stage "deploy" if # needed stages: - test # CentOS7 STAGE test:centos7.3: stage: test image: centos:7.3.1611 before_script: - echo "Running centos7.3 'before_script'..." - yum -y -q -e 0 install tcl - yum -y -q -e 0 install glibc-common - yum -y -q -e 0 install glibc-devel - yum -y -q -e 0 install make - yum -y -q -e 0 install libicu - yum -y -q -e 0 install libjpeg-turbo - yum -y -q -e 0 install freetype - yum -y -q -e 0 install openssl - mkdir -p /scicore/soft/modules - ln -s /export/soft/apps/centos7/generic /scicore/soft/apps - ln -s /export/soft/modules/centos7/generic/all /scicore/soft/modules - source /export/soft/lua_lmod/centos7/lmod/lmod/init/bash - module use /scicore/soft/modules/all - module load foss/2018b - module load CMake/3.12.1-GCCcore-7.3.0 - module load Python/3.6.6-foss-2018b - module load Eigen/3.3.1 - module load Boost/1.68.0-foss-2018b-Python-3.6.6 - module load LibTIFF/.4.0.9-GCCcore-7.3.0 - module load libpng/.1.6.34-GCCcore-7.3.0 - module load HH-suite/3.2.0-foss-2018b-Boost-1.68.0-Python-3.6.6 - module load Perl/5.28.0-GCCcore-7.3.0 - module load OpenMM/7.1.1-foss-2018b-Python-3.6.6 - module load SQLite/3.24.0-GCCcore-7.3.0 - module load dssp/2.2.1-foss-2018b-Boost-1.68.0-Python-3.6.6 - module load msms/2.6.1-linux-x86_64 - module load ClustalW2/2.1-foss-2018b - module load networkx/2.5.1-foss-2018b-Python-3.6.6 - echo "... done running centos7.3 'before_script'." script: - echo "Testing on CentOS 7..." - echo " Building OST..." - mkdir build-ci - cd build-ci - cmake .. -DENABLE_MM=1 -DOPEN_MM_LIBRARY=$EBROOTOPENMM/lib/libOpenMM.so -DOPEN_MM_PLUGIN_DIR=$EBROOTOPENMM/lib/plugins -DOPEN_MM_INCLUDE_DIR=$EBROOTOPENMM/include -DCOMPILE_TMTOOLS=1 -DENABLE_INFO=OFF -DENABLE_GFX=OFF -DENABLE_GUI=OFF -DUSE_NUMPY=1 -DUSE_RPATH=1 -DPython_ROOT_DIR=$EBROOTPYTHON -DEIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include -DFFTW_LIBRARY=$EBROOTFFTW/lib/libfftw3f.a -DFFTW_INCLUDE_DIR=$EBROOTFFTW/include -DSQLITE3_LIBRARY=$EBROOTSQLITE/lib/libsqlite3.so -DSQLITE3_INCLUDE_DIR=$EBROOTSQLITE/include -DBOOST_ROOT=$EBROOTBOOST -DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.so -DPNG_PNG_INCLUDE_DIR=$EBROOTLIBPNG/include -DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so -DZLIB_INCLUDE_DIR=$EBROOTZLIB/include -DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include -DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.so -DZLIB_INCLUDE_DIR=$EBROOTZLIB/include -DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so -DOPTIMIZE=1 -DCMAKE_C_FLAGS='-L${EBROOTLIBPNG}/lib/ -L${EBROOTLIBTIFF}/lib/ -L${EBROOTZLIB}/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include' -DCMAKE_CXX_FLAGS='-L${EBROOTLIBPNG}/lib/ -L${EBROOTLIBTIFF}/lib/ -L${EBROOTZLIB}/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include' -DCMAKE_EXE_LINKER_FLAGS=" -pthread" - make -j 2 - echo " ... done building OST." - echo " Running unit tests for OST..." - make check - echo " ... done running unit tests for OST..." - echo "... done testing on CentOS 7."