Commit 67c620e2 authored by Markus Rampp's avatar Markus Rampp

CI: restructure .gitlab-ci.yml, add small run test from tutorial, add coverage

parent 739090fd
Pipeline #5438 passed with stage
example*
build
CMakeCache.txt
CMakeFiles
Makefile
......
......@@ -7,7 +7,8 @@ before_script:
# tests have been done.
stages:
- build
# - coverage
- test
- coverage
# default build (without CUDA)
build-gcc-mpi-nocuda:
......
#!/bin/bash
ARCHITECTURE=$1
DEBUG=${2:-no}
. /etc/profile.d/modules.sh
module use /afs/ipp/common/usr/modules.2014/@sys/modulefiles/GPU
module load cmake
echo "building BioEM with ARCH=$ARCHITECTURE"
case "$ARCHITECTURE" in
intel-mpi)
module load intel/15.0 impi/5.0.3 fftw/3.3.4 boost/intel/1.56
rm -rf build/; mkdir build
cd build
cmake .. -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc
make VERBOSE=1 -j 2
;;
gcc-mpi)
module load gcc/4.9 impi/5.0.3 fftw/gcc/3.3.4 boost/gcc/1.56
rm -rf build/; mkdir build
cd build
cmake .. -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS_DEBUG='-g -Wall --coverage' -DCMAKE_C_FLAGS_DEBUG='-g -Wall --coverage'
make VERBOSE=1 -j 2
;;
gcc-mpi-cuda)
module load gcc/4.9 cuda/7.5 impi/5.0.3 fftw/gcc/3.3.4 boost/gcc/1.56
rm -rf build/; mkdir build
cd build
cmake .. -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DUSE_CUDA=on -DCUDA_CUDA_LIBRARY=$CUDA_HOME/lib64/stubs/libcuda.so
make VERBOSE=1 -j 2
;;
*)
echo "ARCHITECTURE $ARCHITECTURE not defined for build"
exit 1
;;
esac
module list
#!/bin/bash
INPUT_DIR=$1
OUTPUT_DIR=$2
. /etc/profile.d/modules.sh
module load gcc/4.9
mkdir $OUTPUT_DIR
lcov --no-checksum --capture --directory $INPUT_DIR --output-file coverage.info
lcov -r coverage.info */boost/* --output-file coverage.info
lcov -r coverage.info /usr/* --output-file coverage.info
lcov -r coverage.info /usr/include/* --output-file coverage.info
lcov -r coverage.info *4.9.3* --output-file coverage.info
genhtml coverage.info --output-directory $OUTPUT_DIR
#!/bin/bash
#env
ARCH=$1
NUMPROCS=${2:-4}
NUMTHRDS=${3:-2}
. /etc/profile.d/modules.sh
module load impi
export OMP_NUM_THREADS=$NUMTHRDS
export OMP_PLACES=cores
export OMP_STACKSIZE=128M
cp -r Tutorial_BioEM test1
cd test1
mpiexec -n $NUMPROCS ../build/bioEM --Inputfile Param_Input --Modelfile Model_Text --Particlesfile Text_Image_Form
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