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

.gitignore

 example*
-build
 CMakeCache.txt
 CMakeFiles
 Makefile

.gitlab-ci.yml

@@ -7,7 +7,8 @@ before_script:
 # tests have been done.
 stages:
   - build
-#  - coverage
+  - test
+  - coverage
 
 # default build (without CUDA)
 build-gcc-mpi-nocuda:

.gitlab-ci/build/run_build.sh

+#!/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

.gitlab-ci/test/run_coverage.sh

+#!/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
+
+
+  

.gitlab-ci/test/run_test.sh

+#!/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
+
+
+