Add scripts to compile DTK with sanitizer and modify scripts that all…

…ow jenkins to launch the new job.

docker/jenkins/build.sh

@@ -7,14 +7,25 @@ cd ${TRILINOS_DIR}/DataTransferKit
 [ -d build ] && rm -rf build
 mkdir build && cd build
 # configure trilinos with dtk
+if [ ${SANITIZE} == "undefined" ]
+then . ../scripts/docker_clang_env.sh undefined_sanitizer
+../scripts/docker_cmake -D Trilinos_ENABLE_Fortran=OFF -D TPL_ENABLE_MOAB=OFF
+elif [ ${SANITIZE} == "thread" ]
+then . ../scripts/docker_clang_env.sh thread_sanitizer
+../scripts/docker_cmake -D Trilinos_ENABLE_Fortran=OFF
+else
 ../scripts/docker_cmake -D Trilinos_ENABLE_COVERAGE_TESTING=ON
+fi
 # build
 make -j${NPROC} -i
 # run the unit tests
 ctest -j${NPROC} --no-compress-output -T Test
+if [ -z ${SANITIZE} ]
+then
 # collect coverage data
 lcov --capture --directory DataTransferKit --output-file lcov.info
 # upload it to codecov
 curl -s https://codecov.io/bash -o codecov_bash_uploader
 chmod +x codecov_bash_uploader
 ./codecov_bash_uploader -Z -X gcov -f lcov.info
+fi

docker/jenkins/config.dict

@@ -4,15 +4,16 @@
   'tag': 'latest',
   'name': os.getenv("BUILD_TAG"),
   'cmd': [
-    'sh -c "patch -d /scratch/source/trilinos/release -p1 -i /scratch/source/trilinos/release/DataTransferKit/docker/jenkins/trilinos_stk.patch"',
-    'sh -xe /scratch/source/trilinos/release/DataTransferKit/docker/jenkins/build.sh',
+    'bash -c "patch -d /scratch/source/trilinos/release -p1 -i /scratch/source/trilinos/release/DataTransferKit/docker/jenkins/trilinos_stk.patch"',
+    'bash -xe /scratch/source/trilinos/release/DataTransferKit/docker/jenkins/build.sh',
   ],
   'volumes': [
     os.getenv("WORKSPACE") + ':/scratch/source/trilinos/release/DataTransferKit',
   ],
   'environment': {
     'NPROC': '16',
     'CODECOV_TOKEN': os.getenv("CODECOV_TOKEN"),
+    'SANITIZE': os.getenv("SANITIZE"),
     'JENKINS_URL': os.getenv("JENKINS_URL"),
     'BUILD_NUMBER': os.getenv("BUILD_NUMBER"),
     'BUILD_URL': os.getenv("BUILD_URL"),

scripts/docker_clang_env.sh

@@ -0,0 +1,19 @@
+# Use clang instead of gcc
+export OMPI_CC=/usr/bin/clang-3.9
+export OMPI_CXX=/usr/bin/clang++-3.9
+export CC=mpicc
+export CXX=mpicxx
+
+# Add clang OpenMP runtime library to LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+
+SANITIZER=$1
+if [ "$SANITIZER" == "undefined_sanitizer" ]
+  then FLAGS="-fsanitize=address -fsanitize=undefined -fsanitize-blacklist=/scratch/source/trilinos/release/DataTransferKit/scripts/undefined_blacklist.txt"
+  # Suppress leak sanitizer on functions we have no control of.
+  export LSAN_OPTIONS=suppressions=/scratch/source/trilinos/release/DataTransferKit/scripts/leak_blacklist.txt
+elif [ "$SANITIZER" == "thread_sanitizer" ]
+  then FLAGS="-fsanitize=thread"
+fi
+
+export SANITIZER_FLAGS="$FLAGS"

scripts/docker_cmake

@@ -7,7 +7,7 @@ ARGS=(
     -D BUILD_SHARED_LIBS=ON
     ### COMPILERS AND FLAGS ###
     -D CMAKE_CXX_FLAGS="-Wall -Wpedantic"
-    -D DataTransferKit_CXX_FLAGS="-Wall -Wno-shadow -Wpedantic"
+    -D DataTransferKit_CXX_FLAGS="-Wall -Wno-shadow -Wpedantic ${SANITIZER_FLAGS}"
     ### TPLs ###
     -D TPL_ENABLE_MPI=ON
     -D TPL_ENABLE_BLAS=ON

scripts/leak_blacklist.txt

@@ -0,0 +1,3 @@
+leak:libmpi.so
+leak:libopen-pal.so
+leak:exe

scripts/undefined_blacklist.txt

@@ -0,0 +1,3 @@
+# This two problems seem related
+src:/scratch/source/trilinos/release/packages/stk/stk_mesh/*
+src:/usr/bin/../lib/gcc/x86_64-linux-gnu/5.4.0/../../../../include/c\+\+/5.4.0/bits/*