Fix docker MPI issues? (#185) (#207)

* Fix docker MPI issues due to lack of SYS_PTRACE permissions (disable Vader) (Closes #185)

* Disable Infiniband for OpenMPI

* enable tcp via loopback

* Set RelWithDebInfo as default build type

CMakeModules/BuildType.cmake

@@ -1,6 +1,6 @@
 # Set a default build type if none was specified.
 # If inside git repository build debug, otherwise release.
-set(default_build_type "Release")
+set(default_build_type "RelWithDebInfo")
 if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
   set(default_build_type "Debug")
 endif()

container/charliecloud/parpe_base/install_parpe.sh

@@ -36,7 +36,7 @@ CC=mpicc CXX=mpiCC cmake \
       -DCERES_INCLUDE_DIRS="/usr/include/;/usr/include/eigen3" \
       -DMPI_INCLUDE_DIRS=/usr/include/openmpi-x86_64/ \
       -DBUILD_TESTS=ON \
-      "-DTESTS_MPIEXEC_COMMAND=mpiexec;--allow-run-as-root;-n;4;--oversubscribe" \
+      "-DTESTS_MPIEXEC_COMMAND=mpiexec;--allow-run-as-root;-n;4;--oversubscribe;--mca;btl_vader_single_copy_mechanism;none;--mca;btl;^openib;--mca;oob_tcp_if_include;lo;--mca;btl_tcp_if_include;lo;--mca;orte_base_help_aggregate;0" \
       ..
 make -j12 VERBOSE=1
 

examples/parpeamici/steadystate/run-examples.sh

@@ -10,6 +10,10 @@ HDF5_FILE_TEST=$2
 MPIEXEC="mpiexec --oversubscribe -n 5"
 # Allow running as root in docker
 grep docker /proc/1/cgroup -qa && MPIEXEC="${MPIEXEC} --allow-run-as-root"
+# If we are running in docker, we generally don't have SYS_PTRACE permissions
+# and thus, cannot use vader. Also disable Infiniband.
+grep docker /proc/1/cgroup -qa && mpiexec --version | grep open-mpi && MPIEXEC="${MPIEXEC} --oversubscribe --mca btl_vader_single_copy_mechanism none --mca btl ^openib -mca oob_tcp_if_include lo --mca btl_tcp_if_include lo --mca orte_base_help_aggregate 0"
+
 
 rm -f test.log
 

shippable.yml

@@ -44,7 +44,7 @@ build:
         - CTEST_OUTPUT_ON_FAILURE=1 make ExperimentalMemCheck; cat Testing/Temporary/MemoryChecker.*.log
 
         # coverage report
-        - cd $PARPE_BASE/build && make parpe_coverage_cobertura
+        - cd $PARPE_BASE/build && CTEST_OUTPUT_ON_FAILURE=1 make parpe_coverage_cobertura
         - mkdir -p $PARPE_BASE/shippable/codecoverage && cp $PARPE_BASE/build/parpe_coverage_cobertura.xml $PARPE_BASE/shippable/codecoverage
 
 #    on_failure: