Fix unit tests environment variables (espressomd#4607)

Description of changes:
- properly set unit test environment variables related to sanitizers
- address Open MPI version 4.x singleton mode bug on NUMA architectures
   - disable MCA binding policy on unit tests running in singleton mode on affected NUMA architectures
   - print a warning in pypresso when running in singleton mode on affected NUMA architectures (can be disabled with a CMake option)

CMakeLists.txt

@@ -96,6 +96,10 @@ if(CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND NOT APPLE)
     "Build with memory sanitizer (experimental; requires a memory-sanitized Python interpreter)"
     OFF)
 endif()
+option(
+  ESPRESSO_ADD_OMPI_SINGLETON_WARNING
+  "Add a runtime warning in the pypresso script for NUMA architectures that aren't supported in singleton mode by Open MPI 4.x"
+  ON)
 option(WARNINGS_ARE_ERRORS "Treat warnings as errors during compilation" OFF)
 option(WITH_CCACHE "Use ccache compiler invocation." OFF)
 option(WITH_PROFILER "Enable profiler annotations." OFF)
@@ -280,11 +284,38 @@ find_package(MPI 3.0 REQUIRED)
 find_package(MpiexecBackend)
 
 # OpenMPI checks the number of processes against the number of CPUs
-if("${MPIEXEC_BACKEND_NAME}" STREQUAL "OpenMPI" AND "${MPIEXEC_BACKEND_VERSION}"
-                                                    VERSION_GREATER_EQUAL 2.0.0)
-  set(MPIEXEC_OVERSUBSCRIBE "-oversubscribe")
-else()
-  set(MPIEXEC_OVERSUBSCRIBE "")
+set(MPIEXEC_OVERSUBSCRIBE "")
+# Open MPI 4.x has a bug on NUMA archs that prevents running in singleton mode
+set(ESPRESSO_MPIEXEC_GUARD_SINGLETON_NUMA OFF)
+set(ESPRESSO_CPU_MODEL_NAME_OMPI_SINGLETON_NUMA_PATTERN "AMD (EPYC|Ryzen)")
+
+if("${MPIEXEC_BACKEND_NAME}" STREQUAL "OpenMPI")
+  if("${MPIEXEC_BACKEND_VERSION}" VERSION_GREATER_EQUAL 2.0.0)
+    set(MPIEXEC_OVERSUBSCRIBE "-oversubscribe")
+  endif()
+  if("${MPIEXEC_BACKEND_VERSION}" VERSION_GREATER_EQUAL 4.0
+     AND "${MPIEXEC_BACKEND_VERSION}" VERSION_LESS 5.0)
+    if(NOT DEFINED ESPRESSO_CPU_MODEL_NAME)
+      if(CMAKE_SYSTEM_NAME STREQUAL Linux)
+        if(EXISTS /proc/cpuinfo)
+          file(READ /proc/cpuinfo ESPRESSO_CPU_INFO)
+          string(REGEX
+                 REPLACE ".*\n[Mm]odel name[ \t]*:[ \t]+([^\n]+).*" "\\1"
+                         ESPRESSO_CPU_MODEL_NAME_STRING "${ESPRESSO_CPU_INFO}")
+        else()
+          set(ESPRESSO_CPU_MODEL_NAME_STRING "__unreadable")
+        endif()
+      else()
+        set(ESPRESSO_CPU_MODEL_NAME_STRING "__unaffected")
+      endif()
+      set(ESPRESSO_CPU_MODEL_NAME "${ESPRESSO_CPU_MODEL_NAME_STRING}"
+          CACHE INTERNAL "")
+    endif()
+    if(ESPRESSO_CPU_MODEL_NAME MATCHES
+       "^${ESPRESSO_CPU_MODEL_NAME_OMPI_SINGLETON_NUMA_PATTERN}")
+      set(ESPRESSO_MPIEXEC_GUARD_SINGLETON_NUMA ON)
+    endif()
+  endif()
 endif()
 
 # OpenMPI cannot run two jobs in parallel in a Docker container, because the

cmake/unit_test.cmake

@@ -30,12 +30,14 @@ function(UNIT_TEST)
   else()
     set(SANITIZERS_HALT_ON_ERROR "halt_on_error=0")
   endif()
-  set(UBSAN_OPTIONS "UBSAN_OPTIONS=suppressions=${CMAKE_SOURCE_DIR}/maintainer/CI/ubsan.supp:${SANITIZERS_HALT_ON_ERROR}:print_stacktrace=1")
-  set(ASAN_OPTIONS "ASAN_OPTIONS=${SANITIZERS_HALT_ON_ERROR}:detect_leaks=0:allocator_may_return_null=1")
-  set(MSAN_OPTIONS "MSAN_OPTIONS=${SANITIZERS_HALT_ON_ERROR}")
+  list(APPEND TEST_ENV_VARIABLES "UBSAN_OPTIONS=suppressions=${CMAKE_SOURCE_DIR}/maintainer/CI/ubsan.supp:${SANITIZERS_HALT_ON_ERROR}:print_stacktrace=1")
+  list(APPEND TEST_ENV_VARIABLES "ASAN_OPTIONS=${SANITIZERS_HALT_ON_ERROR}:detect_leaks=0:allocator_may_return_null=1")
+  list(APPEND TEST_ENV_VARIABLES "MSAN_OPTIONS=${SANITIZERS_HALT_ON_ERROR}")
+  if(NOT TEST_NUM_PROC AND ESPRESSO_MPIEXEC_GUARD_SINGLETON_NUMA AND "${TEST_DEPENDS}" MATCHES "(^|;)([Bb]oost::mpi|MPI::MPI_CXX)($|;)")
+    list(APPEND TEST_ENV_VARIABLES "OMPI_MCA_hwloc_base_binding_policy=none")
+  endif()
   set_tests_properties(
-    ${TEST_NAME} PROPERTIES ENVIRONMENT
-                            "${UBSAN_OPTIONS} ${ASAN_OPTIONS} ${MSAN_OPTIONS}")
+    ${TEST_NAME} PROPERTIES ENVIRONMENT "${TEST_ENV_VARIABLES}")
 
   add_dependencies(check_unit_tests ${TEST_NAME})
 endfunction(UNIT_TEST)

doc/sphinx/installation.rst

@@ -61,6 +61,15 @@ are required to be able to compile and use |es|:
         Other MPI implementations like Intel MPI should also work, although
         they are not actively tested in |es| continuous integration.
 
+        Open MPI version 4.x is known to not properly support the MCA binding
+        policy "numa" in singleton mode on a few NUMA architectures.
+        On affected systems, e.g. AMD Ryzen or AMD EPYC, Open MPI halts with
+        a fatal error when setting the processor affinity in ``MPI_Init``.
+        This issue can be resolved by setting the environment variable
+        ``OMPI_MCA_hwloc_base_binding_policy`` to a value other than "numa",
+        such as "l3cache" to bind to a NUMA shared memory block, or to
+        "none" to disable binding (can cause performance loss).
+
     Python
         |es|'s main user interface relies on Python 3.
 
@@ -720,6 +729,11 @@ The following options are available:
 * ``WITH_VALGRIND_INSTRUMENTATION``: Build with valgrind instrumentation
   markers
 
+* ``ESPRESSO_ADD_OMPI_SINGLETON_WARNING``: Add a runtime warning in the
+  pypresso and ipypresso scripts that is triggered in singleton mode
+  with Open MPI version 4.x on unsupported NUMA environments
+  (see :term:`MPI installation requirements <MPI>` for details).
+
 When the value in the :file:`CMakeLists.txt` file is set to ON, the
 corresponding option is created; if the value of the option is set to OFF,
 the corresponding option is not created. These options can also be modified

doc/sphinx/running.rst

@@ -245,8 +245,7 @@ Parallel computing
 
 Many algorithms in |es| are designed to work with multiple MPI ranks.
 However, not all algorithms benefit from MPI parallelization equally.
-Several algorithms only use MPI rank 0 (e.g. :ref:`Reaction methods`), while
-a small subset simply don't support MPI (e.g. :ref:`Dipolar direct sum`).
+Several algorithms only use MPI rank 0 (e.g. :ref:`Reaction methods`).
 |es| should work with most MPI implementations on the market;
 see the :term:`MPI installation requirements <MPI>` for details.
 

src/python/pypresso.cmakein

@@ -14,6 +14,15 @@ else
 fi
 export PYTHONPATH
 
+# Open MPI 4.x cannot run in singleton mode on some NUMA systems
+if [ "@ESPRESSO_ADD_OMPI_SINGLETON_WARNING@" = "ON" ] && [ "@ESPRESSO_MPIEXEC_GUARD_SINGLETON_NUMA@" = "ON" ]; then
+  if [ -z "${OMPI_COMM_WORLD_SIZE}" ] && [ "${OMPI_MCA_hwloc_base_binding_policy}" = "numa" ]; then
+    if test -f /proc/cpuinfo && grep --quiet -P "^[Mm]odel name[ \t]*:[ \t]+@ESPRESSO_CPU_MODEL_NAME_OMPI_SINGLETON_NUMA_PATTERN@( |$)" /proc/cpuinfo; then
+      echo "warning: if Open MPI fails to set processor affinity, set environment variable OMPI_MCA_hwloc_base_binding_policy to \"none\" or \"l3cache\""
+    fi
+  fi
+fi
+
 if [ "@CMAKE_CXX_COMPILER_ID@" != "GNU" ] && [ "@WITH_ASAN@" = "ON" ]; then
   asan_lib=$("@CMAKE_CXX_COMPILER@" /dev/null -### -o /dev/null -fsanitize=address 2>&1 | grep -o '[" ][^" ]*libclang_rt.asan[^" ]*[^s][" ]' | sed 's/[" ]//g' | sed 's/\.a$/.so/g')
   export DYLD_INSERT_LIBRARIES="$asan_lib"

src/script_interface/tests/CMakeLists.txt

@@ -42,9 +42,9 @@ unit_test(NAME ParallelExceptionHandler_test SRC
 unit_test(NAME packed_variant_test SRC packed_variant_test.cpp DEPENDS
           Espresso::script_interface)
 unit_test(NAME ObjectList_test SRC ObjectList_test.cpp DEPENDS
-          Espresso::script_interface Espresso::core)
+          Espresso::script_interface Espresso::core Boost::mpi)
 unit_test(NAME ObjectMap_test SRC ObjectMap_test.cpp DEPENDS
-          Espresso::script_interface Espresso::core)
+          Espresso::script_interface Espresso::core Boost::mpi)
 unit_test(NAME serialization_mpi_guard_test SRC
           serialization_mpi_guard_test.cpp DEPENDS Espresso::script_interface
           Boost::mpi MPI::MPI_CXX NUM_PROC 2)