Complete rewrite of ParaView visualization adaptor

.github/workflows/README.md

@@ -0,0 +1,11 @@
+Debug github actions.
+
+Add the following step before the failing step.
+ssh into the tmate session immediately. 
+Otherwise the session times out and doesn't accept any input.
+
+```
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v2
+```
+

.github/workflows/centos-system-ci.yml

@@ -131,23 +131,10 @@ jobs:
         export DISPLAY=:99.0
         ../util/xvfb-initd.sh start
         sleep 3
-        make run-demos
-        ../util/xvfb-initd.sh stop
-
-    - name: Test out-of-source simulation
-      shell: bash
-      working-directory: build
-      run: |
-        . scl_source enable devtoolset-7 || true
-        . scl_source enable llvm-toolset-6.0 || true
-        . /etc/profile.d/modules.sh || true
-        module load mpi
-        . $INSTALL_DIR/bin/thisbdm.sh
         biodynamo new test-sim
         . ../test/util.inc
-        export DISPLAY=:99.0
-        ../util/xvfb-initd.sh start
         run_cmake_simulation test-sim
+        make run-demos
         ../util/xvfb-initd.sh stop
 
     - name: Notify Slack

.github/workflows/macos-system-ci.yml

@@ -92,6 +92,9 @@ jobs:
           -B build
         cmake --build build --parallel --config Release --target notebooks
 
+    # - name: Setup tmate session
+    #   uses: mxschmitt/action-tmate@v2
+
     - name: System tests BioDynaMo
       shell: zsh {0}
       working-directory: build

.github/workflows/ubuntu-system-ci.yml

@@ -108,42 +108,28 @@ jobs:
           -B build
         cmake --build build --parallel --config Release
 
-    - name: Valgrind tests BioDynaMo
-      shell: bash
-      working-directory: build
-      run: |
-        . $INSTALL_DIR/bin/thisbdm.sh
-        export DISPLAY=:99.0
-        ../util/xvfb-initd.sh start
-        sleep 3
-        make run-valgrind
-        ../util/xvfb-initd.sh stop
-
-    - name: System tests BioDynaMo
+    - name: Run valgrind and system tests
       shell: bash
       working-directory: build
       run: |
+        ps -ef
         . $INSTALL_DIR/bin/thisbdm.sh
         sudo git config --system user.name "Test User"
         sudo git config --system user.email user@test.com
         export DISPLAY=:99.0
         ../util/xvfb-initd.sh start
         sleep 3
-        make run-demos
-        ../util/xvfb-initd.sh stop
-
-    - name: Test out-of-source simulation
-      shell: bash
-      working-directory: build
-      run: |
-        . $INSTALL_DIR/bin/thisbdm.sh
-        export DISPLAY=:99.0
-        ../util/xvfb-initd.sh start
-        sleep 3
+        ps -ef
         biodynamo new test-sim
         . ../test/util.inc
         run_cmake_simulation test-sim
+        ps -ef
+        make run-valgrind
+        ps -ef
+        make run-demos
+        ps -ef
         ../util/xvfb-initd.sh stop
+        ps -ef
 
     - name: Notify Slack
       uses: 8398a7/action-slack@v3

CMakeLists.txt

@@ -292,10 +292,16 @@ if(paraview)
     # compatible binaries
     if(APPLE)
       find_package(ParaView 5.5 CONFIG COMPONENTS vtkPVPythonCatalyst vtkPVVTKExtensionsDefault
-            vtkPVServerManagerRendering PATHS ${CMAKE_THIRD_PARTY_DIR}/paraview)
+            vtkPVServerManagerRendering PATHS ${CMAKE_THIRD_PARTY_DIR}/paraview ENV{ParaView_DIR})
+      if(${ParaView_FOUND})
+        include_directories(${ParaView_PREFIX_PATH}/include/paraview-5.5)
+      endif()
     else()
       find_package(ParaView 5.8 CONFIG COMPONENTS Catalyst PythonCatalyst VTKExtensionsIOCore
-            PATHS ${CMAKE_THIRD_PARTY_DIR}/paraview)
+              PATHS ${CMAKE_THIRD_PARTY_DIR}/paraview ENV{ParaView_DIR})
+      if(${ParaView_FOUND})
+        include_directories(${ParaView_PREFIX_PATH}/include/paraview-5.8)
+      endif()
     endif()
 
     # Check if ParaView was found in the system. If that's not the case then we will proceed
@@ -322,13 +328,14 @@ if(paraview)
       if(APPLE)
         find_package(ParaView 5.5 CONFIG COMPONENTS vtkPVPythonCatalyst vtkPVVTKExtensionsDefault
               vtkPVServerManagerRendering PATHS ${CMAKE_THIRD_PARTY_DIR}/paraview)
+        include_directories(${ParaView_PREFIX_PATH}/include/paraview-5.5)
       else()
         find_package(ParaView 5.8 CONFIG COMPONENTS Catalyst PythonCatalyst VTKExtensionsIOCore
               PATHS ${CMAKE_THIRD_PARTY_DIR}/paraview)
+        include_directories(${ParaView_PREFIX_PATH}/include/paraview-5.8)
       endif()
     endif()
 
-    include_directories(${ParaView_PREFIX_PATH}/include/paraview-5.8)
     add_definitions("-DUSE_PARAVIEW")
 endif()
 
@@ -467,6 +474,7 @@ if (LINUX)
   set(FS_LIB stdc++fs)
 endif()
 build_shared_library(biodynamo
+                   SELECTION selection-libbiodynamo.xml
                    SOURCES ${LIB_SOURCES}
                    HEADERS ${HEADERS}
                    LIBRARIES ${BDM_REQUIRED_LIBRARIES} ${ROOT_LIBRARIES} ${FS_LIB})
@@ -481,6 +489,7 @@ if(paraview)
   # resolve missing python symbols when creating binaries
   set(REQUIRED_PARAVIEW_LIBRARIES "${ParaView_LIBRARIES};${Python_LIBRARIES}")
   build_shared_library(VisualizationAdaptor
+                    SELECTION selection-libVisualizationAdaptor.xml
                     SOURCES ${PV_SOURCES}
                     HEADERS ${PV_HEADERS}
                     LIBRARIES ${REQUIRED_PARAVIEW_LIBRARIES} biodynamo
@@ -558,6 +567,7 @@ if (test)
                          ${CMAKE_SOURCE_DIR}/test/unit/core/sim_object/*.cc
                          ${CMAKE_SOURCE_DIR}/test/unit/core/util/*.cc
                          ${CMAKE_SOURCE_DIR}/test/unit/core/visualization/*.cc
+                         ${CMAKE_SOURCE_DIR}/test/unit/core/visualization/paraview/*.cc
                          ${CMAKE_SOURCE_DIR}/test/unit/neuroscience/*.cc)
   file(GLOB TEST_HEADERS ${CMAKE_SOURCE_DIR}/test/unit/*.h
                          ${CMAKE_SOURCE_DIR}/test/unit/test_util/*.h
@@ -572,7 +582,9 @@ if (test)
                          ${CMAKE_SOURCE_DIR}/test/unit/core/sim_object/*.h
                          ${CMAKE_SOURCE_DIR}/test/unit/core/util/*.h
                          ${CMAKE_SOURCE_DIR}/test/unit/core/visualization/*.h
+                         ${CMAKE_SOURCE_DIR}/test/unit/core/visualization/paraview/*.h
                          ${CMAKE_SOURCE_DIR}/test/unit/neuroscience/*.h)
+  # NB: Remove stdc++fs after switching to c++17  
   bdm_add_test_executable(biodynamo-unit-tests
                           SOURCES ${TEST_SOURCES}
                           HEADERS ${TEST_HEADERS}

cmake/BioDynaMo.cmake

@@ -58,68 +58,69 @@ endfunction(get_implicit_dependencies)
 # and external simulation projects.
 # \param TARGET target name for the executable
 # \param SOURCES list of source files
-# \param LIBRARIES list of libraries that should be linked to the executable.
-#        can also be a target name of a library
+# \param LIBRARIES list of *shared* libraries that should be linked to the executable.
+#        can also be a target name of a library.
+#        STATIC libraries not compiled with -fPIC must be linked in a separate command using 
+#        target_link_libraries(${TARGET} static-lib-wo-fpic)
 function(bdm_add_executable TARGET)
   cmake_parse_arguments(ARG "" "" "SOURCES;HEADERS;LIBRARIES" ${ARGN} )
 
   if(dict)
-    # generate dictionary using genreflex
-    set(DICT_FILE "${CMAKE_CURRENT_BINARY_DIR}/${TARGET}_dict")
-
-    # Since the location of the CMake files differ in the build and installation
-    # directory, we check if BDM_CMAKE_DIR is already set (in build directory
-    # case). Otherwise, set it to the installation directory
-    if(NOT DEFINED BDM_CMAKE_DIR)
-      set(BDM_CMAKE_DIR $ENV{BDMSYS}/share/cmake)
-    endif()
-    REFLEX_GENERATE_DICTIONARY(${DICT_FILE} ${ARG_HEADERS} SELECTION ${BDM_CMAKE_DIR}/selection.xml)
-
-    # generate executable
-    add_executable(${TARGET} ${ARG_SOURCES} ${DICT_FILE}.cc)
-    if (OPENCL_FOUND)
-      # Do this here; we don't want libbiodynamo.so to contain any OpenCL symbols
-      set(ARG_LIBRARIES ${ARG_LIBRARIES} ${OPENCL_LIBRARIES})
-      target_compile_definitions(${TARGET} PUBLIC -DUSE_OPENCL)
-    endif()
-    target_link_libraries(${TARGET} ${ARG_LIBRARIES})
-    if (DEFINED CMAKE_INSTALL_LIBDIR)
-      add_custom_command(TARGET ${TARGET}
-            POST_BUILD
-            COMMAND ${CMAKE_COMMAND} -E copy ${DICT_FILE}_rdict.pcm ${CMAKE_INSTALL_BINDIR})
+    build_shared_library(${TARGET}
+                         SELECTION selection.xml
+                         HEADERS ${ARG_HEADERS}
+                         SOURCES ${ARG_SOURCES}
+                         LIBRARIES ${ARG_LIBRARIES})
+    file(WRITE ${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/${TARGET}-main.cc "int main(int argc, const char** argv);")
+    add_executable(${TARGET}-bin ${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/${TARGET}-main.cc)
+    target_link_libraries(${TARGET}-bin ${TARGET})
+    if (LINUX)
+      set_target_properties(${TARGET}-bin PROPERTIES LINK_FLAGS "-Wl,-rpath,$ORIGIN")
+    else()
+      set_target_properties(${TARGET}-bin PROPERTIES LINK_FLAGS "-Wl,-rpath,@loader_path")
     endif()
+    set_target_properties(${TARGET}-bin PROPERTIES OUTPUT_NAME ${TARGET})
   else()
     add_executable(${TARGET} ${ARG_SOURCES})
     target_link_libraries(${TARGET} ${ARG_LIBRARIES})
   endif()
 endfunction(bdm_add_executable)
 
 # function build_shared_library( TARGET
+#                                SELECTION selection.xml
 #                                SOURCES source1 source2 ...
 #                                HEADERS header1 header2 ...
 #                                LIBRARIES lib1 lib2 ...
 #                                PLUGIN <"TRUE">)
 # build shared library with ROOT dictionaries. If ARG_PLUGIN is set, we will
 # always generate dictionaries (as required by ROOT's plugin manager)
 function(build_shared_library TARGET)
-  cmake_parse_arguments(ARG "" "" "SOURCES;HEADERS;LIBRARIES;PLUGIN" ${ARGN} )
+  cmake_parse_arguments(ARG "" "" "SELECTION;SOURCES;HEADERS;LIBRARIES;PLUGIN" ${ARGN} )
 
   # We always need dictionaries for the plugins (plugin manager requires class
   # information)
   if(dict OR DEFINED ARG_PLUGIN)
     # generate dictionary using genreflex
     set(DICT_FILE "${CMAKE_CURRENT_BINARY_DIR}/lib${TARGET}_dict")
+    set(BDM_DICT_FILE "${CMAKE_CURRENT_BINARY_DIR}/lib${TARGET}_bdm_dict.cc")
 
     # Since the location of the CMake files differ in the build and installation
     # directory, we check if BDM_CMAKE_DIR is already set (in build directory
     # case). Otherwise, set it to the installation directory
     if(NOT DEFINED BDM_CMAKE_DIR)
       set(BDM_CMAKE_DIR $ENV{BDMSYS}/share/cmake)
     endif()
-    REFLEX_GENERATE_DICTIONARY(${DICT_FILE} ${ARG_HEADERS} SELECTION ${BDM_CMAKE_DIR}/selection-lib${TARGET}.xml)
-
+    REFLEX_GENERATE_DICTIONARY(${DICT_FILE} ${ARG_HEADERS} SELECTION ${BDM_CMAKE_DIR}/${ARG_SELECTION})
+    if (BDM_OUT_OF_SOURCE) 
+      set(BDM_DICT_BIN_PATH "$ENV{BDMSYS}/bin")
+    else()
+      set(BDM_DICT_BIN_PATH "${PROJECT_SOURCE_DIR}/cmake")
+    endif()
+    add_custom_command(OUTPUT "${BDM_DICT_FILE}"
+                       COMMAND ${BDM_DICT_BIN_PATH}/bdm-dictionary ${BDM_DICT_FILE} ${ARG_HEADERS}
+                       DEPENDS ${ARG_HEADERS} ${BDM_DICT_BIN_PATH}/bdm-dictionary)
     # generate shared library
-    add_library(${TARGET} SHARED ${ARG_SOURCES} ${DICT_FILE}.cc)
+    add_library(${TARGET} SHARED ${ARG_SOURCES} ${DICT_FILE}.cc ${BDM_DICT_FILE})
     target_link_libraries(${TARGET} ${ARG_LIBRARIES})
     if (DEFINED CMAKE_INSTALL_LIBDIR)
       add_custom_command(TARGET ${TARGET}

cmake/Installation.cmake

@@ -114,6 +114,9 @@ install(TARGETS biodynamo
 
 if(test)
     install(TARGETS biodynamo-unit-tests
+            LIBRARY
+            DESTINATION ${DIRNAME}/lib)
+    install(TARGETS biodynamo-unit-tests-bin
             RUNTIME
             DESTINATION ${DIRNAME}/bin)
 endif()

cmake/Testing.cmake

@@ -17,6 +17,8 @@ ExternalProject_Add(
   gtest
   URL "${CMAKE_SOURCE_DIR}/third_party/gtest-1.7.0.zip"
   PREFIX "${CMAKE_CURRENT_BINARY_DIR}/gtest"
+  CMAKE_ARGS
+    -DCMAKE_CXX_FLAGS="-fPIC"
   CMAKE_CACHE_ARGS
     -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
     -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
@@ -80,11 +82,11 @@ function(bdm_add_test_executable TEST_TARGET)
 
   # add valgrind test
   if (valgrind AND VALGRIND_FOUND AND NOT coverage)
-    # filter out SchedulerTest.Backup because of timing issue
+    # filter out tests that would take too long if tested under valgrind 
     add_test(NAME "valgrind_${TEST_TARGET}"
-    COMMAND  ${CMAKE_BINARY_DIR}/launcher.sh ${CMAKE_SOURCE_DIR}/util/valgrind.sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TEST_TARGET} -- --gtest_filter=-*DeathTest.*:IOTest.InvalidRead:SchedulerTest.Backup:ResourceManagerTest.SortAndApplyOnAllElementsParallel*:InlineVector*:NeuriteElementBehaviour.*:MechanicalInteraction.*:DiffusionTest.*Convergence*:SimObjectVectorTest.Equality:SchedulerTest::LoadAndBalanceAfterEnvironment)
+    COMMAND  ${CMAKE_BINARY_DIR}/launcher.sh ${CMAKE_SOURCE_DIR}/util/valgrind.sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TEST_TARGET} -- --gtest_filter=-*DeathTest.*:IOTest.InvalidRead:SchedulerTest.Backup:ResourceManagerTest.SortAndApplyOnAllElementsParallel*:InlineVector*:NeuriteElementBehaviour.*:MechanicalInteraction.*:DiffusionTest.*Convergence*:ParaviewIntegrationTest*:SimObjectVectorTest.Equality:SchedulerTest::LoadAndBalanceAfterEnvironment)
     add_custom_target(run-valgrind
-    COMMAND  ${CMAKE_BINARY_DIR}/launcher.sh ${CMAKE_SOURCE_DIR}/util/valgrind.sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TEST_TARGET} -- --gtest_filter=-*DeathTest.*:IOTest.InvalidRead:SchedulerTest.Backup:ResourceManagerTest.SortAndApplyOnAllElementsParallel*:InlineVector*:NeuriteElementBehaviour.*:MechanicalInteraction.*:DiffusionTest.*Convergence*:SimObjectVectorTest.Equality:SchedulerTest::LoadAndBalanceAfterEnvironment)
+    COMMAND  ${CMAKE_BINARY_DIR}/launcher.sh ${CMAKE_SOURCE_DIR}/util/valgrind.sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TEST_TARGET} -- --gtest_filter=-*DeathTest.*:IOTest.InvalidRead:SchedulerTest.Backup:ResourceManagerTest.SortAndApplyOnAllElementsParallel*:InlineVector*:NeuriteElementBehaviour.*:MechanicalInteraction.*:DiffusionTest.*Convergence*:ParaviewIntegrationTest*:SimObjectVectorTest.Equality:SchedulerTest::LoadAndBalanceAfterEnvironment)
     add_dependencies(run-valgrind biodynamo-unit-tests)
   endif()
 

cmake/UseBioDynaMo.cmake.in

@@ -40,7 +40,6 @@ SET(cuda_default @cuda@)
 SET(opencl_default @opencl@)
 SET(dict_default @dict@)
 SET(numa_default @numa@)
-SET(paraview_default @paraview@)
 SET(sbml_default @sbml@)
 SET(vtune_default @vtune@)
 SET(tcmalloc_default @tcmalloc@)
@@ -51,7 +50,6 @@ option(cuda      "Enable CUDA code generation for GPU acceleration" @cuda@)
 option(opencl    "Enable OpenCL code generation for GPU acceleration" @opencl@)
 option(dict      "Build with ROOT dictionaries" @dict@)
 option(numa      "Enable Numa support" @numa@)
-option(paraview  "Enable ParaView" @paraview@)
 option(sbml      "Enable SBML support" @sbml@)
 option(vtune     "Enable VTune performance analysis" @vtune@)
 option(tcmalloc  "Use tcmalloc." @tcmalloc@)
@@ -73,10 +71,6 @@ if (numa AND NOT numa_default)
     MESSAGE(FATAL_ERROR "One of the option which you provided (-Dnuma=${numa}) is not compatible with \
 BioDynaMo. BioDynaMo was built by setting -Dnuma to ${numa_default}. Please change -Dnuma to -Dnuma=${numa_default}.")
 endif()
-if (paraview AND NOT paraview_default)
-    MESSAGE(FATAL_ERROR "One of the option which you provided (-Dparaview=${paraview}) is not compatible with \
-BioDynaMo. BioDynaMo was built by setting -Dparaview to ${paraview_default}. Please change -Dparaview to -Dparaview=${paraview_default}.")
-endif()
 if (sbml AND NOT sbml_default)
     MESSAGE(FATAL_ERROR "One of the option which you provided (-Dsbml=${sbml}) is not compatible with \
 BioDynaMo. BioDynaMo was built by setting -Dsbml to ${sbml_default}. Please use -Dsbml=${sbml_default}.")
@@ -164,10 +158,6 @@ if(opencl)
   find_package(OpenCL)
 endif()
 
-if (paraview)
-  find_package(GLUT)
-endif()
-
 if(numa)
   find_package(Numa REQUIRED)
   if (NUMA_FOUND)
@@ -178,16 +168,6 @@ if(numa)
   endif()
 endif()
 
-if(paraview)
-  find_package(ParaView 5.3 QUIET OPTIONAL_COMPONENTS vtkPVPythonCatalyst)
-  if(${ParaView_FOUND})
-    message(STATUS "Found ParaView")
-  else()
-    message(WARNING "ParaView not found")
-    set(paraview OFF CACHE "Build with ParaView support." BOOL)
-  endif()
-endif()
-
 find_package(ROOT REQUIRED COMPONENTS Geom Gui Eve GenVector)
 verify_root()
 if (dict)
@@ -270,6 +250,7 @@ include(${ROOT_USE_FILE})
 fix_rootcling_omp_issue()
 fix_macos_opencl_header_issue()
 
+list(REMOVE_ITEM ROOT_LIBRARIES "$ENV{BDMSYS}/third_party/root/lib/libEve.so")
 set(BDM_REQUIRED_LIBRARIES ${BDM_REQUIRED_LIBRARIES} biodynamo ${ROOT_LIBRARIES})
 
 include_directories("$ENV{BDMSYS}/include")