Support for SONATA reports (#225)

* Select report type at runtime (Bin, SONATA)
  - Revert SONATA_ENABLE cmake changes
  - Add ReportHandler class
* Refactor report module
  - Split nrnreport into different classes
  - Allow sonata reports to coexist with current reportinglib
  - Adapt integration tests for sonata reports
* Move sort_spikes after sonata_write_spikes
* Error messages on integration tests
* Fixed an issue where clang invoking the linker will always add mentioned libraries into the ELF
  header of the executable, this causes special-core to fail at load with libraries not found. By
  forcing the `--as-needed` flag, we reproduce the gcc behavior, which adds libraries only
  when needed and relies on the loader to recursively resolve libraries.
* Choose between reportinglib and sonata reports
  - If CORENRN_ENABLE_REPORTING variable is present, try to find a reporting library
   (reportinglib or sonata_reports) and allow its usage. Error if neither is found.
* Adapt tests to changes when choosing reporting library
* Add population name to the write_spikes
* Adapt report.conf file to CLI11
Co-authored-by: Tristan Carel <[email protected]>
Co-authored-by: Blanco Alonso Jorge <[email protected]>
Co-authored-by: Omar Awile <[email protected]>
Co-authored-by: Pramod Kumbhar <[email protected]>

Author: 5 people

CMake/config/CompilerFlagsHelpers.cmake

@@ -100,6 +100,15 @@ foreach(COMPILER_LANGUAGE ${SUPPORTED_COMPILER_LANGUAGE_LIST})
 			set(CMAKE_${COMPILER_LANGUAGE}_GEN_NATIVE "-march=native")
 		endif()
 
+    ## CLANG
+	elseif(CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_CLANG)
+		## Force same ld behavior as when called from gcc
+		## --as-needed forces the linker to check whether a dynamic library mentioned in the command line is actually
+		## needed by the objects being linked. Symbols needed in shared objects are already linked when building that
+		## library.
+		set(CMAKE_EXE_LINKER_FLAGS "-Wl,--as-needed")
+		set(CMAKE_SHARED_LINKER_FLAGS "-Wl,--as-needed")
+
 	## rest of the world
 	else()
 		set(CMAKE_${COMPILER_LANGUAGE}_WARNING_ALL "-Wall")

CMakeLists.txt

@@ -56,8 +56,7 @@ add_subdirectory(${CORENEURON_PROJECT_SOURCE_DIR}/external/CLI11)
 # =============================================================================
 option(CORENRN_ENABLE_OPENMP "Build the CORE NEURON with OpenMP implementation" ON)
 option(CORENRN_ENABLE_TIMEOUT "Enable nrn_timeout implementation" ON)
-option(CORENRN_ENABLE_REPORTINGLIB "Enable use of ReportingLib for soma reports" OFF)
-option(CORENRN_ENABLE_SONATA "Enable SONATA output format" OFF)
+option(CORENRN_ENABLE_REPORTING "Enable use of ReportingLib for soma reports" OFF)
 option(CORENRN_ENABLE_MPI "Enable MPI-based execution" ON)
 option(CORENRN_ENABLE_SOA "Enable SoA Memory Layout" ON)
 option(CORENRN_ENABLE_HOC_EXP "Enable wrapping exp with hoc_exp()" OFF)
@@ -158,19 +157,30 @@ if(NOT CORENRN_ENABLE_TIMEOUT)
   add_definitions("-DDISABLE_TIMEOUT")
 endif()
 
-if ( CORENRN_ENABLE_SONATA AND CORENRN_ENABLE_REPORTINGLIB )
-  message(FATAL_ERROR "Can't have enabled both SONATA reports and reportinglib")
-endif()
-
-if(CORENRN_ENABLE_REPORTINGLIB)
-  find_package(reportinglib REQUIRED)
+if(CORENRN_ENABLE_REPORTING)
+  find_package(reportinglib)
+  find_package(sonata)
+  find_program (H5DUMP_EXECUTABLE h5dump)
+  if(NOT reportinglib_FOUND AND NOT sonata_FOUND)
+    message(SEND_ERROR "Neither reportinglib nor SONATA libraries were found")
+  elseif(reportinglib_FOUND AND sonata_FOUND)
+    add_definitions("-DENABLE_BIN_REPORTS")
+    add_definitions("-DENABLE_SONATA_REPORTS")
+  elseif(reportinglib_FOUND)
+    add_definitions("-DENABLE_BIN_REPORTS")
+    set(ENABLE_BIN_REPORTS ON)
+  else() # sonata_FOUND
+    if(TARGET sonata::sonata_report)
+      add_definitions("-DENABLE_SONATA_REPORTS")
+      set(ENABLE_SONATA_REPORTS ON)
+      set(reportinglib_INCLUDE_DIR "")
+      set(reportinglib_LIBRARY "")
+    else()
+      message(SEND_ERROR "SONATA library was found but without reporting support")
+    endif()
+  endif()
   include_directories(${reportinglib_INCLUDE_DIR})
-  add_definitions("-DENABLE_REPORTING")
-endif()
-if(CORENRN_ENABLE_SONATA)
-    find_package(sonata QUIET PATHS ${sonata_DIR}/share/sonata/CMake)
-    include_directories(${sonatareport_INCLUDE_DIR})
-    add_definitions("-DENABLE_SONATA_REPORTS -DENABLE_REPORTING")
+  include_directories(${sonatareport_INCLUDE_DIR})
 endif()
 
 if(MINGW)
@@ -297,15 +307,12 @@ if(cmake_generator_tolower MATCHES "makefile")
   message(STATUS "Caliper             | ${CORENRN_ENABLE_CALIPER_PROFILING}")
   message(STATUS "Likwid              | ${CORENRN_ENABLE_LIKWID_PROFILING}")
   message(STATUS "Unit Tests          | ${CORENRN_ENABLE_UNIT_TESTS}")
-  message(STATUS "ReportingLib        | ${CORENRN_ENABLE_REPORTINGLIB}")
-  message(STATUS "  SONATA support    | ${CORENRN_ENABLE_SONATA}")
-  if(CORENRN_ENABLE_REPORTINGLIB)
-    message(STATUS "  INC               | ${reportinglib_INCLUDE_DIR}")
-    message(STATUS "  LIB               | ${reportinglib_LIBRARY}")
-  endif()
-  if(CORENRN_ENABLE_SONATA)
-    message(STATUS "  INC               | ${sonatareport_INCLUDE_DIR}")
-    message(STATUS "  LIB               | ${sonatareport_LIBRARY}")
+  message(STATUS "Reporting           | ${CORENRN_ENABLE_REPORTING}")
+  if(CORENRN_ENABLE_REPORTING)
+    message(STATUS "  sonatareport_INC  | ${sonatareport_INCLUDE_DIR}")
+    message(STATUS "  sonatareport_LIB  | ${sonatareport_LIBRARY}")
+    message(STATUS "  reportinglib_INC  | ${reportinglib_INCLUDE_DIR}")
+    message(STATUS "  reportinglib_LIB  | ${reportinglib_LIBRARY}")
   endif()
 
   message(STATUS "--------------+--------------------------------------------------------------")

coreneuron/CMakeLists.txt

@@ -24,6 +24,7 @@ file(GLOB CORENEURON_CODE_FILES
                   "apps/corenrn_parameters.cpp"
                   "gpu/*.cpp"
                   "io/*.cpp"
+                  "io/reports/*.cpp"
                   "mechanism/*.cpp"
                   "mpi/*.cpp"
                   "network/*.cpp"
@@ -211,12 +212,14 @@ add_dependencies(coreneuron scopmath)
 # coreneuron executable
 include_directories(${CORENEURON_PROJECT_SOURCE_DIR})
 add_executable(nrniv-core "apps/coreneuron.cpp")
+
 target_link_libraries(nrniv-core
-        corenrnmech
-        ${MPI_C_LIBRARIES}
-        ${MPI_CXX_LIBRARIES}
-        ${reportinglib_LIBRARY}
-        ${sonatareport_LIBRARY})
+            corenrnmech
+            ${reportinglib_LIBRARY}
+            ${sonatareport_LIBRARY}
+            ${MPI_C_LIBRARIES}
+            ${MPI_CXX_LIBRARIES})
+
 set_target_properties(nrniv-core PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 
 # =============================================================================

coreneuron/apps/main1.cpp

@@ -34,6 +34,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 
 #include <cstring>
 #include <climits>
+#include <memory>
 #include <vector>
 
 #include "coreneuron/engine.h"
@@ -51,7 +52,10 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include "coreneuron/io/prcellstate.hpp"
 #include "coreneuron/utils/nrnmutdec.h"
 #include "coreneuron/utils/nrn_stats.h"
-#include "coreneuron/io/nrnreport.hpp"
+#include "coreneuron/io/reports/nrnreport.hpp"
+#include "coreneuron/io/reports/binary_report_handler.hpp"
+#include "coreneuron/io/reports/report_handler.hpp"
+#include "coreneuron/io/reports/sonata_report_handler.hpp"
 #include "coreneuron/gpu/nrn_acc_manager.hpp"
 #include "coreneuron/utils/profile/profiler_interface.h"
 #include "coreneuron/network/partrans.hpp"
@@ -395,6 +399,22 @@ static void trajectory_return() {
     }
 }
 
+std::unique_ptr<ReportHandler> create_report_handler(ReportConfiguration& config) {
+    std::unique_ptr<ReportHandler> report_handler;
+    if (std::strcmp(config.format, "Bin") == 0) {
+        report_handler = std::make_unique<BinaryReportHandler>(config);
+    } else if (std::strcmp(config.format, "SONATA") == 0) {
+        report_handler = std::make_unique<SonataReportHandler>(config);
+    }
+    else {
+        if (nrnmpi_myid == 0) {
+            printf(" WARNING : Report name '%s' has unknown format: '%s'.\n", config.name, config.format);
+        }
+        return nullptr;
+    }
+    return report_handler;
+}
+
 }  // namespace coreneuron
 
 /// The following high-level functions are marked as "extern C"
@@ -434,6 +454,7 @@ extern "C" int run_solve_core(int argc, char** argv) {
     Instrumentor::phase_begin("main");
 
     std::vector<ReportConfiguration> configs;
+    std::vector<std::unique_ptr<ReportHandler> > report_handlers;
     bool reports_needs_finalize = false;
 
     report_mem_usage("After mk_mech");
@@ -514,7 +535,11 @@ extern "C" int run_solve_core(int argc, char** argv) {
         // register all reports into reportinglib
         double min_report_dt = INT_MAX;
         for (size_t i = 0; i < configs.size(); i++) {
-            register_report(dt, tstop, delay, configs[i]);
+            std::unique_ptr<ReportHandler> report_handler = create_report_handler(configs[i]);
+            if(report_handler) {
+                report_handler->create_report(dt, tstop, delay);
+                report_handlers.push_back(std::move(report_handler));
+            }
             if (configs[i].report_dt < min_report_dt) {
                 min_report_dt = configs[i].report_dt;
             }

coreneuron/io/nrn_setup.cpp

@@ -46,7 +46,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include "coreneuron/io/nrn_checkpoint.hpp"
 #include "coreneuron/permute/node_permute.h"
 #include "coreneuron/permute/cellorder.hpp"
-#include "coreneuron/io/nrnsection_mapping.h"
+#include "coreneuron/io/nrnsection_mapping.hpp"
 #include "coreneuron/utils/nrnoc_aux.hpp"
 
 // callbacks into nrn/src/nrniv/nrnbbcore_write.cpp