Added support for SONATA reports (#211)

  - Call records_write_spikes
  - Change SONATA reportinglib library name
  - Move from find_package() module mode to config mode
    - Removed Findsonatareport.cmake file
    - find_package(sonata) found through config file (sonata_DIR needs to be passed to cmake)

Author: jorblancoa

CMakeLists.txt

@@ -50,6 +50,7 @@ include(CTest)
 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_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)
@@ -139,11 +140,20 @@ 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)
   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")
+endif()
 
 if(MINGW)
   add_definitions("-DMINGW")
@@ -247,8 +257,14 @@ if(cmake_generator_tolower MATCHES "makefile")
   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}")
   endif()
 
   message(STATUS "--------------+--------------------------------------------------------------")

apps/CMakeLists.txt

@@ -11,7 +11,8 @@ target_link_libraries(nrniv-core
                       corenrnmech
                       ${MPI_C_LIBRARIES}
                       ${MPI_CXX_LIBRARIES}
-                      ${reportinglib_LIBRARY})
+                      ${reportinglib_LIBRARY}
+                      ${sonatareport_LIBRARY})
 set_target_properties(nrniv-core PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 
 # main program required for building special-core

coreneuron/CMakeLists.txt

@@ -162,6 +162,7 @@ add_library(corenrnmech
 target_link_libraries(coreneuron
                       ${MPI_CXX_LIBRARIES}
                       ${reportinglib_LIBRARY}
+                      ${sonatareport_LIBRARY}
                       ${link_cudacoreneuron}
                       ${CUDA_LIBRARIES}
                       ${CALIPER_LIB}

coreneuron/nrniv/output_spikes.cpp

@@ -41,6 +41,9 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include "coreneuron/nrnmpi/nrnmpi_impl.h"
 #include "coreneuron/nrnmpi/nrnmpidec.h"
 #include "coreneuron/utils/string_utils.h"
+#ifdef ENABLE_SONATA_REPORTS
+#include "reportinglib/records.h"
+#endif
 
 namespace coreneuron {
 std::vector<double> spikevec_time;
@@ -158,6 +161,9 @@ void output_spikes_parallel(const char* outpath) {
     if (nrnmpi_myid == 0) {
         remove(fname.c_str());
     }
+#ifdef ENABLE_SONATA_REPORTS
+    records_write_spikes(spikevec_time, spikevec_gid);
+#else
     sort_spikes(spikevec_time, spikevec_gid);
     nrnmpi_barrier();
 
@@ -211,7 +217,9 @@ void output_spikes_parallel(const char* outpath) {
 
     MPI_File_close(&fh);
     free(spike_data);
+#endif
 }
+
 #endif
 
 void output_spikes_serial(const char* outpath) {

coreneuron/utils/reports/nrnreport.cpp

@@ -35,8 +35,12 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include "coreneuron/nrnoc/mech_mapping.hpp"
 #include "coreneuron/nrnoc/membfunc.h"
 #ifdef ENABLE_REPORTING
+#ifdef ENABLE_SONATA_REPORTS
+#include "reportinglib/records.h"
+#else
 #include "reportinglib/Records.h"
 #endif
+#endif
 #include <iostream>
 #include <vector>
 #include <algorithm>

tests/jenkins/Jenkinsfile

@@ -317,4 +317,11 @@ pipeline {
             }
         }
     }
+    post {
+        always {
+            dir("${WORKSPACE}") {
+                deleteDir()
+            }
+        }
+    }
 }

tests/unit/cmdline_interface/CMakeLists.txt

@@ -11,7 +11,8 @@ target_link_libraries(cmd_interface_test_bin
                       ${MPI_CXX_LIBRARIES}
                       ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}
                       coreneuron
-                      ${reportinglib_LIBRARY})
+                      ${reportinglib_LIBRARY}
+                      ${sonatareport_LIBRARY})
 
 add_test(NAME cmd_interface_test
          COMMAND ${TEST_EXEC_PREFIX} ${CMAKE_CURRENT_BINARY_DIR}/cmd_interface_test_bin)

tests/unit/interleave_info/CMakeLists.txt

@@ -11,7 +11,8 @@ target_link_libraries(interleave_info_bin
                       ${MPI_CXX_LIBRARIES}
                       ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}
                       coreneuron
-                      ${reportinglib_LIBRARY})
+                      ${reportinglib_LIBRARY}
+                      ${sonatareport_LIBRARY})
 
 add_test(NAME interleave_info_constructor_test
          COMMAND ${TEST_EXEC_PREFIX} ${CMAKE_CURRENT_BINARY_DIR}/interleave_info_bin)

tests/unit/queueing/CMakeLists.txt

@@ -11,6 +11,7 @@ target_link_libraries(queuing_test_bin
                       ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}
                       ${Boost_SYSTEM_LIBRARY}
                       coreneuron
-                      ${reportinglib_LIBRARY})
+                      ${reportinglib_LIBRARY}
+                      ${sonatareport_LIBRARY})
 
 add_test(NAME queuing_test COMMAND ${TEST_EXEC_PREFIX} ${CMAKE_CURRENT_BINARY_DIR}/queuing_test_bin)

tests/unit/sdprintf/CMakeLists.txt

@@ -11,7 +11,8 @@ add_executable(sdprintf_test_bin ${sdprintf_test_src})
 target_link_libraries(sdprintf_test_bin
                       ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}
                       coreneuron
-                      ${reportinglib_LIBRARY})
+                      ${reportinglib_LIBRARY}
+                      ${sonatareport_LIBRARY})
 
 add_test(NAME sdprintf_test
          COMMAND ${TEST_EXEC_PREFIX} ${CMAKE_CURRENT_BINARY_DIR}/sdprintf_test_bin)