Coreneuron source code reorganization (#229)

* Initial version of coreneuron source code reorganization
  - reorganized most source files into topical subdirs as discussed with development team
  - fixed up source code includes to reflect changes
  - fixed up CMake files to reflect changes
  - updated nmodl submodules to reflect changes
  - Rearranged mechanism related code into subfolders `mechanism` and `mechanism/mech`
    to ensure that the files later used for mod generation are kept seperately. This
    corrects an issue when building coreneuron and simplifies the cmake files
* Cleaned up issues in header includes
  - removed unnecessary headers
  - fixed relative header includes
  - fixed C header includes to new style
     (e.g. `<string.h>` --> `<cstring>`)
* Updated nmodl and mod2c and fixed issue when building with nmodl
* Update many header names and remove nrnoc_decl.h
* Updated mod2c/nmodl to fix stdlib header includes

Author: Omar Awile

CMake/NmodlHelper.cmake

@@ -89,12 +89,18 @@ macro(nmodl_to_cpp_target)
 
   list(APPEND NMODL_${mod2c_KEY}_MODS "${mod2c_modname_}")
   if(CORENRN_ENABLE_NMODL AND NMODL_FOUND)
+    string(FIND "${NMODL_EXTRA_FLAGS_LIST}" "passes" pos)
+    if(pos EQUAL -1)
+      set(NMODL_FLAGS "passes;--inline;${NMODL_EXTRA_FLAGS_LIST}")
+    else()
+      string(REPLACE "passes" "passes;--inline" NMODL_FLAGS "${NMODL_EXTRA_FLAGS_LIST}")
+    endif()
     add_custom_command(OUTPUT ${mod2c_output_} ${mod2c_wrapper_output_}
                        DEPENDS ${mod2c_MODFILE} ${CORENRN_NMODL_BINARY}
                        COMMAND ${CMAKE_COMMAND} -E copy "${mod2c_source_}"
                                "${CMAKE_CURRENT_BINARY_DIR}"
                        COMMAND ${CORENRN_NMODL_COMMAND} "${mod2c_modname_}" -o "${CMAKE_CURRENT_BINARY_DIR}"
-                               host ${nmodl_modearg} passes --inline ${NMODL_EXTRA_FLAGS_LIST}
+                               host ${nmodl_modearg} ${NMODL_FLAGS}
                        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
   else()
     add_custom_command(OUTPUT ${mod2c_output_}

CMakeLists.txt

@@ -215,7 +215,6 @@ endif()
 # Add main directories
 # =============================================================================
 add_subdirectory(coreneuron)
-add_subdirectory(apps)
 add_subdirectory(extra)
 
 if(CORENRN_ENABLE_UNIT_TESTS)

apps/CMakeLists.txt

@@ -18,28 +18,33 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 # =============================================================================
 file(GLOB_RECURSE CORENEURON_HEADER_FILES "*.h*")
 file(GLOB_RECURSE CORENEURON_TEMPLATE_FILES "*.ipp")
-file(GLOB_RECURSE CORENEURON_CODE_FILES
-                  "nrniv/*.c*"
-                  "nrnmpi/*.c*"
-                  "nrnoc/*.c*"
-                  "nrnomp/*.c*"
-                  "utils/*.c*")
+file(GLOB CORENEURON_CODE_FILES
+                  "apps/main1.cpp"
+                  "gpu/*.cpp"
+                  "io/*.cpp"
+                  "mechanism/*.cpp"
+                  "mpi/*.cpp"
+                  "network/*.cpp"
+                  "permute/*.cpp"
+                  "sim/*.cpp")
+file(GLOB_RECURSE CORENEURON_UTILS_FILES "utils/*.c*")
+list(APPEND CORENEURON_CODE_FILES ${CORENEURON_UTILS_FILES})
 file(GLOB_RECURSE CORENEURON_CUDA_FILES "*.cu")
-file(GLOB_RECURSE SCOPMATH_CODE_FILES "scopmath_core/*.c*")
+file(GLOB SCOPMATH_CODE_FILES "sim/scopmath/*.cpp")
 
-set(DIMPLIC_CODE_FILE "mech/dimplic.cpp")
-set(ENGINEMECH_CODE_FILE "mech/enginemech.cpp")
+set(DIMPLIC_CODE_FILE "mechanism/mech/dimplic.cpp")
+set(ENGINEMECH_CODE_FILE "mechanism/mech/enginemech.cpp")
 
 # for external mod files we need to generate modl_ref function in mod_func.c
-set(MODFUNC_PERL_SCRIPT "${CMAKE_CURRENT_SOURCE_DIR}/mech/mod_func.c.pl")
+set(MODFUNC_PERL_SCRIPT "mechanism/mech/mod_func.c.pl")
 
 # as openacc limits passing function pointers as arguments, mod2c translated files depend on a
 # _kinderiv.h file that is constructed by kinderiv.py
 set(KINDERIV_PYTHON_SCRIPT "${CMAKE_CURRENT_SOURCE_DIR}/kinderiv.py")
 set(KINDERIV_HEADER_FILE "${CMAKE_CURRENT_BINARY_DIR}/_kinderiv.h")
 
 set(NMODL_UNITS_FILE "${CMAKE_BINARY_DIR}/share/nrnunits.lib")
-set(INBUILT_MOD_PATH "${CMAKE_CURRENT_SOURCE_DIR}/mech/modfile")
+set(INBUILT_MOD_PATH "mechanism/mech/modfile")
 set(INBUILT_MOD_FILES expsyn.mod exp2syn.mod hh.mod netstim.mod passive.mod pattern.mod stim.mod)
 
 # Has helper macro for generating cpp file from mod2c
@@ -85,8 +90,8 @@ if(CORENRN_ENABLE_GPU)
       ${CMAKE_CURRENT_BINARY_DIR}/netstim_inhpoisson.cpp
       ${CMAKE_CURRENT_BINARY_DIR}/pattern.cpp
       ${CMAKE_CURRENT_SOURCE_DIR}/utils/randoms/nrnran123.cpp
-      ${CMAKE_CURRENT_SOURCE_DIR}/nrniv/nrn_setup.cpp
-      ${CMAKE_CURRENT_SOURCE_DIR}/nrniv/global_vars.cpp)
+      ${CMAKE_CURRENT_SOURCE_DIR}/io/nrn_setup.cpp
+      ${CMAKE_CURRENT_SOURCE_DIR}/io/global_vars.cpp)
 
   set_source_files_properties(${DIMPLIC_CODE_FILE}
                               ${NMODL_INBUILT_MOD_OUTPUTS}
@@ -193,6 +198,20 @@ add_custom_command(TARGET coreneuron
                    COMMENT "Running nrnivmodl-core with halfgap.mod")
 add_dependencies(coreneuron scopmath)
 
+# =============================================================================
+# create nrnivmodl-core
+# =============================================================================
+# 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})
+set_target_properties(nrniv-core PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+
 # =============================================================================
 # Extract link definitions to be used with nrnivmodl-core
 # =============================================================================
@@ -212,13 +231,17 @@ configure_file(${ENGINEMECH_CODE_FILE} ${CMAKE_BINARY_DIR}/share/coreneuron/engi
 
 configure_file("engine.h" ${CMAKE_BINARY_DIR}/include/coreneuron/engine.h)
 configure_file("enginemech.h" ${CMAKE_BINARY_DIR}/include/coreneuron/enginemech.h)
-configure_file("nrniv/profiler_interface.h"
+configure_file("utils/profile/profiler_interface.h"
                ${CMAKE_BINARY_DIR}/include/coreneuron/nrniv/profiler_interface.h)
-configure_file("nrnoc/nrnoc_ml.ispc" ${CMAKE_BINARY_DIR}/include/coreneuron/nrnoc/nrnoc_ml.ispc)
+configure_file("mechanism/nrnoc_ml.ispc" ${CMAKE_BINARY_DIR}/include/coreneuron/mechanism/nrnoc_ml.ispc)
 
 # TODO : this doesn't get re-copied if source changes
 file(COPY "utils/randoms" DESTINATION ${CMAKE_BINARY_DIR}/include/coreneuron/utils)
 
+# main program required for building special-core
+file(COPY apps/coreneuron.cpp DESTINATION ${CMAKE_BINARY_DIR}/share/coreneuron)
+
+
 # =============================================================================
 # Install main targets
 # =============================================================================
@@ -253,3 +276,7 @@ install(PROGRAMS ${CORENRN_NMODL_BINARY} DESTINATION bin)
 if(NOT CORENRN_ENABLE_NMODL)
   install(FILES ${NMODL_UNITS_FILE} DESTINATION share/mod2c)
 endif()
+
+# install nrniv-core app
+install(TARGETS nrniv-core DESTINATION bin)
+install(FILES apps/coreneuron.cpp DESTINATION share/coreneuron)

coreneuron/CMakeLists.txt

@@ -27,7 +27,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 */
 
 #include <coreneuron/enginemech.h>
-#include "coreneuron/nrniv/profiler_interface.h"
+#include "coreneuron/utils/profile/profiler_interface.h"
 
 int main(int argc, char** argv) {
     coreneuron::Instrumentor::init_profile();

apps/coreneuron.cpp renamed to coreneuron/apps/coreneuron.cpp

@@ -32,33 +32,33 @@ THE POSSIBILITY OF SUCH DAMAGE.
  * @brief File containing main driver routine for CoreNeuron
  */
 
+#include <cstring>
+#include <climits>
 #include <vector>
-#include <string.h>
+
 #include "coreneuron/engine.h"
 #include "coreneuron/utils/randoms/nrnran123.h"
 #include "coreneuron/nrnconf.h"
-#include "coreneuron/nrnoc/fast_imem.h"
-#include "coreneuron/nrnoc/multicore.h"
-#include "coreneuron/nrnoc/nrnoc_decl.h"
-#include "coreneuron/nrnmpi/nrnmpi.h"
+#include "coreneuron/sim/fast_imem.hpp"
+#include "coreneuron/sim/multicore.hpp"
+#include "coreneuron/mpi/nrnmpi.h"
 #include "coreneuron/nrniv/nrniv_decl.h"
-#include "coreneuron/nrniv/nrnmutdec.h"
-#include "coreneuron/nrniv/output_spikes.h"
-#include "coreneuron/nrniv/nrn_checkpoint.h"
-#include "coreneuron/utils/endianness.h"
+#include "coreneuron/mechanism/register_mech.hpp"
+#include "coreneuron/io/output_spikes.hpp"
+#include "coreneuron/io/nrn_checkpoint.hpp"
 #include "coreneuron/utils/memory_utils.h"
-#include "coreneuron/nrniv/nrnoptarg.h"
+#include "coreneuron/io/nrnoptarg.hpp"
+#include "coreneuron/io/prcellstate.hpp"
+#include "coreneuron/utils/nrnmutdec.h"
 #include "coreneuron/utils/sdprintf.h"
-#include "coreneuron/nrniv/nrn_stats.h"
-#include "coreneuron/utils/reports/nrnreport.h"
-#include "coreneuron/nrniv/nrn_acc_manager.h"
-#include "coreneuron/nrniv/profiler_interface.h"
-#include "coreneuron/nrniv/partrans.h"
-#include "coreneuron/nrniv/multisend.h"
-#include "coreneuron/utils/file_utils.h"
-#include "coreneuron/nrniv/nrn2core_direct.h"
-#include <string.h>
-#include <climits>
+#include "coreneuron/utils/nrn_stats.h"
+#include "coreneuron/io/nrnreport.hpp"
+#include "coreneuron/gpu/nrn_acc_manager.hpp"
+#include "coreneuron/utils/profile/profiler_interface.h"
+#include "coreneuron/network/partrans.hpp"
+#include "coreneuron/network/multisend.hpp"
+#include "coreneuron/io/file_utils.hpp"
+#include "coreneuron/io/nrn2core_direct.h"
 
 extern "C" {
 const char* corenrn_version() {

coreneuron/nrniv/main1.cpp renamed to coreneuron/apps/main1.cpp

@@ -42,15 +42,14 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include <array>
 
 #include "coreneuron/utils/randoms/nrnran123.h"      //Random Number Generator
-#include "coreneuron/scopmath_core/newton_struct.h"  //Newton Struct
-#include "coreneuron/nrnoc/membdef.h"                //static definitions
-#include "coreneuron/nrnoc/nrnoc_ml.h"               //Memb_list and mechs info
+#include "coreneuron/sim/scopmath/newton_struct.h"  //Newton Struct
+#include "coreneuron/membrane_definitions.h"                //static definitions
+#include "coreneuron/mechanism/mechanism.hpp"               //Memb_list and mechs info
 
-#include "coreneuron/nrniv/memory.h"  //Memory alignments and padding
+#include "coreneuron/utils/memory.h"  //Memory alignments and padding
 #include "coreneuron/nrnconf.h"
-#include "coreneuron/nrnoc/multicore.h"
-#include "coreneuron/nrnoc/nrnoc_decl.h"
-#include "coreneuron/nrnoc/mech_mapping.hpp"
+#include "coreneuron/sim/multicore.hpp"
+#include "coreneuron/mechanism/mech_mapping.hpp"
 
 namespace coreneuron {
 

coreneuron/coreneuron.hpp

@@ -1,16 +1,16 @@
 #include <queue>
 #include <utility>
 
-#include "coreneuron/nrnoc/multicore.h"
-#include "coreneuron/nrniv/netcon.h"
-#include "coreneuron/nrniv/nrn_acc_manager.h"
+#include "coreneuron/sim/multicore.hpp"
+#include "coreneuron/network/netcon.hpp"
 #include "coreneuron/nrniv/nrniv_decl.h"
-#include "coreneuron/nrniv/vrecitem.h"
-#include "coreneuron/nrniv/profiler_interface.h"
-#include "coreneuron/nrniv/cellorder.h"
-#include "coreneuron/nrniv/cuda_profile.h"
-#include "coreneuron/scopmath_core/newton_struct.h"
+#include "coreneuron/utils/vrecitem.h"
+#include "coreneuron/utils/profile/profiler_interface.h"
+#include "coreneuron/permute/cellorder.hpp"
+#include "coreneuron/utils/profile/cuda_profile.h"
+#include "coreneuron/sim/scopmath/newton_struct.h"
 #include "coreneuron/coreneuron.hpp"
+#include "coreneuron/utils/nrnoc_aux.hpp"
 
 #ifdef _OPENACC
 #include <openacc.h>

coreneuron/nrniv/nrn_acc_manager.cpp renamed to coreneuron/gpu/nrn_acc_manager.cpp

@@ -5,7 +5,8 @@
 #include <openacc.h>
 #endif
 
-#include "coreneuron/nrnoc/multicore.h"
+#include "coreneuron/sim/multicore.hpp"
+
 namespace coreneuron {
 void setup_nrnthreads_on_device(NrnThread* threads, int nthreads);
 void update_nrnthreads_on_host(NrnThread* threads, int nthreads);

coreneuron/nrniv/nrn_acc_manager.h renamed to coreneuron/gpu/nrn_acc_manager.hpp

@@ -26,9 +26,9 @@ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
 THE POSSIBILITY OF SUCH DAMAGE.
 */
 
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstdio>
+#include <cstring>
+#include <cstdlib>
 #include <sys/stat.h>
 #include <errno.h>
 

coreneuron/utils/file_utils.cpp renamed to coreneuron/io/file_utils.cpp

@@ -1,15 +1,14 @@
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
 #include <map>
 #include <string>
 #include <algorithm>
 
 #include "coreneuron/utils/randoms/nrnran123.h"
 #include "coreneuron/nrnconf.h"
-#include "coreneuron/nrniv/nrniv_decl.h"
-#include "coreneuron/nrnoc/membfunc.hpp"
-#include "coreneuron/nrniv/nrn_assert.h"
-#include "coreneuron/nrniv/nrn2core_direct.h"
+#include "coreneuron/mechanism/membfunc.hpp"
+#include "coreneuron/utils/nrn_assert.h"
+#include "coreneuron/io/nrn2core_direct.h"
 
 void* (*nrn2core_get_global_dbl_item_)(void*, const char*& name, int& size, double*& val);
 int (*nrn2core_get_global_int_item_)(const char* name);

coreneuron/utils/file_utils.h renamed to coreneuron/io/file_utils.hpp

@@ -26,28 +26,32 @@ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
 THE POSSIBILITY OF SUCH DAMAGE.
 */
 
-#include <string.h>
+#include <cstring>
 #include <map>
-#include <string>
 #include <iostream>
 #include <fstream>
 #include <sstream>
+
 #include "coreneuron/nrnconf.h"
-#include "coreneuron/nrnoc/multicore.h"
-#include "coreneuron/nrnoc/membdef.h"
-#include "coreneuron/nrnoc/nrnoc_decl.h"
+#include "coreneuron/sim/multicore.hpp"
+#include "coreneuron/membrane_definitions.h"
+#include "coreneuron/mechanism/register_mech.hpp"
 #include "coreneuron/nrniv/nrniv_decl.h"
-#include "coreneuron/nrniv/nrn_assert.h"
+#include "coreneuron/utils/nrn_assert.h"
 #include "coreneuron/utils/sdprintf.h"
-#include "coreneuron/mech/cfile/cabvars.h"
-#include "coreneuron/nrniv/nrn2core_direct.h"
+#include "coreneuron/mechanism/mech/cfile/cabvars.h"
+#include "coreneuron/io/nrn2core_direct.h"
 #include "coreneuron/coreneuron.hpp"
+#include "coreneuron/mechanism//eion.hpp"
 
 static char banner[] = "Duke, Yale, and the BlueBrain Project -- Copyright 1984-2019";
 
 namespace coreneuron {
 int nrn_nobanner_;
 
+// NB: this should go away
+extern const char* nrn_version(int);
+
 int nrn_need_byteswap;
 // following copied (except for nrn_need_byteswap line) from NEURON ivocvect.cpp
 #define BYTEHEADER   \

coreneuron/nrniv/global_vars.cpp renamed to coreneuron/io/global_vars.cpp

@@ -25,23 +25,24 @@ CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
 THE POSSIBILITY OF SUCH DAMAGE.
 */
-#include "coreneuron/nrnoc/multicore.h"
-#include "coreneuron/nrniv/nrniv_decl.h"
-#include "coreneuron/nrnoc/nrnoc_decl.h"
-#include "coreneuron/nrniv/nrn_filehandler.h"
-#include "coreneuron/nrniv/nrn_checkpoint.h"
-#include "coreneuron/nrniv/netcvode.h"
-#include "coreneuron/nrniv/vrecitem.h"
-#include "coreneuron/mech/mod2c_core_thread.h"
-#include "coreneuron/utils/file_utils.h"
-#include "coreneuron/nrniv/node_permute.h"
-#include "coreneuron/coreneuron.hpp"
-
 #include <iostream>
-#include <fstream>
 #include <sstream>
 #include <cassert>
-#include <stdio.h>
+
+#include "coreneuron/sim/multicore.hpp"
+#include "coreneuron/nrniv/nrniv_decl.h"
+#include "coreneuron/io/nrn_filehandler.hpp"
+#include "coreneuron/io/nrn_checkpoint.hpp"
+#include "coreneuron/io/nrn_setup.hpp"
+#include "coreneuron/network/netcvode.hpp"
+#include "coreneuron/network/netpar.hpp"
+#include "coreneuron/utils/vrecitem.h"
+#include "coreneuron/mechanism/mech/mod2c_core_thread.hpp"
+#include "coreneuron/io/file_utils.hpp"
+#include "coreneuron/permute/node_permute.h"
+#include "coreneuron/coreneuron.hpp"
+#include "coreneuron/utils/nrnoc_aux.hpp"
+
 namespace coreneuron {
 bool nrn_checkpoint_arg_exists;
 int _nrn_skip_initmodel;