* Move coreneuron towards c++ (#82)

- coreneuron namespace added
- change ivocvect vector compatibility and declarations
- core_read and core_write to be out of coreneuron namespace
- change public API of coreneuron to explose core_psolve
- add pulbic header
- kinderiv.h has prototype declaration for euler methods
- changes to integrate with neurodamus: psolve_core renamed and added --skip-mpi-finalize command line option
- OpenACC pragma annotation was missing for kernels using euler
- cudaMemset wrong pointer (bug fix) 
- user provided flags should take precedence
- change tests to comply to new changes
- link with mod2c generated files

Author: fouriaux

apps/coreneuron.cpp

@@ -26,12 +26,11 @@ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
 THE POSSIBILITY OF SUCH DAMAGE.
 */
 
-
-extern int main1(int argc, char** argv, char** env);
+#include <coreneuron/engine.h>
 extern "C" {extern void modl_reg(void);}
 
-int main(int argc, char** argv, char** env) {
-  return main1(argc, argv, env);
+int main(int argc, char** argv) {
+  return solve_core(argc, argv);
 }
 
 /// Declare an empty function if Neurodamus mechanisms are not used, otherwise register them in mechs/cfile/mod_func.c

coreneuron/CMakeLists.txt

@@ -55,7 +55,7 @@ set(MOD2C env "MODLUNIT=${MOD2C_UNITS}" ${MOD2C})
 macro(mod2c_target name input)
     get_filename_component(mod2c_source_ ${input} ABSOLUTE)
     get_filename_component(mod2c_modname_ ${input} NAME)
-    string(REGEX REPLACE "\\.mod$" ".c" mod2c_cname_ "${mod2c_modname_}")
+    string(REGEX REPLACE "\\.mod$" ".cpp" mod2c_cname_ "${mod2c_modname_}")
 
     set(mod2c_output_ "${CMAKE_CURRENT_BINARY_DIR}/${mod2c_cname_}")
     list(APPEND MOD2C_${name}_OUTPUTS "${mod2c_output_}")
@@ -192,7 +192,7 @@ mod2c_from_file(OPTMECH "${ADDITIONAL_MECHS}" "${ADDITIONAL_MECHPATH}")
 
 # For 'non-standard' mod files, need to generate registering function in mod_func.c
 
-set(MOD_FUNC_C    "${CMAKE_CURRENT_BINARY_DIR}/mod_func.c")
+set(MOD_FUNC_C    "${CMAKE_CURRENT_BINARY_DIR}/mod_func.cpp")
 set(MOD_FUNC_C_PL "${CMAKE_CURRENT_SOURCE_DIR}/mech/mod_func.c.pl")
 
 # ... pass as argument to the perl script the list of mod file names;
@@ -221,7 +221,7 @@ add_custom_command(OUTPUT "${KINDERIV_H}"
 
 if (EXPORT_MECHS_FUNCTIONS)
   # Create C file with all "get function pointers" methods
-  set(MOD_FUNC_PTRS_C    "${CMAKE_CURRENT_BINARY_DIR}/mod_func_ptrs.c")
+  set(MOD_FUNC_PTRS_C    "${CMAKE_CURRENT_BINARY_DIR}/mod_func_ptrs.cpp")
   set(MOD_FUNC_PTRS_C_PL "${CMAKE_CURRENT_SOURCE_DIR}/mech/mod_func_ptrs.c.pl")
 
   # ... pass as argument to the perl script the list of mods full paths;
@@ -236,10 +236,10 @@ set(GENERATED_MECH_C_FILES ${MOD_FUNC_C} ${MOD_FUNC_PTRS_C} ${MOD2C_STDMECH_OUTP
 
 # artificial cells must be on cpu, defaul nrnran123.c is for cpu, nrn_setup.cpp uses nrnran123 for only memory calculation purpose which should use cpu version of nrnran123
 set(NOACC_MECH_C_FILES
-    ${CMAKE_CURRENT_BINARY_DIR}/netstim.c
-    ${CMAKE_CURRENT_BINARY_DIR}/netstim_inhpoisson.c
-    ${CMAKE_CURRENT_BINARY_DIR}/pattern.c
-    ${CMAKE_CURRENT_SOURCE_DIR}/utils/randoms/nrnran123.c
+    ${CMAKE_CURRENT_BINARY_DIR}/netstim.cpp
+    ${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)
 
@@ -291,6 +291,7 @@ set_target_properties(coreneuron PROPERTIES
 install(TARGETS coreneuron
              LIBRARY DESTINATION ${LIB_INSTALL_DIR}
              ARCHIVE DESTINATION ${LIB_INSTALL_DIR} )
+         install(FILES "engine.h" DESTINATION include/coreneuron)
 
 if(ENABLE_DEV_FILES_INSTALLATION)
     install(DIRECTORY .

coreneuron/coreneuron.h

@@ -39,16 +39,14 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include <stdlib.h>
 #include <math.h>
 
+#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/utils/randoms/nrnran123.h"      //Random Number Generator
 
-#if defined(__cplusplus)
 #include "coreneuron/nrniv/memory.h"  //Memory alignments and padding
 
-extern "C" {
-#endif
+namespace coreneuron {
 
 #ifdef EXPORT_MECHS_FUNCTIONS
 // from (auto-generated) mod_func_ptrs.c
@@ -59,18 +57,16 @@ extern mod_f_t get_BA_function(const char* sym, int BA_func_id);
 #endif
 
 // from nrnoc/capac.c
-extern void nrn_init_capacitance(struct NrnThread*, struct Memb_list*, int);
-extern void nrn_cur_capacitance(struct NrnThread* _nt, struct Memb_list* ml, int type);
+extern void nrn_init_capacitance(NrnThread*, Memb_list*, int);
+extern void nrn_cur_capacitance(NrnThread* _nt, Memb_list* ml, int type);
 extern void nrn_alloc_capacitance(double* data, Datum* pdata, int type);
 
 // from nrnoc/eion.c
-extern void nrn_init_ion(struct NrnThread*, struct Memb_list*, int);
-extern void nrn_cur_ion(struct NrnThread* _nt, struct Memb_list* ml, int type);
+extern void nrn_init_ion(NrnThread*, Memb_list*, int);
+extern void nrn_cur_ion(NrnThread* _nt, Memb_list* ml, int type);
 extern void nrn_alloc_ion(double* data, Datum* pdata, int type);
 extern void second_order_cur(NrnThread* _nt, int secondorder);
 
-#if defined(__cplusplus)
-}
-#endif
+} //namespace coreneuron
 
 #endif

coreneuron/engine.h

@@ -0,0 +1,12 @@
+#ifndef CORENEURON_ENGINE_H
+#define CORENEURON_ENGINE_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+    extern int solve_core (int argc, char** argv);
+#ifdef __cplusplus
+    } 
+#endif
+
+#endif

coreneuron/kinderiv.py

@@ -14,7 +14,7 @@
 
 import os
 
-fnames = [f.replace('.mod', '.c') for f in os.listdir('.') if f.endswith('.mod')]
+fnames = [f.replace('.mod', '.cpp') for f in os.listdir('.') if f.endswith('.mod')]
 euler = []
 deriv = []
 kin = []
@@ -47,6 +47,7 @@
     fout.write(' */\n')
 
 fout.write("\n/* declarations */\n")
+fout.write("\nnamespace coreneuron {\n")
 for item in deriv:
   fout.write('#pragma acc routine seq\n')
   fout.write('extern int %s%s(_threadargsproto_);\n' % (item[0], item[1]))
@@ -94,6 +95,8 @@
 fout.write("\n")
 
 fout.write('\n#endif\n')
+
+fout.write("\n} //namespace coreneuron\n")
 fout.close()
 
 # if kf exists and is same as kftmp, just remove kftmp. Otherwise

coreneuron/mech/cfile/cabvars.h

@@ -26,9 +26,8 @@ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
 THE POSSIBILITY OF SUCH DAMAGE.
 */
 
-#ifdef __cplusplus
-extern "C" {
-#endif
+
+namespace coreneuron {
 
 extern void capacitance_reg(void), _passive_reg(void),
 #if EXTRACELLULAR
@@ -44,6 +43,4 @@ static void (*mechanism[])(void) = {/* type will start at 3 */
 #endif
                                     _stim_reg, _hh_reg, _expsyn_reg, _netstim_reg, _exp2syn_reg, 0};
 
-#ifdef __cplusplus
-}
-#endif
+} //namespace coreneuron

coreneuron/mech/mod2c_core_thread.h

@@ -4,9 +4,7 @@
 #include "coreneuron/nrnoc/multicore.h"
 #include "coreneuron/nrnoc/nrnoc_ml.h"
 
-#if defined(__cplusplus)
-extern "C" {
-#endif
+namespace coreneuron {
 
 #if !defined(LAYOUT)
 /* 1 means AoS, >1 means AoSoA, <= 0 means SOA */
@@ -141,8 +139,6 @@ extern void _modl_set_dt_thread(double, NrnThread*);
 
 void nrn_sparseobj_copyto_device(SparseObj* so);
 
-#if defined(__cplusplus)
-}
-#endif
+} // namespace coreneuron
 
 #endif

coreneuron/mech/mod_func.c.pl

@@ -26,6 +26,7 @@
 
 print << "__eof";
 #include <stdio.h>
+namespace coreneuron {
 extern int nrnmpi_myid;
 extern int nrn_nobanner_;
 extern int @{[join ",\n  ", map{"_${_}_reg(void)"} @mods]};
@@ -41,4 +42,5 @@
 
     @{[join "\n", map{" _${_}_reg();"} @mods] }
 }
+} //namespace coreneuron
 __eof

coreneuron/mech/mod_func_ptrs.c.pl

@@ -33,6 +33,7 @@
 #include <string.h>
 #include <stdlib.h>
 #include "coreneuron/coreneuron.h"
+namespace coreneuron {
 __eof
 
 #Get the correct SUFFIX from each mod file for each mechanism
@@ -121,5 +122,6 @@
 {
   return NULL;
 }
+} //namespace coreneuron
 __eof
 

coreneuron/mech/modfile/pattern.mod

@@ -32,8 +32,6 @@ NET_RECEIVE (w) {LOCAL nst
 
 VERBATIM
 
-extern void nrn_fake_fire(int gid, double spiketime, int fake_out);
-
 typedef struct {
 	int size;
 	double* tvec;
@@ -57,16 +55,17 @@ Info* mkinfo(_threadargsproto_) {
 	return info;
 }
 /* for CoreNEURON checkpoint save and restore */
+namespace coreneuron {
 int checkpoint_save_patternstim(_threadargsproto_) {
 	INFOCAST; Info* info = *ip;
 	return info->index;
 }
 void checkpoint_restore_patternstim(int _index, double _te, _threadargsproto_) {
     INFOCAST; Info* info = *ip;
     info->index = _index;
-    artcell_net_send(_tqitem, -1, _nt->_vdata[_ppvar[1*_STRIDE]], _te, 1.0);
+    artcell_net_send(_tqitem, -1, (Point_process*)_nt->_vdata[_ppvar[1*_STRIDE]], _te, 1.0);
 }
-
+} //namespace coreneuron
 ENDVERBATIM
 
 FUNCTION initps() {
@@ -109,7 +108,7 @@ ENDVERBATIM
 VERBATIM
 static void bbcore_write(double* x, int* d, int* xx, int *offset, _threadargsproto_){}
 static void bbcore_read(double* x, int* d, int* xx, int* offset, _threadargsproto_){}
-
+namespace coreneuron {
 void pattern_stim_setup_helper(int size, double* tv, int* gv, _threadargsproto_) {
 	INFOCAST;
 	Info* info = mkinfo(_threadargs_);
@@ -118,6 +117,6 @@ void pattern_stim_setup_helper(int size, double* tv, int* gv, _threadargsproto_)
 	info->tvec = tv;
 	info->gidvec = gv;
 }
-
+} // namespace coreneuron
 ENDVERBATIM