New mpi way

cmake/NeuronFileLists.cmake

@@ -533,8 +533,6 @@ set(NMODL_FILES_LIST
 
 set(IVOS_FILES_LIST listimpl.cpp string.cpp observe.cpp regexp.cpp resource.cpp)
 
-set(MPI_DYNAMIC_INCLUDE nrnmpi_dynam.h nrnmpi_dynam_cinc nrnmpi_dynam_wrappers.inc)
-
 set(NRN_MUSIC_FILES_LIST nrnmusic.cpp)
 
 # =============================================================================
@@ -570,7 +568,7 @@ nrn_create_file_list(NRN_SPARSE13_SRC_FILES ${PROJECT_SOURCE_DIR}/src/sparse13
                      ${SPARSE13_FILES_LIST})
 nrn_create_file_list(NRN_SCOPMATH_SRC_FILES ${PROJECT_SOURCE_DIR}/src/scopmath
                      ${SCOPMATH_FILES_LIST})
-nrn_create_file_list(NRN_NRNMPI_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrnmpi ${NRNMPI_FILES_LIST})
+nrn_create_file_list(NRN_NRNMPI_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrnmpi/lib ${NRNMPI_FILES_LIST})
 nrn_create_file_list(NRN_NRNGNU_SRC_FILES ${PROJECT_SOURCE_DIR}/src/gnu ${NRNGNU_FILES_LIST})
 nrn_create_file_list(NRN_NRNPYTHON_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrnpython
                      ${NRNPYTHON_FILES_LIST})
@@ -579,8 +577,6 @@ nrn_create_file_list(NRN_BIN_SRC_FILES ${PROJECT_SOURCE_DIR}/src/ivoc/ nrnmain.c
 nrn_create_file_list(NRN_BIN_SRC_FILES ${PROJECT_SOURCE_DIR}/src/oc/ ockludge.cpp modlreg.cpp)
 nrn_create_file_list(NRN_MODLUNIT_SRC_FILES ${NRN_MODLUNIT_SRC_DIR} ${MODLUNIT_FILES_LIST})
 nrn_create_file_list(NRN_NMODL_SRC_FILES ${NRN_NMODL_SRC_DIR} ${NMODL_FILES_LIST})
-nrn_create_file_list(NRNMPI_DYNAMIC_INCLUDE_FILE ${PROJECT_SOURCE_DIR}/src/nrnmpi
-                     ${MPI_DYNAMIC_INCLUDE})
 nrn_create_file_list(NRN_IVOS_SRC_FILES ${NRN_IVOS_SRC_DIR} ${IVOS_FILES_LIST})
 nrn_create_file_list(NRN_MUSIC_SRC_FILES ${NRN_MUSIC_SRC_DIR} ${NRN_MUSIC_FILES_LIST})
 list(APPEND NRN_OC_SRC_FILES ${PROJECT_BINARY_DIR}/src/oc/hocusr.h)

src/ivoc/nrnmain.cpp

@@ -16,9 +16,6 @@ void nrnmpi_load_or_exit(bool is_python);
 void nrnmusic_load();
 #endif  // NRN_MUSIC
 #endif  // NRNMPI_DYNAMICLOAD
-#if NRNMPI
-extern "C" void nrnmpi_init(int nrnmpi_under_nrncontrol, int* pargc, char*** pargv);
-#endif
 
 int main(int argc, char** argv, char** env) {
     nrn_main_launch = 1;

src/nrniv/CMakeLists.txt

@@ -156,14 +156,17 @@ set(NRN_NRNIV_LIB_SRC_FILES
     ${NRN_SPARSE13_SRC_FILES}
     ${NRN_SUNDIALS_SRC_FILES})
 
+set(NRN_MPI_LIB_NAME "nrn_mpi" CACHE INTERNAL "")
 if(NRN_ENABLE_MPI)
   list(APPEND NRN_NRNIV_LIB_SRC_FILES ${NRN_PARALLEL_SRC_FILES})
-endif()
 
-if(NRN_ENABLE_MPI_DYNAMIC)
-  list(APPEND NRN_NRNIV_LIB_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrnmpi/nrnmpi_dynam.cpp)
-else()
-  list(APPEND NRN_NRNIV_LIB_SRC_FILES ${NRN_NRNMPI_SRC_FILES})
+  if(NRN_ENABLE_MPI_DYNAMIC)
+    add_library(${NRN_MPI_LIB_NAME} OBJECT ${NRN_NRNMPI_SRC_FILES})
+    target_include_directories(
+      ${NRN_MPI_LIB_NAME} PRIVATE ${MPI_C_INCLUDE_DIRS} ${PROJECT_SOURCE_DIR}/src)
+    set_property(TARGET ${NRN_MPI_LIB_NAME} PROPERTY POSITION_INDEPENDENT_CODE ON)
+    set(CORENRN_MPI_OBJ $<TARGET_OBJECTS:${NRN_MPI_LIB_NAME})
+  endif()
 endif()
 
 if(MINGW)
@@ -268,16 +271,6 @@ add_custom_command(
 add_custom_target(generate_hocusr_header DEPENDS "${PROJECT_BINARY_DIR}/src/oc/hocusr.h")
 add_dependencies(generated_source_files generate_hocusr_header)
 
-# header for dynamic mpi
-if(NRN_ENABLE_MPI_DYNAMIC)
-  add_custom_command(
-    OUTPUT ${NRNMPI_DYNAMIC_INCLUDE_FILE}
-    COMMAND sh mkdynam.sh
-    WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/src/nrnmpi
-    DEPENDS ${PROJECT_SOURCE_DIR}/src/nrnmpi/mkdynam.sh
-            ${PROJECT_SOURCE_DIR}/src/nrnmpi/nrnmpidec.h)
-endif()
-
 # =============================================================================
 # Various macro definitions for compiling different files
 # =============================================================================
@@ -379,13 +372,8 @@ elseif(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
     PROPERTY COMPILE_OPTIONS -O1)
 endif()
 
-if(NRN_ENABLE_MPI_DYNAMIC)
-  set_source_files_properties(${PROJECT_SOURCE_DIR}/src/nrnmpi/nrnmpi_dynam.cpp
-                              PROPERTIES OBJECT_DEPENDS ${NRNMPI_DYNAMIC_INCLUDE_FILE})
-  set_source_files_properties(${PROJECT_SOURCE_DIR}/src/nrnmpi/nrnmpi.cpp
-                              PROPERTIES OBJECT_DEPENDS ${NRNMPI_DYNAMIC_INCLUDE_FILE})
-  set_source_files_properties(${PROJECT_SOURCE_DIR}/src/nrnmpi/bbsmpipack.cpp
-                              PROPERTIES OBJECT_DEPENDS ${NRNMPI_DYNAMIC_INCLUDE_FILE})
+if(NRN_ENABLE_MPI)
+  set(NRN_NRNIV_MPI_DYNAM "../nrnmpi/core/resolve.cpp")
 endif()
 
 if(NRN_ENABLE_MUSIC)
@@ -410,7 +398,7 @@ include_directories(${NRN_INCLUDE_DIRS})
 # =============================================================================
 # All source directories to include
 # =============================================================================
-add_library(nrniv_lib ${NRN_LIBRARY_TYPE} ${NRN_NRNIV_LIB_SRC_FILES})
+add_library(nrniv_lib ${NRN_LIBRARY_TYPE} ${NRN_NRNIV_LIB_SRC_FILES} ${NRN_NRNIV_MPI_DYNAM})
 cpp_cc_configure_sanitizers(TARGET nrniv_lib)
 # Source-directory .cpp needs to find generated .hpp.
 target_include_directories(nrniv_lib PUBLIC "${NRN_OC_GEN}")

src/nrniv/bbsavestate.cpp

@@ -219,13 +219,6 @@ extern PreSyn* nrn_gid2presyn(int gid);
 extern int nrn_gid_exists(int gid);
 
 #if NRNMPI
-extern void nrnmpi_barrier();
-extern void nrnmpi_int_alltoallv(int*, int*, int*, int*, int*, int*);
-extern void nrnmpi_dbl_alltoallv(double*, int*, int*, double*, int*, int*);
-extern int nrnmpi_int_allmax(int);
-extern void nrnmpi_int_allgather(int* s, int* r, int n);
-extern void nrnmpi_int_allgatherv(int* s, int* r, int* n, int* dspl);
-extern void nrnmpi_dbl_allgatherv(double* s, double* r, int* n, int* dspl);
 #else
 static void nrnmpi_barrier() {}
 static void nrnmpi_int_alltoallv(int* s, int* scnt, int* sdispl, int* r, int* rcnt, int* rdispl) {

src/nrniv/multisend.cpp

@@ -367,11 +367,6 @@ double nrn_multisend_receive_time(int type) {  // and others
     return rt;
 }
 
-extern void nrnmpi_multisend_comm();
-extern void nrnmpi_multisend_multisend(NRNMPI_Spike*, int, int*);
-extern int nrnmpi_multisend_single_advance(NRNMPI_Spike*);
-extern int nrnmpi_multisend_conserve(int nsend, int nrecv);
-
 static void nrn_multisend_init() {
     for (int i = 0; i < n_multisend_interval; ++i) {
         multisend_receive_buffer[i]->init(i);

src/nrniv/netpar.cpp

@@ -34,6 +34,55 @@ static int n_multisend_interval;
 int nrnmusic;
 #endif
 
+#ifndef nrn_spikebuf_size
+#define nrn_spikebuf_size 0
+#endif
+
+// Variable from MPI
+#if nrn_spikebuf_size > 0
+typedef struct {
+    int nspike;
+    int gid[nrn_spikebuf_size];
+    double spiketime[nrn_spikebuf_size];
+} NRNMPI_Spikebuf;
+#endif
+
+
+#define icapacity_ nrnmpi_i_capacity_
+#define spikeout_  nrnmpi_spikeout_
+#define spikein_   nrnmpi_spikein_
+#define nout_      nrnmpi_nout_
+#define nin_       nrnmpi_nin_
+extern int nout_;
+extern int* nin_;
+extern int icapacity_;
+extern NRNMPI_Spike* spikeout_;
+extern NRNMPI_Spike* spikein_;
+
+#define spfixout_       nrnmpi_spikeout_fixed_
+#define spfixin_        nrnmpi_spikein_fixed_
+#define spfixin_ovfl_   nrnmpi_spikein_fixed_ovfl_
+#define localgid_size_  nrnmpi_localgid_size_
+#define ag_send_size_   nrnmpi_ag_send_size_
+#define ag_send_nspike_ nrnmpi_send_nspike_
+#define ovfl_capacity_  nrnmpi_ovfl_capacity_
+#define ovfl_           nrnmpi_ovfl_
+extern int localgid_size_;  /* bytes */
+extern int ag_send_size_;   /* bytes */
+extern int ag_send_nspike_; /* spikes */
+extern int ovfl_capacity_;  /* spikes */
+extern int ovfl_;           /* spikes */
+extern unsigned char* spfixout_;
+extern unsigned char* spfixin_;
+extern unsigned char* spfixin_ovfl_;
+//end variables
+
+#if nrn_spikebuf_size > 0
+#define spbufout_ nrnmpi_spbufout_
+#define spbufin_  nrnmpi_spbufin_
+extern NRNMPI_Spikebuf* spbufout_;
+extern NRNMPI_Spikebuf* spbufin_;
+#endif
 static Symbol* netcon_sym_;
 static Gid2PreSyn gid2out_;
 static Gid2PreSyn gid2in_;
@@ -88,11 +137,9 @@ static double set_mindelay(double maxdelay);
 
 #if NRNMPI
 
-#include "../nrnmpi/mpispike.h"
+// #include "../nrnmpi/mpispike.h"
 
 void nrn_timeout(int);
-extern int nrnmpi_int_allmax(int);
-extern void nrnmpi_int_allgather(int*, int*, int);
 void nrn2ncs_outputevent(int netcon_output_index, double firetime);
 bool nrn_use_compress_;  // global due to bbsavestate
 #define use_compress_ nrn_use_compress_
@@ -574,7 +621,7 @@ void nrn_spike_exchange(NrnThread* nt) {
         nrnmpi_barrier();
         nrnmpi_step_wait_ += nrnmpi_wtime() - wt;
     }
-    n = nrnmpi_spike_exchange();
+    n = nrnmpi_spike_exchange(nin_, &nout_, &icapacity_, &spikein_, &spikeout_);
     wt_ = nrnmpi_wtime() - wt;
     wt = nrnmpi_wtime();
     TBUF
@@ -670,7 +717,7 @@ void nrn_spike_exchange_compressed(NrnThread* nt) {
         nrnmpi_barrier();
         nrnmpi_step_wait_ += nrnmpi_wtime() - wt;
     }
-    n = nrnmpi_spike_exchange_compressed();
+    n = nrnmpi_spike_exchange_compressed(nin_, spfixin_ovfl_, spfixout_, spfixin_, ag_send_size_, ag_send_nspike_, localgid_size_, &ovfl_capacity_, &ovfl_);
     wt_ = nrnmpi_wtime() - wt;
     wt = nrnmpi_wtime();
     TBUF

src/nrniv/splitcell.cpp

@@ -21,8 +21,6 @@ the subtrees is no longer required by this implementation.
 #if PARANEURON
 void nrnmpi_split_clear();
 extern void (*nrnmpi_splitcell_compute_)();
-extern void nrnmpi_send_doubles(double*, int cnt, int dest, int tag);
-extern void nrnmpi_recv_doubles(double*, int cnt, int src, int tag);
 extern double nrnmpi_splitcell_wait_;
 
 static int change_cnt_;

src/nrnmpi/core/resolve.cpp

@@ -0,0 +1,25 @@
+#include <dlfcn.h>
+#include <sstream>
+#include "../nrnmpi.h"
+
+// Those functions are part of a mechanism to dynamically load mpi or not
+void mpi_manager_t::resolve_symbols(void* handle) {
+    for (auto* ptr: m_function_ptrs) {
+        assert(!(*ptr));
+        ptr->resolve(handle);
+        assert(*ptr);
+    }
+}
+
+void mpi_function_base::resolve(void* handle) {
+    dlerror();
+    void* ptr = dlsym(handle, m_name);
+    const char* error = dlerror();
+    if (error) {
+        std::ostringstream oss;
+        oss << "Could not get symbol " << m_name << " from handle " << handle << ": " << error;
+        throw std::runtime_error(oss.str());
+    }
+    assert(ptr);
+    m_fptr = ptr;
+}