mingw/windows buildrtability fixes (#209)

* Use CMAKE_SHARED_LIBRARY_SUFFIX instead of .so (required for windows/mingw)
* Fix for exe suffix and make sure to have dlls in bin directory
* adjust runtime output only for coreneuron directory
* define mingw definition

Author: pramodk

CMakeLists.txt

@@ -13,10 +13,10 @@ project(coreneuron)
 set(VERSION_MAJOR "0")
 set(VERSION_MINOR "16")
 set(VERSION_PATCH "0")
-set(VERSION_STRING "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}")
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
+set(VERSION_STRING "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}")
 
 # =============================================================================
 # Settings to enable project as submodule
@@ -144,6 +144,9 @@ if(CORENRN_ENABLE_REPORTINGLIB)
   add_definitions("-DENABLE_REPORTING")
 endif()
 
+if(MINGW)
+  add_definitions("-DMINGW")
+endif()
 
 # =============================================================================
 # NMODL specific options
@@ -153,8 +156,8 @@ if(CORENRN_ENABLE_NMODL)
   include_directories(${nmodl_INCLUDE})
 
   # copy to make nrnivmodl-core work from build as well instal directory
-  configure_file(${nmodl_BINARY} ${CMAKE_BINARY_DIR}/bin/nmodl COPYONLY)
-  set(CORENRN_NMODL_BINARY ${CMAKE_BINARY_DIR}/bin/nmodl)
+  set(CORENRN_NMODL_BINARY ${CMAKE_BINARY_DIR}/bin/nmodl${CMAKE_EXECUTABLE_SUFFIX})
+  configure_file(${nmodl_BINARY} ${CORENRN_NMODL_BINARY} COPYONLY)
 
   # path to python interface
   set(ENV{PYTHONPATH} "${nmodl_PYTHONPATH}:$ENV{PYTHONPATH}")
@@ -165,7 +168,7 @@ if(CORENRN_ENABLE_NMODL)
 else()
   # use mod2c if nmodl not enabled
   include(AddMod2cSubmodule)
-  set(CORENRN_NMODL_BINARY ${CMAKE_BINARY_DIR}/bin/mod2c_core)
+  set(CORENRN_NMODL_BINARY ${CMAKE_BINARY_DIR}/bin/mod2c_core${CMAKE_EXECUTABLE_SUFFIX})
 endif()
 
 

coreneuron/CMakeLists.txt

@@ -10,6 +10,9 @@ include_directories(utils/randoms
                     ${CMAKE_CURRENT_BINARY_DIR}
                     ${CORENEURON_PROJECT_SOURCE_DIR})
 
+# put libraries (e.g. dll) in bin directory
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+
 # =============================================================================
 # gather various source files
 # =============================================================================

coreneuron/nrniv/memory.h

@@ -64,7 +64,11 @@ inline void free_memory(void* pointer) {
 #include <stdlib.h>
 
 inline void alloc_memory(void*& pointer, size_t num_bytes, size_t alignment) {
+#if defined(MINGW)
+    nrn_assert( (pointer = _aligned_malloc(num_bytes, alignment)) != nullptr);
+#else
     nrn_assert(posix_memalign(&pointer, alignment, num_bytes) == 0);
+#endif
 }
 
 inline void calloc_memory(void*& pointer, size_t num_bytes, size_t alignment) {

coreneuron/nrniv/nrn_stats.cpp

@@ -211,7 +211,9 @@ void report_cell_stats(void) {
         nrnmpi_barrier();
     }
 #endif
-    if (nrnmpi_myid == 0)
+    if (nrnmpi_myid == 0) {
         printf("\n\n");
+        fflush(stdout);
+    }
 }
 }  // namespace coreneuron

coreneuron/nrnoc/nrntimeout.cpp

@@ -40,7 +40,7 @@ setitimer will conflict with profiler. In that case,
 user can disable setitimer which is just safety for
 deadlock situations */
 namespace coreneuron {
-#ifdef DISABLE_TIMEOUT
+#if ( defined(DISABLE_TIMEOUT) || defined(MINGW) )
 
 void nrn_timeout(int seconds) {
 }

coreneuron/utils/file_utils.cpp

@@ -32,6 +32,10 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include <sys/stat.h>
 #include <errno.h>
 
+#if defined(MINGW)
+    #define mkdir(dir_name, permission) _mkdir(dir_name)
+#endif
+
 /* adapted from : gist@jonathonreinhart/mkdir_p.c */
 int mkdir_p(const char* path) {
     const int path_len = strlen(path);
@@ -50,6 +54,7 @@ int mkdir_p(const char* path) {
         if (*p == '/') {
             /* temporarily truncate to sub-dir */
             *p = '\0';
+
             if (mkdir(dirpath, S_IRWXU) != 0) {
                 if (errno != EEXIST)
                     return -1;

coreneuron/utils/memory_utils.cpp

@@ -74,6 +74,8 @@ double nrn_mallinfo(void) {
         KERN_SUCCESS)
         return (size_t)0L; /* Can't access? */
     return info.resident_size / (1024.0 * 1024.0);
+#elif defined(MINGW)
+    mbs = -1;
 #else
     std::ifstream file;
     file.open("/proc/self/statm");
@@ -87,8 +89,6 @@ double nrn_mallinfo(void) {
         struct mallinfo m;
         m = mallinfo();
         mbs = (m.hblkhd + m.uordblks) / (1024.0 * 1024.0);
-#else
-        mbs = -1;
 #endif
     }
 #endif

external/mod2c

@@ -118,7 +118,7 @@ $(coremech_lib): $(mod_func_o) $(dimplic_o) $(mod_c_objs) $(mod_ispc_objs) build
 	@printf " => $(C_GREEN)LINKING$(C_RESET) library $(coremech_lib) Mod files: $(mod_files)\n"
 	$(CXX_LINK_SHARED) -I $(incdir) -DADDITIONAL_MECHS $(datadir)/enginemech.cpp -o ${coremech_lib} ${_SONAME} \
 	  $(mod_func_o) $(dimplic_o) $(mod_c_objs) $(mod_ispc_objs) $(libdir)/libscopmath.a $(CORENRNLIB_FLAGS) -Wl,-rpath,$(libdir) $(LDFLAGS)
-	(rm -f $(OUTPUT)/.libs/libcorenrnmech.so ; mkdir -p $(OUTPUT)/.libs ; ln -s ../../${coremech_lib} $(OUTPUT)/.libs/libcorenrnmech.so)
+	(rm -f $(OUTPUT)/.libs/libcorenrnmech@CMAKE_SHARED_LIBRARY_SUFFIX@ ; mkdir -p $(OUTPUT)/.libs ; ln -s ../../${coremech_lib} $(OUTPUT)/.libs/libcorenrnmech@CMAKE_SHARED_LIBRARY_SUFFIX@)
 
 
 # Generic build cpp->.o Need PIC for shared lib