Merge pull request #31 from virtualcell/nonchombo-build

Nonchombo build

Author: jcschaff

.github/workflows/cd.yml

@@ -2,7 +2,6 @@
 /build-dockcross-win64/
 /.project
 /.cproject
-/svnversion.txt
 /build-win64/
 /.DS_Store
 /build-linux64/
@@ -14,6 +13,7 @@
 /singularity/
 /cmake-build*
 /build*
+/debug-build*
 /.idea/
 /nfsim/
 /all_solvers/*

.gitignore

@@ -4,7 +4,17 @@
 #
 ##############################################
 if (APPLE)
-	set(CMAKE_OSX_ARCHITECTURES "x86_64")
+	execute_process(COMMAND uname -m OUTPUT_VARIABLE PROCESSOR_ARCHITECTURE OUTPUT_STRIP_TRAILING_WHITESPACE)
+	message("Processor Architecture: ${PROCESSOR_ARCHITECTURE}")
+	if (PROCESSOR_ARCHITECTURE STREQUAL "arm64")
+		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__arm64__")
+		set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__arm64__")
+		set(CMAKE_OSX_ARCHITECTURES "arm64")
+	else()
+		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__x86_64__")
+		set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__x86_64__")
+		set(CMAKE_OSX_ARCHITECTURES "x86_64")
+	endif()
 #	set(CMAKE_Fortran_OSX_DEPLOYMENT_TARGET_FLAG "-mmacosx-version-min=10.7" CACHE PATH "")
 #	set(CMAKE_OSX_DEPLOYMENT_TARGET "10.7" CACHE PATH "")
 #############################################
@@ -31,7 +41,7 @@ elseif (LINUX)
 		set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64")
 		set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m64")
 		set (CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -m64")
-	endif()	
+	endif()
 endif()
 
 cmake_minimum_required(VERSION 3.13)
@@ -45,10 +55,6 @@ if(POLICY CMP0057)
   cmake_policy(SET CMP0057 NEW)
 endif()
 
-set(SVERSION "unversionedbuild")
-message("svnversion ${SVERSION}")
-add_definitions(-DSVNVERSION=svn${SVERSION})
-
 #include (LocalJNI.cmake)
 
 set(RULE_MESSAGES OFF)
@@ -152,10 +158,8 @@ endif()
 set(WINDOWS FALSE)
 if (${CMAKE_SYSTEM_NAME} MATCHES Windows)
 	set(WINDOWS TRUE)
-#	set(WIN32 TRUE)
-	if (${CMAKE_GENERATOR} MATCHES "Unix Makefiles") 
-		set(MINGW TRUE)
-	endif (${CMAKE_GENERATOR} MATCHES "Unix Makefiles") 
+	set(WIN32 TRUE)
+	set(MINGW TRUE)
 endif()
 
 set (ARCH_64bit FALSE)
@@ -240,6 +244,9 @@ if (${OPTION_TARGET_MOVINGBOUNDARY_SOLVER} OR
 		add_subdirectory(hdf5-1.8.11)
 	else()
 		set(HDF5_USE_STATIC_LIBRARIES ON)
+		if(WINDOWS OR WIN32 OR WIN64)
+			set(HDF5_USE_STATIC_LIBRARIES OFF)
+		endif ()
 		#CMakeList.txt that comes with hdf5 switches library name if compiled with debug
 		find_package(HDF5 COMPONENTS HL CXX C)
 		set(HDF_VERSION ${HDF5_VERSION})

CMakeLists.txt

@@ -1,5 +1,5 @@
 #ifndef DIVIDEBYZEROEXCEPTION_H
-#define DIVIDEBYZEROEXCEPTION_CPP
+#define DIVIDEBYZEROEXCEPTION_H
 
 #include "ExpressionException.h"
 

ExpressionParser/DivideByZeroException.h

@@ -38,6 +38,17 @@ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
 #include <front/fdecs.h>
 
+#ifdef WIN64
+double drand48_windows()
+{
+	const long NUM_RAND = RAND_MAX+1;
+	const double RAND_TOTAL_MAX = NUM_RAND*NUM_RAND - 1.0;
+	long r = (NUM_RAND)*rand()+rand();
+	return r / RAND_TOTAL_MAX;
+}
+#define drand48 drand48_windows
+#endif
+
 LOCAL	boolean    track_comp_and_repair3d(int*,int*,int*,INTERFACE*,Front*);
 LOCAL	boolean	repair_intfc3d_in_box(INTERFACE*,int*,int*,Front*);
 LOCAL	boolean 	set_reconstruction_boxes(int*,int*,int**,int,RECT_BOX**,

FronTierLib/front/fgb3d.c

@@ -703,6 +703,7 @@ IMPORT	void	strip_bdry_curves(INTERFACE*, int);
 IMPORT	void	cut_surface(SURFACE*,boolean (*func)(POINTER,double*),POINTER,boolean);
 IMPORT	void	install_hsbdry_on_surface(SURFACE*,int);
 IMPORT	boolean	surfaces_matched(SURFACE*,SURFACE*);
+IMPORT  void    install_subdomain_bdry_curves(INTERFACE*);
 
 	/* fscat3d2.c*/
 IMPORT	boolean	f_intfc_communication3d2(Front*);
@@ -888,6 +889,7 @@ IMPORT	void	tangent(POINT*,BOND*,CURVE*,double*,Front*);
 IMPORT	void	user_print_rp_node(RP_NODE*,RPROBLEM*);
 IMPORT	void	user_print_rproblem(RPROBLEM*);
 IMPORT	void	user_free_rp_node(RP_NODE*,RPROBLEM*);
+IMPORT  void    assign_curve_boundary_type(CURVE*,int,int*);
 
 #if defined(USE_OVERTURE)
         /* foverture_patch.c */

FronTierLib/front/fprotos.h

@@ -39,6 +39,7 @@ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
 #include <intfc/int.h>
 #include <intfc/iprotos.h>
+#include <fprotos.h>
 
 LOCAL   void 	assign_blk_crx(BLK_CRX*,int,int,int,const EG_CRX*,boolean);
 LOCAL	void 	assign_two_comp_domain(double (*func)(POINTER,double*),POINTER,

FronTierLib/intfc/imksurf.c

@@ -64,6 +64,9 @@ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 #include <sys/stat.h>
 #ifndef WIN32
 #include <sys/utsname.h>
+#else
+#include <process.h>
+#define getpid _getpid
 #endif
 	static const char *scan_float_fmt = "%lf";
 

FronTierLib/util/simpleio.c

@@ -436,7 +436,7 @@ void VCellCVodeSolver::cvodeSolve(bool bPrintProgress, FILE* outputFile, void (*
 					if (outputCount * (NEQ + 1) * bytesPerSample > MaxFileSizeBytes){ 
 						/* if more than one gigabyte, then fail */ 
 						char msg[100];
-						sprintf(msg, "output exceeded maximum %ld bytes", MaxFileSizeBytes);
+						sprintf(msg, "output exceeded maximum %d bytes", MaxFileSizeBytes);
 						throw VCell::Exception(msg);
 					}
 					writeData(Time, outputFile);

IDAWin/VCellCVodeSolver.cpp

@@ -9,6 +9,11 @@ if (SUPPORTS_MATLAB)
 	option(BUILD_INCLUDE_MATLAB_DIRS "Include matlab integration directory" OFF)
 endif (SUPPORTS_MATLAB)
 
+if (MINGW)
+	add_definitions(-DMINGW)
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DMINGW")
+endif (MINGW)
+
 if(DEFINED CMAKE_BUILD_TYPE)
    SET(CMAKE_BUILD_TYPE ${CMAKE_BUILD_TYPE} CACHE STRING "Choose the type of build, options are: None(CMAKE_CXX_FLAGS or CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel.")
 else()