Merge pull request #31 from virtualcell/nonchombo-build

Nonchombo build
virtualcell · May 25, 2024 · 8b020bb · 8b020bb
2 parents 603ace6 + bb4fe00
commit 8b020bb
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diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml
diff --git a/.gitignore b/.gitignore
@@ -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/*

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -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})

diff --git a/ExpressionParser/DivideByZeroException.h b/ExpressionParser/DivideByZeroException.h
@@ -1,5 +1,5 @@
 #ifndef DIVIDEBYZEROEXCEPTION_H
-#define DIVIDEBYZEROEXCEPTION_CPP
+#define DIVIDEBYZEROEXCEPTION_H
 
 #include "ExpressionException.h"
 

diff --git a/FronTierLib/front/fgb3d.c b/FronTierLib/front/fgb3d.c
@@ -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**,

diff --git a/FronTierLib/front/fprotos.h b/FronTierLib/front/fprotos.h
@@ -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 */

diff --git a/FronTierLib/intfc/imksurf.c b/FronTierLib/intfc/imksurf.c
@@ -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,

diff --git a/FronTierLib/util/simpleio.c b/FronTierLib/util/simpleio.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";
 

diff --git a/IDAWin/VCellCVodeSolver.cpp b/IDAWin/VCellCVodeSolver.cpp
@@ -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);

diff --git a/MBSolver/CMakeLists.txt b/MBSolver/CMakeLists.txt
@@ -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()

diff --git a/MBSolver/Solver/include/CoordVect.h b/MBSolver/Solver/include/CoordVect.h
@@ -2,6 +2,7 @@
 #define _COORDVECT_H_
 
 #include <array>
+#include <ostream>
 #include <MovingBoundaryTypes.h>
 #include <IndexVect.h>
 namespace moving_boundary

diff --git a/MBSolver/Solver/include/Distance.h b/MBSolver/Solver/include/Distance.h
@@ -1,5 +1,6 @@
 #ifndef Distance_h
 #define Distance_h
+#include <limits>
 #include <cmath>
 #include <TPoint.h>
 #include <cassert>

diff --git a/MBSolver/Solver/include/IndexVect.h b/MBSolver/Solver/include/IndexVect.h
@@ -2,6 +2,8 @@
 #define _INDEXVECT_H_
 
 #include <array>
+#include <ostream>
+#include <cstddef>
 #include <MovingBoundaryTypes.h>
 
 class IndexVect
@@ -13,7 +15,7 @@ class IndexVect
   IndexVect ();
   IndexVect (int a, int b);
   IndexVect (const IndexVect& rhs);
-  IndexVect(std::array<size_t, DIM> p);
+  explicit IndexVect(std::array<std::size_t, DIM> p);
 
   IndexVect& operator= (const IndexVect& rhs);
 

diff --git a/MBSolver/Solver/include/MBridge/MBPatch.h b/MBSolver/Solver/include/MBridge/MBPatch.h
@@ -1,5 +1,6 @@
 #ifndef MBPatch_h
 #define MBPatch_h
+#include <limits>
 #include <vector>
 #include <iostream>
 #include <MBridge/MBMatlabGenerator.h>

diff --git a/MBSolver/Solver/include/MPoint.h b/MBSolver/Solver/include/MPoint.h
@@ -1,6 +1,7 @@
 #ifndef MPoint_h
 #define MPoint_h
 #pragma warning ( disable : 4996)
+#include <limits>
 #include <cassert>
 #include <array>
 #include <stdexcept>

diff --git a/MBSolver/Solver/include/Modulo.h b/MBSolver/Solver/include/Modulo.h
@@ -1,6 +1,8 @@
 #ifndef Modulo_h
 #define Modulo_h
 
+#include <limits>
+
 namespace vcell_util {
 	/**
 	* modulo integer type

diff --git a/MBSolver/Solver/include/World.h b/MBSolver/Solver/include/World.h
@@ -1,6 +1,7 @@
 #ifndef World_h
 #define World_h
 #include <MovingBoundaryTypes.h>
+#include <limits>
 #include <TPoint.h>
 #include <Universe.h>
 #include <SVector.h>

diff --git a/MBSolver/Solver/include/version.h b/MBSolver/Solver/include/version.h
diff --git a/MBSolver/Solver/src/CoordVect.cpp b/MBSolver/Solver/src/CoordVect.cpp
@@ -2,6 +2,7 @@
 #include <IndexVect.h>
 #include <math.h>
 #include <istream>
+#include <limits>
 #include <World.h>
 #include <MeshElementNode.h>
 #include <MovingBoundaryTypes.h>

diff --git a/MBSolver/Solver/src/IndexVect.cpp b/MBSolver/Solver/src/IndexVect.cpp
@@ -26,7 +26,7 @@ IndexVect::IndexVect (const IndexVect &iv)
 	}
 }
 
-IndexVect::IndexVect(std::array<size_t, 2> p)
+IndexVect::IndexVect(std::array<std::size_t, 2> p)
 {
 	for (int i = 0; i < DIM; ++ i)
 	{

diff --git a/MBSolver/Solver/src/MapTable.cpp b/MBSolver/Solver/src/MapTable.cpp
@@ -1,3 +1,4 @@
+#include <stdexcept>
 #include <algorithm>
 #include <MapTable.h>
 #include <MTExpression.h>
@@ -7,7 +8,7 @@ using VCell::MTExpression;
 double MapTable::operator[](std::string name) const {
 	auto iter = values.find(name);
 	if (iter == values.end( )) {
-		throw new std::domain_error("no such name"); 
+		throw std::domain_error("no such name");
 	}
 	return iter->second;
 }

diff --git a/MBSolver/Solver/src/Mesh.cpp b/MBSolver/Solver/src/Mesh.cpp
@@ -1,5 +1,6 @@
 #include <cstdint>
 #include <stdexcept>
+#include <limits>
 #pragma warning ( disable: 4018 )
 #include <Mesh.h>
 #include <VCellException.h>

diff --git a/MBSolver/Solver/src/MeshElementNode.cpp b/MBSolver/Solver/src/MeshElementNode.cpp
@@ -1,5 +1,6 @@
 #include <MPoint.h>
 #include <sstream>
+#include <limits>
 #include <cstring>
 #include <exception>
 #include <algorithm>

diff --git a/MBSolver/Solver/src/MovingBoundaryParabolicProblem.cpp b/MBSolver/Solver/src/MovingBoundaryParabolicProblem.cpp
@@ -1,10 +1,12 @@
 //#pragma warning ( disable: 4996 )
 #pragma warning ( disable: 4244 )
 #pragma warning ( disable: 4267 )
+#include <VCELL/SimulationMessaging.h>
 #include <MPoint.h>
 #include <boost/logic/tribool.hpp>
 #include <World.h>
 #include <VoronoiMesh.h>
+#include <limits>
 #include <cstring>
 #include <sstream>
 #include <iomanip>
@@ -28,7 +30,6 @@
 #include <IndexVect.h>
 
 #include <ExplicitSolver.h>
-#include <VCELL/SimulationMessaging.h>
 #include <MBridge/FronTierAdapt.h>
 #include <MBridge/Figure.h>
 #include <MBridge/MBPatch.h>

diff --git a/MBSolver/Solver/src/Polygon.cpp b/MBSolver/Solver/src/Polygon.cpp
@@ -1,3 +1,4 @@
+#include <limits>
 #include <cstdint>
 #include <Volume.h>
 #include <Edge.h>
@@ -16,7 +17,8 @@ namespace {
 	template <typename V>
 	struct vectorWriter {
 		std::ostream &os;
-		vectorWriter(std::ostream &os_) 
+
+		explicit vectorWriter(std::ostream &os_)
 			:os(os_) {}
 		void operator( )(V v) {
 			vcell_persist::save(os,v);

diff --git a/MBSolver/Solver/src/ReportClient.cpp b/MBSolver/Solver/src/ReportClient.cpp
@@ -2,6 +2,7 @@
 #include <map>
 #include <set>
 #include <iomanip>
+#include <limits>
 #include <algo.h>
 #include <Mesh.h>
 #include <MeshElementNode.h>
@@ -13,7 +14,6 @@
 #include <ReportClient.h>
 #include <Universe.h>
 #include <TextReportClient.h>
-#include <version.h>
 #include <flex.h>
 #include <vhdf5/dataset.h>
 #include <vhdf5/attribute.h>
@@ -27,6 +27,7 @@
 #include <MBridge/Figure.h>
 #include <Hdf5OutputWriter.h>
 #include <VCELL/SimulationMessaging.h>
+#include <VCELL/GitDescribe.h>
 #pragma GCC diagnostic ignored "-Winvalid-offsetof"
 using moving_boundary::World ;
 using moving_boundary::CoordinateType;
@@ -804,11 +805,8 @@ namespace {
 				H5::DataSet runTime = vcellH5::primitiveWrite(baseGroup,"runTime",totalTime);
 				//annotate version info - we place on runTime node to allow easy exclusion when doing
 				//h5diff (see --exclude-path)
-				const vcell_util::Version & version = vcell_util::Version::get( );
-				vcellH5::writeAttribute(runTime,"svnVersion",version.svn);
-				vcellH5::writeAttribute(runTime,"compileDate",version.compileDate);
-				vcellH5::writeAttribute(runTime,"compileTime",version.compileTime);
-
+                std::string gitVersion(g_GIT_DESCRIBE);
+				vcellH5::writeAttribute(runTime,"gitVersion", gitVersion);
 				unsigned int lastTimeIndex = static_cast<unsigned int>(genTimes.size( ));
 				vcellH5::primitiveWrite(baseGroup,"lastTimeIndex",lastTimeIndex);
 

diff --git a/MBSolver/Solver/src/Voronoi32.cpp b/MBSolver/Solver/src/Voronoi32.cpp
@@ -4,6 +4,7 @@
 #include <vector>
 #include <algorithm>
 #include <fstream>
+#include <limits>
 #include "Voronoi.h"
 #include "SVector.h"
 #include "algo.h"

diff --git a/MBSolver/Solver/src/World.cpp b/MBSolver/Solver/src/World.cpp
@@ -2,6 +2,7 @@
 #include <Logger.h>
 #include <NumericConvert.h>
 #include <map>
+#include <limits>
 #include <list>
 #include <iomanip>
 #include <boost/math/common_factor.hpp>
@@ -224,7 +225,7 @@ namespace moving_boundary {
 	template struct WorldMax<int16_t>;
 	template struct WorldMax<int32_t>;
 	template struct WorldMax<long long>;
-
+
 	#ifdef COMPILE_64
 	template struct World<int64_t,2>;
 	template struct WorldMax<int64_t>;