Backport OpenBLAS and CMake changes to 1.2.7

daleroberts · daleroberts · commit a3ca7e895325 · 2025-11-21T13:52:50.000+11:00
diff --git a/dynadjust/CMakeLists.txt b/dynadjust/CMakeLists.txt
diff --git a/dynadjust/FindXercesC.cmake b/dynadjust/FindXercesC.cmake
@@ -21,8 +21,14 @@ SET (PKG_MGR_PATH_INCLUDE /usr/include)
 
 # SET THE ROOT DIRECTORY WHERE XERCES-C++ IS INSTALLED
 IF (CMAKE_SYSTEM_NAME MATCHES "Darwin")
-  # Apple
-  SET (XERCESC_ROOT_DIR /usr/local/Cellar/xerces-c/3.2.2)
+  # Apple - try homebrew locations first
+  IF (EXISTS /opt/homebrew/opt/xerces-c)
+    SET (XERCESC_ROOT_DIR /opt/homebrew/opt/xerces-c)
+  ELSEIF (EXISTS /usr/local/opt/xerces-c)
+    SET (XERCESC_ROOT_DIR /usr/local/opt/xerces-c)
+  ELSE()
+    SET (XERCESC_ROOT_DIR /usr/local/Cellar/xerces-c/3.2.2)
+  ENDIF()
   SET (XERCESC_LIBRARY_DIR ${XERCESC_ROOT_DIR}/lib)
   SET (XERCESC_INCLUDE_DIR ${XERCESC_ROOT_DIR}/include)
 
@@ -75,4 +81,9 @@ IF (EXISTS ${XERCESC_INCLUDE_DIR})
   ENDIF ()
 ENDIF ()
 
+# Set CMake-style variables for compatibility
+SET(XercesC_INCLUDE_DIRS ${XERCESC_INCLUDE_DIR})
+SET(XercesC_LIBRARIES ${XERCESC_LIBRARY})
+SET(XercesC_FOUND ${XERCESC_FOUND})
+
 mark_as_advanced(XERCESC_LIBRARY)
diff --git a/dynadjust/cmake/StaticBuildOptimizations.cmake b/dynadjust/cmake/StaticBuildOptimizations.cmake
@@ -0,0 +1,2 @@
+# Static build optimisations for DynAdjust
+# This file is included when BUILD_STATIC is ON
diff --git a/dynadjust/dynadjust/dnaadjust/CMakeLists.txt b/dynadjust/dynadjust/dnaadjust/CMakeLists.txt
@@ -1,7 +1,7 @@
 # <dnaadjust/...> build rules
 project (dnaadjust)
 
-add_definitions(-DBUILD_DNAADJUST_DLL -DBUILD_EXPORTDNATYPES -DMULTI_THREAD_ADJUST -DMKL_ILP64 -fopenmp)
+add_definitions(-DBUILD_DNAADJUST_DLL -DBUILD_EXPORTDNATYPES -DMULTI_THREAD_ADJUST -DMKL_ILP64)
 
 include_directories (${PROJECT_SOURCE_DIR})
 
diff --git a/dynadjust/dynadjust/dnaadjust/dnaadjust.cpp b/dynadjust/dynadjust/dnaadjust/dnaadjust.cpp
@@ -208,9 +208,9 @@ void dna_adjust::InitialiseAdjustment()
 	
 	// Confidence interval
 	double conf(projectSettings_.a.confidence_interval * 0.01);
-	normal dist(0.0, 1.0);
+	boost::math::normal normal_dist(0.0, 1.0);
 	conf += (1.0 - conf) / 2.0;
-	criticalValue_ = quantile(dist, conf);
+	criticalValue_ = boost::math::quantile(normal_dist, conf);
 
 	potentialOutlierCount_ = 0;
 
diff --git a/dynadjust/dynadjust/dnaadjust/dnaadjust.hpp b/dynadjust/dynadjust/dnaadjust/dnaadjust.hpp
@@ -29,7 +29,8 @@
 	#endif
 #endif
 
-#include <mkl.h>
+// MKL/BLAS/LAPACK is included via dnamatrix_contiguous.hpp
+// #include <mkl.h>
 
 #include <exception>
 #include <stdexcept>
diff --git a/dynadjust/dynadjust/dnaadjust/precompile.h b/dynadjust/dynadjust/dnaadjust/precompile.h
@@ -11,7 +11,8 @@
 
 // Support MKL inverse oly if compiler is Intel
 #if defined(__ICC) || defined(__INTEL_COMPILER)		// Intel compiler
-#include <mkl.h>
+// MKL/BLAS/LAPACK is included via dnamatrix_contiguous.hpp
+// #include <mkl.h>
 #endif
 
 #include <include/config/dnaexports.hpp>
diff --git a/dynadjust/dynadjust/dnaadjustwrapper/CMakeLists.txt b/dynadjust/dynadjust/dnaadjustwrapper/CMakeLists.txt
@@ -4,7 +4,7 @@ project (dnaadjustwrapper)
 # build dnaadjust library first
 add_subdirectory (${CMAKE_SOURCE_DIR}/dynadjust/dnaadjust ${CMAKE_BINARY_DIR}/dynadjust/dnaadjust)
 
-add_definitions (-DBUILD_ADJUST_EXE -DMULTI_THREAD_ADJUST -DMKL_ILP64 -fopenmp)
+add_definitions (-DBUILD_ADJUST_EXE -DMULTI_THREAD_ADJUST -DMKL_ILP64)
 
 include_directories (${PROJECT_SOURCE_DIR})
 
diff --git a/dynadjust/dynadjust/dnaadjustwrapper/dnaadjustwrapper.cpp b/dynadjust/dynadjust/dnaadjustwrapper/dnaadjustwrapper.cpp
@@ -1164,8 +1164,8 @@ int main(int argc, char* argv[])
 						cout << "   " << leafStr<string>(p.a.bst_file) << "  last modified on  " << ctime(&t_bst);
 						cout << "   " << leafStr<string>(p.a.bms_file) << "  last modified on  " << ctime(&t_bms) << endl;
 						cout << "   " << leafStr<string>(p.a.seg_file) << "  created on  " << ctime(&t_seg) << endl;
-						cout << "  Run 'segment " << p.g.network_name << " [options]' to re-create the segmentation file, or re-run" << endl << 
-							"  adjust using the --" << SEG_FILE << " option if the file " << basename(p.a.seg_file) << " must\n  be used." << endl << endl;
+						cout << "  Run 'segment " << p.g.network_name << " [options]' to re-create the segmentation file, or re-run" << endl <<
+							"  adjust using the --" << SEG_FILE << " option if the file " << path(p.a.seg_file).filename().string() << " must\n  be used." << endl << endl;
 						cout_mutex.unlock();
 						return EXIT_FAILURE;
 					}
diff --git a/dynadjust/dynadjust/dnaimport/CMakeLists.txt b/dynadjust/dynadjust/dnaimport/CMakeLists.txt
@@ -1,7 +1,7 @@
 # <dnaimport/...> build rules
 project (dnaimport)
 
-add_definitions(-DBUILD_DNAIMPORT_DLL -DBUILD_EXPORTDNATYPES -DMKL_ILP64 -fopenmp)
+add_definitions(-DBUILD_DNAIMPORT_DLL -DBUILD_EXPORTDNATYPES -DMKL_ILP64)
 
 include_directories (${PROJECT_SOURCE_DIR})
 
diff --git a/dynadjust/dynadjust/dnaimport/dnainterop.hpp b/dynadjust/dynadjust/dnaimport/dnainterop.hpp
@@ -29,7 +29,8 @@
 #endif
 #endif
 
-#include <mkl.h>
+// MKL/BLAS/LAPACK is included via dnamatrix_contiguous.hpp
+// #include <mkl.h>
 
 #include <exception>
 #include <system_error>
diff --git a/dynadjust/dynadjust/dnaplot/CMakeLists.txt b/dynadjust/dynadjust/dnaplot/CMakeLists.txt
@@ -1,7 +1,7 @@
 # <dnaplot/...> build rules
 project (dnaplot)
 
-add_definitions(-DBUILD_DNAPLOT_DLL -DBUILD_EXPORTDNATYPES -DMKL_ILP64 -fopenmp)
+add_definitions(-DBUILD_DNAPLOT_DLL -DBUILD_EXPORTDNATYPES -DMKL_ILP64)
 
 include_directories (${PROJECT_SOURCE_DIR})
 
diff --git a/dynadjust/dynadjust/dnaplotwrapper/CMakeLists.txt b/dynadjust/dynadjust/dnaplotwrapper/CMakeLists.txt
@@ -4,7 +4,7 @@ project (dnaplotwrapper)
 # build dnaplot library first
 add_subdirectory (${CMAKE_SOURCE_DIR}/dynadjust/dnaplot ${CMAKE_BINARY_DIR}/dynadjust/dnaplot)
 
-add_definitions (-DBUILD_PLOT_EXE -DMKL_ILP64 -fopenmp)
+add_definitions (-DBUILD_PLOT_EXE -DMKL_ILP64)
 
 include_directories (${PROJECT_SOURCE_DIR})
 
diff --git a/dynadjust/dynadjust/dnareftran/CMakeLists.txt b/dynadjust/dynadjust/dnareftran/CMakeLists.txt
@@ -1,7 +1,7 @@
 # <dnareftran/...> build rules
 project (dnareftran)
 
-add_definitions(-DBUILD_DNAREFTRAN_DLL -DBUILD_EXPORTDNATYPES -DMKL_ILP64 -fopenmp)
+add_definitions(-DBUILD_DNAREFTRAN_DLL -DBUILD_EXPORTDNATYPES -DMKL_ILP64)
 
 include_directories (${PROJECT_SOURCE_DIR})
 
diff --git a/dynadjust/dynadjust/dynadjust/dynadjust.cpp b/dynadjust/dynadjust/dynadjust/dynadjust.cpp
@@ -17,6 +17,7 @@
 #include <boost/program_options/parsers.hpp>
 #include <boost/program_options/variables_map.hpp>
 #include <boost/filesystem.hpp>
+#include <libgen.h>
 #include <boost/algorithm/string/predicate.hpp>
 
 using namespace std;
@@ -208,7 +209,7 @@ int main(int argc, char* argv[])
 
 	if (vm.count(PROJECT_FILE) && vm.count(NETWORK_NAME))
 	{
-		if (equals(basename(p.g.project_file), p.g.network_name))
+		if (equals(path(p.g.project_file).stem().string(), p.g.network_name))
 		{
 			cout << endl << "- Error: project file name doesn't match network name.  Provide" << endl;  
 			cout << endl << "         either a project file path or the network name. " << endl << endl;  
diff --git a/dynadjust/include/config/dnaoptions-interface.hpp b/dynadjust/include/config/dnaoptions-interface.hpp
@@ -291,7 +291,7 @@ const char* const NTV2_SUB_NAME = "sub-grid-name";
 const char* const NTV2_CREATED = "creation-date";
 const char* const NTV2_UPDATED = "update-date";
 
-const char* const MAP_FILE = "map-file";
+const char* const MAP_FILE_OPT = "map-file";
 const char* const ASL_FILE = "asl-file";
 const char* const AML_FILE = "aml-file";
 const char* const DST_FILE = "dst-file";
diff --git a/dynadjust/include/config/dnaprojectfile.cpp b/dynadjust/include/config/dnaprojectfile.cpp
@@ -769,7 +769,7 @@ void CDnaProjectFile::LoadSettingImport(const settingMode mSetting, const string
   			break;
 		}
 	}
-	else if (iequals(var, MAP_FILE))
+	else if (iequals(var, MAP_FILE_OPT))
 	{
 		if (val.empty())
 			return;
diff --git a/dynadjust/include/functions/dnafilepathfuncs.hpp b/dynadjust/include/functions/dnafilepathfuncs.hpp
@@ -63,7 +63,7 @@ T formPath(const T& folder, const T file)
 template <typename T>
 T leafStr(const T& filePath)
 {
-	return path(filePath).leaf().string();
+	return path(filePath).filename().string();
 }
 
 #endif //DNAFILEPATHFUNCS_H_
diff --git a/dynadjust/include/functions/dnaprocessfuncs.cpp b/dynadjust/include/functions/dnaprocessfuncs.cpp
@@ -22,9 +22,7 @@
 
 #include <include/functions/dnaprocessfuncs.hpp>
 
-#include <boost/process.hpp>
-
-using namespace boost::process;
+#include <cstdlib>
 
 bool run_command(const string& executable_path, const UINT16& quiet)
 {	
@@ -60,15 +58,18 @@ bool run_command(const string& executable_path, const UINT16& quiet)
 	}
 	return EXIT_SUCCESS;
 
-#elif defined(__linux) || defined(sun) || defined(__unix__) || defined(__APPLE__)		
+#elif defined(__linux) || defined(sun) || defined(__unix__) || defined(__APPLE__)
 
 	int return_value(0);
-		
-	if (quiet)
-		return_value = boost::process::system(executable_path, boost::process::std_out > boost::process::null);
-	else
-		return_value = boost::process::system(executable_path, boost::process::std_out > stdout);
-		
+
+	if (quiet) {
+		// Redirect stdout and stderr to /dev/null
+		std::string cmd = executable_path + " > /dev/null 2>&1";
+		return_value = std::system(cmd.c_str());
+	} else {
+		return_value = std::system(executable_path.c_str());
+	}
+
 	return (return_value == EXIT_SUCCESS);
 
 #endif
diff --git a/dynadjust/include/math/dnamatrix_contiguous.cpp b/dynadjust/include/math/dnamatrix_contiguous.cpp
diff --git a/dynadjust/include/math/dnamatrix_contiguous.hpp b/dynadjust/include/math/dnamatrix_contiguous.hpp
diff --git a/dynadjust/include/measurement_types/dnageometries.hpp b/dynadjust/include/measurement_types/dnageometries.hpp
diff --git a/dynadjust/include/thread/dnathreading.hpp b/dynadjust/include/thread/dnathreading.hpp

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+# Static build optimisations for DynAdjust`
	`2`	`+# This file is included when BUILD_STATIC is ON`