Performance improvements

.github/workflows/build_and_test.yml

@@ -1145,8 +1145,9 @@ jobs:
           # Source Intel OneAPI environment
           source /opt/intel/oneapi/setvars.sh
 
-          # Modify PATH to use our binaries
+          # Modify PATH and LD_LIBRARY_PATH to use our binaries
           export PATH="../bin:$PATH"
+          export LD_LIBRARY_PATH="../bin:${LD_LIBRARY_PATH:-}"
 
           # Run the test script and capture output
           set +e  # Don't exit on error
@@ -1169,8 +1170,9 @@ jobs:
           # Source Intel OneAPI environment
           source /opt/intel/oneapi/setvars.sh
 
-          # Modify PATH to use our binaries
+          # Modify PATH and LD_LIBRARY_PATH to use our binaries
           export PATH="../bin:$PATH"
+          export LD_LIBRARY_PATH="../bin:${LD_LIBRARY_PATH:-}"
 
           # Run the test script and capture output
           set +e  # Don't exit on error

dynadjust/CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.15)
-project(dynadjust VERSION 1.3.0)
+project(dynadjust VERSION 1.4.1)
 
 option(USE_MKL "Use Intel MKL (Linux and Windows)" OFF)
 option(BUILD_TESTING "Enable testing" OFF)
@@ -59,17 +59,23 @@ if(BUILD_TESTING)
     set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 endif()
 
-# Set output directories for all platforms to use ../bin/
-set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
-set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
-set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
+# Set output directories for all platforms to use ../bin/ (unless overridden)
+if(NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY)
+    set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
+endif()
+if(NOT CMAKE_LIBRARY_OUTPUT_DIRECTORY)
+    set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
+endif()
+if(NOT CMAKE_ARCHIVE_OUTPUT_DIRECTORY)
+    set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
+endif()
 
 # For multi-config generators (Visual Studio, Xcode)
 foreach(OUTPUTCONFIG ${CMAKE_CONFIGURATION_TYPES})
     string(TOUPPER ${OUTPUTCONFIG} OUTPUTCONFIG_UPPER)
-    set(CMAKE_RUNTIME_OUTPUT_DIRECTORY_${OUTPUTCONFIG_UPPER} ${CMAKE_SOURCE_DIR}/../bin)
-    set(CMAKE_LIBRARY_OUTPUT_DIRECTORY_${OUTPUTCONFIG_UPPER} ${CMAKE_SOURCE_DIR}/../bin)
-    set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY_${OUTPUTCONFIG_UPPER} ${CMAKE_SOURCE_DIR}/../bin)
+    set(CMAKE_RUNTIME_OUTPUT_DIRECTORY_${OUTPUTCONFIG_UPPER} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
+    set(CMAKE_LIBRARY_OUTPUT_DIRECTORY_${OUTPUTCONFIG_UPPER} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
+    set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY_${OUTPUTCONFIG_UPPER} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
 endforeach()
 
 if (BUILD_STATIC)
@@ -189,7 +195,7 @@ else()
 endif()
 message(STATUS "Found XercesC (${XercesC_INCLUDE_DIRS} ${XercesC_LIBRARIES})")
 
-# Static builds need ICU for Xerces transcoding (glibc iconv can't dlopen gconv modules in static binaries)
+# Static builds need ICU for Xerces transcoding (glibc iconv can't dlopen gconv modules in static binaries).
 if(BUILD_STATIC AND UNIX AND NOT APPLE)
     find_package(ICU COMPONENTS uc data)
     if(ICU_FOUND)
@@ -300,10 +306,13 @@ message(STATUS "Found Boost version: ${Boost_VERSION}")
 # Set up libraries
 # ----------------------------------------------------------------------------
 
+find_package(Threads REQUIRED)
+
 set(DNA_LIBRARIES
     ${Boost_LIBRARIES}
     ${XercesC_LIBRARIES}
     ${XERCES_ICU_LIBRARIES}
+    Threads::Threads
 )
 
 # ----------------------------------------------------------------------------
@@ -608,6 +617,23 @@ if(BUILD_STATIC)
             endif()
         endforeach()
 
+        # For MKL builds, add static MKL libraries (MKL::MKL is an imported
+        # target that the generic .a finder above cannot resolve)
+        if(USE_MKL AND MKL_FOUND AND DEFINED ENV{MKLROOT})
+            set(MKL_LIB_DIR "$ENV{MKLROOT}/lib")
+            if(ILP64)
+                set(MKL_INTERFACE_LIB "${MKL_LIB_DIR}/libmkl_intel_ilp64.a")
+            else()
+                set(MKL_INTERFACE_LIB "${MKL_LIB_DIR}/libmkl_intel_lp64.a")
+            endif()
+            list(APPEND STATIC_LIBS_LIST
+                "-Wl,--start-group"
+                "${MKL_INTERFACE_LIB}"
+                "${MKL_LIB_DIR}/libmkl_sequential.a"
+                "${MKL_LIB_DIR}/libmkl_core.a"
+                "-Wl,--end-group")
+        endif()
+
         message("")
         message(STATUS "STATIC_LIBS_LIST=${STATIC_LIBS_LIST}")
 
@@ -916,6 +942,13 @@ if (BUILD_TESTING)
     target_link_libraries(test_snx_file_writer PRIVATE ${DNA_LIBRARIES})
     target_compile_definitions(test_snx_file_writer PRIVATE __BINARY_NAME__="test_snx_file_writer" __BINARY_DESC__="Unit tests for SNX file writer")
 
+    # Test: test_format_elapsed_time
+    add_executable(test_format_elapsed_time
+        ${UNIT_TEST_DIR}/test_format_elapsed_time.cpp
+    )
+    target_include_directories(test_format_elapsed_time PRIVATE ${UNIT_TEST_DIR} ${CMAKE_SOURCE_DIR}/include)
+    target_compile_definitions(test_format_elapsed_time PRIVATE __BINARY_NAME__="test_format_elapsed_time" __BINARY_DESC__="Unit tests for FormatElapsedTime helper")
+
     # Register unit tests with CTest
     add_test(NAME unit-MatrixTest COMMAND $<TARGET_FILE:test_matrix>)
     add_test(NAME unit-MsrToStnSortTest COMMAND $<TARGET_FILE:test_msr_to_stn_sort>)
@@ -931,6 +964,7 @@ if (BUILD_TESTING)
     add_test(NAME unit-AslFileLoaderTest COMMAND $<TARGET_FILE:test_asl_file_loader>)
     add_test(NAME unit-BmsFileLoaderTest COMMAND $<TARGET_FILE:test_bms_file_loader>)
     add_test(NAME unit-SnxFileWriterTest COMMAND $<TARGET_FILE:test_snx_file_writer>)
+    add_test(NAME unit-FormatElapsedTimeTest COMMAND $<TARGET_FILE:test_format_elapsed_time>)
 
     # ........................................................................
     # Functional tests
@@ -974,7 +1008,10 @@ if (BUILD_TESTING)
     add_test (NAME import-urban-network COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -n urban urban-network.stn urban-network.msr --flag-unused-stations)
     add_test (NAME geoid-urban-network COMMAND $<TARGET_FILE:${DNAGEOID_TARGET}> urban -g urban-network-geoid.gsb --export-dna-geo)
     add_test (NAME segment-urban-network COMMAND $<TARGET_FILE:${DNASEGMENT_TARGET}> urban --min 50 --max 150 --test-integrity)
-    add_test (NAME adjust-urban-network-verbose COMMAND $<TARGET_FILE:${DNAADJUST_TARGET}> urban --verbose 3)
+    add_test (NAME import-urban-network-verbose COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -n urban_verbose urban-network.stn urban-network.msr --flag-unused-stations)
+    add_test (NAME geoid-urban-network-verbose COMMAND $<TARGET_FILE:${DNAGEOID_TARGET}> urban_verbose -g urban-network-geoid.gsb --export-dna-geo)
+    add_test (NAME segment-urban-network-verbose COMMAND $<TARGET_FILE:${DNASEGMENT_TARGET}> urban_verbose --min 50 --max 150 --test-integrity)
+    add_test (NAME adjust-urban-network-verbose COMMAND $<TARGET_FILE:${DNAADJUST_TARGET}> urban_verbose --verbose 3)
     add_test (NAME adjust-urban-network COMMAND $<TARGET_FILE:${DNAADJUST_TARGET}> urban --output-adj-msr --phased --stn-corrections --export-sinex-file --export-xml-stn-file --export-dna-stn-file --output-pos-uncertainty --export-dna-msr --export-xml-msr)
     add_test (NAME plot-urban-network-01 COMMAND $<TARGET_FILE:${DNAPLOT_TARGET}> urban --phased --label-sta --correction-arrows --label-corr --compute-corrections --scale-arrows 10.5 --error-ellipse --positional-uncertainty --scale-ellipse-c 10.5)
     add_test (NAME plot-urban-network-02 COMMAND $<TARGET_FILE:${DNAPLOT_TARGET}> urban --phased --label-sta --label-constraints --correction-arrows --label-corr --compute-corrections --scale-arrows 10.5 --error-ellipse --positional-uncertainty --scale-ellipse-c 10.5 --block-number 2 --alternate-name)
@@ -1098,14 +1135,36 @@ if (BUILD_TESTING)
     add_test (NAME test-urban-phased-network COMMAND $<TARGET_FILE:${DNADIFF_TARGET}> urban.phased.adj urban.phased.adj.expected --skip-to-marker "M Station 1" -t 0.001)
     add_test (NAME test-urban-thread-network COMMAND $<TARGET_FILE:${DNADIFF_TARGET}> urban_mt.phased-mt.adj urban_mt.phased-mt.adj.expected --skip-to-marker "M Station 1" -t 0.01 -v)
 
-    # 8. Source tag preservation in --export-xml (issue #317)
+    # Source tag preservation in --export-xml (issue #317)
     # Import XML data with <Source> tags and verify they are preserved in export
     add_test (NAME import-source-test COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -n srctest source-test-stn.xml source-test-msr.xml --export-xml -r GDA2020)
     add_test (NAME check-source-import COMMAND bash check_source_tags.sh srctestmsr.xml CAMPAIGN_2023A CAMPAIGN_2023B EMPTY)
     # Transform to a different frame and verify <Source> tags survive reftran
     add_test (NAME reftran-source-test COMMAND $<TARGET_FILE:${DNAREFTRAN_TARGET}> srctest -r itrf2014 -e 01.01.2020 --export-xml)
     add_test (NAME check-source-reftran COMMAND bash check_source_tags.sh srctest.ITRF2014.01.01.2020msr.xml CAMPAIGN_2023A CAMPAIGN_2023B EMPTY)
 
+    # 8a. XML import with and without xsi:noNamespaceSchemaLocation (issue #346)
+    # Verify dnaimport handles XML files regardless of whether the schema location
+    # attribute is present. Strip the attribute and import each sample data pair.
+
+    # gnss-network: with schema location (original files)
+    add_test (NAME import-xml-gnss-with-xsd COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -n xsd_gnss gnss-networkstn.xml gnss-networkmsr.xml -r GDA2020)
+    # gnss-network: without schema location
+    add_test (NAME import-xml-gnss-strip COMMAND bash strip_schema_location.sh gnss-networkstn.xml gnss-networkstn-noxsd.xml)
+    add_test (NAME import-xml-gnss-strip-msr COMMAND bash strip_schema_location.sh gnss-networkmsr.xml gnss-networkmsr-noxsd.xml)
+    add_test (NAME import-xml-gnss-without-xsd COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -n xsd_gnss gnss-networkstn-noxsd.xml gnss-networkmsr-noxsd.xml -r GDA2020)
+    set_tests_properties(import-xml-gnss-strip import-xml-gnss-strip-msr PROPERTIES FIXTURES_SETUP gnss_strip)
+    set_tests_properties(import-xml-gnss-without-xsd PROPERTIES FIXTURES_REQUIRED gnss_strip)
+
+    # urban-network: with schema location
+    add_test (NAME import-xml-urban-with-xsd COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -n xsd_urban urban-networkstn.xml urban-networkmsr.xml -r GDA2020)
+    # urban-network: without schema location
+    add_test (NAME import-xml-urban-strip COMMAND bash strip_schema_location.sh urban-networkstn.xml urban-networkstn-noxsd.xml)
+    add_test (NAME import-xml-urban-strip-msr COMMAND bash strip_schema_location.sh urban-networkmsr.xml urban-networkmsr-noxsd.xml)
+    add_test (NAME import-xml-urban-without-xsd COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -n xsd_urban urban-networkstn-noxsd.xml urban-networkmsr-noxsd.xml -r GDA2020)
+    set_tests_properties(import-xml-urban-strip import-xml-urban-strip-msr PROPERTIES FIXTURES_SETUP urban_strip)
+    set_tests_properties(import-xml-urban-without-xsd PROPERTIES FIXTURES_REQUIRED urban_strip)
+
     # 9. gnss reference frame transformations
     add_test (NAME ref-gnss01-network COMMAND $<TARGET_FILE:${DNAREFTRAN_TARGET}> gnss -r itrf2014 -e 01.01.2020)
     add_test (NAME ref-gnss02-network COMMAND $<TARGET_FILE:${DNAREFTRAN_TARGET}> gnss -r itrf1988 -e 03.12.1995)
@@ -1744,16 +1803,8 @@ if (BUILD_TESTING)
     add_test (NAME import-no-frame COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -n sample -r itrf1975 dsg.stn dsg.msr)
     # no stations and measurements (generated above)
     add_test (NAME import-no-data COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -n null ./null.stn ./null.msr)
-    # no DynaML.xsd - remove file in platform-independent manner (using CMake command) by setting up a test dependency
-    add_test (NAME import-no-xsd-file-remove COMMAND ${CMAKE_COMMAND} -E remove DynaML.xsd)
-    add_test (NAME import-no-xsd-file COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -n gnss gnss-networkstn.xml gnss-networkmsr.xml)
-    set_tests_properties(import-no-xsd-file PROPERTIES DEPENDS import-no-xsd-file-remove TIMEOUT 5)
-    # Restore DynaML.xsd after testing its absence
-    add_test (NAME import-no-xsd-file-restore COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/../sampleData/DynaML.xsd DynaML.xsd)
-    set_tests_properties(import-no-xsd-file-restore PROPERTIES DEPENDS import-no-xsd-file)
     # no geoid file
     add_test (NAME import-no-geoid COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -n geoid --geo-file ./nofile.geo)
-    set_tests_properties(import-no-geoid PROPERTIES DEPENDS import-no-xsd-file-restore)
     # no project file
     add_test (NAME import-no-project COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -p ./nofile.dnaproj)
     # measurement stns not in station file
@@ -1765,7 +1816,7 @@ if (BUILD_TESTING)
     add_test (NAME import-misc-network-size COMMAND $<TARGET_FILE:${DNAIMPORT_TARGET}> -n contig --import-contiguous-stn-msr 5000 --export-dna)
 
     set_tests_properties(import-no-option import-invalid-option import-invalid-file import-nearby import-no-files import-no-frame
-        import-no-data import-no-xsd-file import-no-geoid import-no-project import-no-stns import-no-help
+        import-no-data import-no-geoid import-no-project import-no-stns import-no-help
         import-misc-block-size import-misc-network-size import-misc-07
         PROPERTIES WILL_FAIL TRUE)
 
@@ -1942,6 +1993,9 @@ if (BUILD_TESTING)
     set_tests_properties(
         import-urban-network geoid-urban-network segment-urban-network adjust-urban-network
         PROPERTIES RUN_SERIAL TRUE)
+    set_tests_properties(
+        import-urban-network-verbose geoid-urban-network-verbose segment-urban-network-verbose adjust-urban-network-verbose
+        PROPERTIES RUN_SERIAL TRUE)
     set_tests_properties(
         import-urban-network-thread reftran-urban-network-thread geoid-urban-network-thread segment-urban-network-thread adjust-urban-network-thread-01
         PROPERTIES RUN_SERIAL TRUE)
@@ -1986,7 +2040,7 @@ if (BUILD_TESTING)
         unit-AmlFileLoaderTest unit-BmsFileTest unit-NetworkDataLoaderTest
         unit-MeasurementProcessorTest unit-DynAdjustPrinterTest unit-GNSSNstatSortTest
         unit-BstFileLoaderTest unit-AslFileLoaderTest unit-BmsFileLoaderTest
-        unit-SnxFileWriterTest
+        unit-SnxFileWriterTest unit-FormatElapsedTimeTest
     )
     set_tests_properties(${UNIT_TESTS} PROPERTIES
         RUN_SERIAL FALSE
@@ -2007,4 +2061,3 @@ endif ()
 
 message ("")
 message ("")
-

dynadjust/cmake/StaticBuildOptimizations.cmake

@@ -6,20 +6,59 @@ function(optimize_static_target TARGET_NAME)
     if(CMAKE_BUILD_TYPE STREQUAL "Release" OR CMAKE_BUILD_TYPE STREQUAL "RelWithDebInfo")
         set_property(TARGET ${TARGET_NAME} PROPERTY INTERPROCEDURAL_OPTIMIZATION TRUE)
     endif()
-    
+
     # Platform-specific optimizations
     if(UNIX AND NOT APPLE)
-        # Linux-specific optimizations
         target_link_options(${TARGET_NAME} PRIVATE
-            -static
-            -Wl,--gc-sections      # Remove unused sections
-            -Wl,--as-needed         # Only link libraries that are actually used
-            -Wl,-O2                 # Optimize at link time
-            -Wl,--strip-all         # Strip all symbols
+            -static-libgcc
+            -static-libstdc++
+            -Wl,--as-needed
+            -Wl,-O2
+            -Wl,--strip-all
+            # glibc 2.34+ merged libpthread into libc; libpthread.a is an
+            # empty stub. libstdc++.a references ALL pthread functions via
+            # weak aliases (__gthrw_), and glibc defines them as WEAK (W)
+            # in libc.a. LLD will not pull a weak-defined archive member to
+            # satisfy a weak-undefined reference, leaving every pthread
+            # symbol at address 0 and crashing at runtime.
+            # Fix: add a strong undefined reference (-u) for each symbol.
+            # This forces LLD to pull in each object from libc.a, making
+            # the weak-defined symbol available for the weak refs to bind to.
+            -Wl,-u,pthread_once
+            -Wl,-u,pthread_getspecific
+            -Wl,-u,pthread_setspecific
+            -Wl,-u,pthread_create
+            -Wl,-u,pthread_join
+            -Wl,-u,pthread_equal
+            -Wl,-u,pthread_self
+            -Wl,-u,pthread_detach
+            -Wl,-u,pthread_cancel
+            -Wl,-u,pthread_mutex_lock
+            -Wl,-u,pthread_mutex_trylock
+            -Wl,-u,pthread_mutex_unlock
+            -Wl,-u,pthread_mutex_init
+            -Wl,-u,pthread_mutex_destroy
+            -Wl,-u,pthread_cond_init
+            -Wl,-u,pthread_cond_broadcast
+            -Wl,-u,pthread_cond_signal
+            -Wl,-u,pthread_cond_wait
+            -Wl,-u,pthread_cond_timedwait
+            -Wl,-u,pthread_cond_destroy
+            -Wl,-u,pthread_key_create
+            -Wl,-u,pthread_key_delete
+            -Wl,-u,pthread_mutexattr_init
+            -Wl,-u,pthread_mutexattr_settype
+            -Wl,-u,pthread_mutexattr_destroy
+            -Wl,-u,pthread_attr_init
+            -Wl,-u,pthread_attr_destroy
+            -Wl,-u,pthread_attr_setdetachstate
+            -Wl,-u,pthread_exit
+            -Wl,-u,__pthread_key_create
         )
+        target_link_libraries(${TARGET_NAME} PRIVATE pthread m dl)
         target_compile_options(${TARGET_NAME} PRIVATE
-            -ffunction-sections     # Put each function in its own section
-            -fdata-sections         # Put each data item in its own section
+            -ffunction-sections
+            -fdata-sections
         )
     elseif(APPLE)
         # macOS-specific optimizations

dynadjust/dynadjust.rc

@@ -25,8 +25,8 @@ LANGUAGE LANG_ENGLISH, SUBLANG_ENGLISH_US
 //
 
 VS_VERSION_INFO VERSIONINFO
- FILEVERSION 1,3,0,0
- PRODUCTVERSION 1,3,0,0
+ FILEVERSION 1,4,1,0
+ PRODUCTVERSION 1,4,1,0
  FILEFLAGSMASK 0x3fL
 #ifdef _DEBUG
  FILEFLAGS 0x1L
@@ -42,12 +42,12 @@ BEGIN
         BLOCK "040904b0"
         BEGIN
             VALUE "FileDescription", "DynAdjust is a rigorous, high performance least squares adjustment application."
-            VALUE "FileVersion", "1.3.0.0"
+            VALUE "FileVersion", "1.4.1.0"
             VALUE "InternalName", "DynAdjust"
             VALUE "LegalCopyright", "Copyright 2025 Geoscience Australia"
             VALUE "OriginalFilename", "DynAdjust"
             VALUE "ProductName", "DynAdjust"
-            VALUE "ProductVersion", "1.3.0.0"
+            VALUE "ProductVersion", "1.4.1.0"
         END
     END
     BLOCK "VarFileInfo"