Merge branch 'main' into bugfix/biagas/fix_python_testing_windows_main

.github/workflows/main.yml

@@ -0,0 +1,36 @@
+name: Basic
+
+on:
+  push:
+    branches: ["mcm86-30jul24-gh-actions-ci"]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install HDF5
+      run: |
+        wget -q https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.4/bin/unix/hdf5-1.14.4-3-ubuntu-2204_gcc.tar.gz
+        mkdir hdf5-1.14.4-3
+        tar -xf hdf5-1.14.4-3-ubuntu-2204_gcc.tar.gz
+        tar -xf hdf5/HDF5-1.14.4.3-Linux.tar.gz --strip-components=4 -C hdf5-1.14.4-3
+        rm -rf hdf5
+
+    - name: Build Silo
+      run: |
+        export PATH="$PWD/hdf5-1.14.4-3/bin:$PATH"
+        mkdir build
+        cd build
+        env LDFLAGS=-Wl,-rpath,`pwd`/../hdf5-1.14.4-3/lib FFLAGS=-fallow-argument-mismatch FCFLAGS=-fallow-argument-mismatch ../configure --with-hdf5=`pwd`/../hdf5-1.14.4-3/include,`pwd`/../hdf5-1.14.4-3/lib --enable-pythonmodule --enable-json --prefix=`pwd`/myinstall
+        make -j 8 install
+
+    - name: Check Silo
+      run: |
+        export PATH="$PWD/hdf5-1.14.4-3/bin:$PATH"
+        cd build
+        make -j 8 check

CMake/SiloFindHDF5.cmake

@@ -84,7 +84,7 @@ if(HDF5_FOUND)
 
             add_custom_command(TARGET copy_deps POST_BUILD
                  COMMAND ${CMAKE_COMMAND} -E copy_if_different
-                 ${HDF5_DLL} ${Silo_BINARY_DIR}/bin/$<CONFIG>)
+                 ${HDF5_DLL} ${Silo_BINARY_DIR}/bin/$<$<BOOL:${is_multi_config}>:$<CONFIG>>/)
         endif()
     endif()
 

CMake/SiloFindPython.cmake

@@ -58,18 +58,25 @@
 ###
 
 
-if(DEFINED SILO_PYTHON_DIR)
+if(SILO_PYTHON_DIR)
     # help CMake find the specified python
-    set(Python_ROOT ${SILO_PYTHON_DIR})
+    set(Python_ROOT_DIR ${SILO_PYTHON_DIR})
+
+    # prefer python3
+    if(EXISTS ${SILO_PYTHON_DIR}/bin/python3)
+        set(Python_EXECUTABLE ${SILO_PYTHON_DIR}/bin/python3)
+    elseif(EXISTS ${SILO_PYTHON_DIR}/bin/python)
+        set(Python_EXECUTABLE ${SILO_PYTHON_DIR}/bin/python)
+    endif()
 endif()
 
 find_package(Python COMPONENTS Interpreter Development)
 
 if(Python_FOUND)
+    # Need to ensure these vars are available by testing, so make
+    # them live in PARENT_SCOPE.
+    set(Python_EXECUTABLE ${Python_EXECUTABLE} PARENT_SCOPE)
     if(WIN32)
-        # Need to ensure these vars are available by testing, so make
-        # them live in PARENT_SCOPE.
-        set(Python_EXECUTABLE ${Python_EXECUTABLE} PARENT_SCOPE)
         if(TARGET Python::Module)
             get_target_property(PYTHON_DLL Python::Module IMPORTED_LOCATION)
             if(PYTHON_DLL)

CMake/SiloFindQt5.cmake → CMake/SiloFindQt6.cmake

@@ -53,20 +53,20 @@
 ##############################################################################
 
 ###
-# Uses find_package to find the Qt5 library
-#   If SILO_QT5_DIR is defined, uses it to tell CMake where to look.
+# Uses find_package to find the Qt6 library
+#   If SILO_QT6_DIR is defined, uses it to tell CMake where to look.
 ###
 
 
-if(DEFINED SILO_QT5_DIR AND EXISTS ${SILO_QT5_DIR})
+if(DEFINED SILO_QT6_DIR AND EXISTS ${SILO_QT6_DIR})
     # set the variable needed for CMake to find this version of Qt
-    set(Qt5_DIR ${SILO_QT5_DIR})
+    set(Qt6_DIR ${SILO_QT6_DIR})
 endif()
 
-find_package(Qt5 COMPONENTS Core Gui Widgets CONFIG)
+find_package(Qt6 COMPONENTS Core Gui Widgets CONFIG)
 
-if(NOT Qt5_FOUND)
-    message(WARNING "An explicit request for silex was made and it requires Qt, but Qt could not be found.  You may want to try setting SILO_QT5_DIR")
+if(NOT Qt6_FOUND)
+    message(WARNING "An explicit request for silex was made and it requires Qt, but Qt could not be found.  You may want to try setting SILO_QT6_DIR")
 endif()
 
 
@@ -81,24 +81,24 @@ endif()
 ##
 # Windows
 ##
-if(Qt5_FOUND AND WIN32)
+if(Qt6_FOUND AND WIN32)
     # the windeployqt target will be executed as a POST build step for SILEX
-    if(TARGET Qt5::qmake AND NOT TARGET Qt5::windeployqt)
-        get_target_property(_qt5_qmake_location Qt5::qmake IMPORTED_LOCATION)
+    if(TARGET Qt6::qmake AND NOT TARGET Qt6::windeployqt)
+        get_target_property(_qt6_qmake_location Qt6::qmake IMPORTED_LOCATION)
 
         execute_process(
-            COMMAND "${_qt5_qmake_location}" -query QT_INSTALL_PREFIX
+            COMMAND "${_qt6_qmake_location}" -query QT_INSTALL_PREFIX
             RESULT_VARIABLE return_code
-            OUTPUT_VARIABLE qt5_install_prefix
+            OUTPUT_VARIABLE qt6_install_prefix
             OUTPUT_STRIP_TRAILING_WHITESPACE
         )
 
-        set(imported_location "${qt5_install_prefix}/bin/windeployqt.exe")
+        set(imported_location "${qt6_install_prefix}/bin/windeployqt.exe")
 
         if(EXISTS ${imported_location})
-            add_executable(Qt5::windeployqt IMPORTED)
+            add_executable(Qt6::windeployqt IMPORTED)
 
-            set_target_properties(Qt5::windeployqt PROPERTIES
+            set_target_properties(Qt6::windeployqt PROPERTIES
                 IMPORTED_LOCATION ${imported_location}
             )
         endif()

CMake/SiloFindSzip.cmake

@@ -75,15 +75,16 @@ if(SZIP_FOUND)
     set(HAVE_LIBSZ 1)
     if(WIN32)
         get_target_property(SZIP_DLL szip IMPORTED_LOCATION_RELEASE )
-        if(SILO_ENABLE_SILEX OR SILEX_ENABLE_BROWSER)
+
+        if(SILO_ENABLE_SILEX OR SILO_ENABLE_BROWSER)
             install(FILES ${SZIP_DLL} DESTINATION bin
                     PERMISSIONS OWNER_READ OWNER_WRITE
                                 GROUP_READ GROUP_WRITE
                                 WORLD_READ)
 
             add_custom_command(TARGET copy_deps POST_BUILD
                  COMMAND ${CMAKE_COMMAND} -E copy_if_different
-                 ${SZIP_DLL} ${Silo_BINARY_DIR}/bin/$<CONFIG>)
+                 ${SZIP_DLL} ${Silo_BINARY_DIR}/bin/$<$<BOOL:${is_multi_config}>:$<CONFIG>>/)
         endif()
     endif()
 else()

CMake/SiloFindZlib.cmake

@@ -61,7 +61,7 @@
 
 if(DEFINED SILO_ZLIB_DIR AND EXISTS ${SILO_ZLIB_DIR}/zlib-config.cmake)
     # this works for zlib with CMake
-    find_package(ZLIB PATHS ${SILO_ZLIB_DIR} CONFIG)
+    find_package(ZLIB PATHS ${SILO_ZLIB_DIR} CONFIG NO_DEFAULT_PATH)
 else()
     if(DEFINED SILO_ZLIB_DIR AND EXISTS ${SILO_ZLIB_DIR})
         # help CMake find the specified zlib
@@ -76,15 +76,16 @@ if(ZLIB_FOUND)
     set(HAVE_ZLIB_H 1)
     if(WIN32)
         get_target_property(ZLIB_DLL zlib IMPORTED_LOCATION_RELEASE)
-        if(SILO_ENABLE_SILEX OR SILEX_ENABLE_BROWSER)
+
+        if(SILO_ENABLE_SILEX OR SILO_ENABLE_BROWSER)
             install(FILES ${ZLIB_DLL} DESTINATION bin
                     PERMISSIONS OWNER_READ OWNER_WRITE
                                 GROUP_READ GROUP_WRITE
                                 WORLD_READ)
 
             add_custom_command(TARGET copy_deps POST_BUILD
                  COMMAND ${CMAKE_COMMAND} -E copy_if_different
-                 ${ZLIB_DLL} ${Silo_BINARY_DIR}/bin/$<CONFIG>)
+                 ${ZLIB_DLL} ${Silo_BINARY_DIR}/bin/$<$<BOOL:${is_multi_config}>:$<CONFIG>>/)
         endif()
     endif()
 else()

CMakeLists.txt

@@ -297,11 +297,11 @@ check_symbol_exists(stat64 "sys/stat.h" HAVE_STAT64)
 check_symbol_exists(stat "sys/stat.h" HAVE_STAT)
 
 if (HAVE_STAT64)
-	add_definitions(-DHAVE_STAT64)
+    add_definitions(-DHAVE_STAT64)
 endif()
 
 if (HAVE_STAT)
-	add_definitions(-DHAVE_STAT)
+    add_definitions(-DHAVE_STAT)
 endif()
 
 ###-----------------------------------------------------------------------------

config-site/steppenwolf.cmake

@@ -55,9 +55,7 @@
 ###
 # config-site for STEPPENWOLF, a Windows system.
 ###
-message("steppenwolf.cmake being processed")
 
-###
 # Helpers for TP lib location
 ###
 set(TP_DIR C:/A_Visit/ForRegression/visit-deps/windowsbuild/MSVC2022)
@@ -78,9 +76,9 @@ silo_option_default(VAR SILO_HDF5_SZIP_DIR VALUE ${TP_DIR}/szip/2.1.1/cmake)
 silo_option_default(VAR SILO_ZLIB_DIR VALUE ${TP_DIR}/zlib/1.2.13/cmake)
 
 ##
-# QT5 (must be the location of Qt5Config.cmake)
+# QT6 (must be the location of Qt6Config.cmake)
 ##
-#silo_option_default(VAR SILO_QT5_DIR VALUE ${TP_DIR}/Qt/5.14.2/lib/cmake/Qt5)
+silo_option_default(VAR SILO_QT6_DIR VALUE ${TP_DIR}/Qt/6.4.2/lib/cmake/Qt6)
 
 ##
 # python
@@ -97,6 +95,5 @@ silo_option_default(VAR SILO_ENABLE_FORTRAN VALUE OFF TYPE BOOL)
 silo_option_default(VAR SILO_ENABLE_PYTHON_MODULE VALUE ON TYPE BOOL)
 
 # enable tests
-#silo_option_default(VAR SILO_ENABLE_TESTS VALUE ON TYPE BOOL)
-
+silo_option_default(VAR SILO_ENABLE_TESTS VALUE ON TYPE BOOL)
 

docs/requirements.txt

@@ -17,13 +17,13 @@ docutils==0.17.1
     #   myst-parser
     #   sphinx
     #   sphinx-rtd-theme
-idna==3.4
+idna==3.7
     # via requests
 imagesize==1.4.1
     # via sphinx
 importlib-metadata==6.8.0
     # via sphinx
-jinja2==3.1.2
+jinja2==3.1.4
     # via
     #   myst-parser
     #   sphinx
@@ -47,7 +47,7 @@ pytz==2023.3.post1
     # via babel
 pyyaml==6.0.1
     # via myst-parser
-requests==2.31.0
+requests==2.32.2
     # via sphinx
 snowballstemmer==2.2.0
     # via sphinx
@@ -70,7 +70,7 @@ sphinxcontrib-qthelp==1.0.3
     # via sphinx
 sphinxcontrib-serializinghtml==1.1.5
     # via sphinx
-urllib3==2.0.7
+urllib3==2.2.2
     # via requests
-zipp==3.17.0
+zipp==3.19.1
     # via importlib-metadata

src/hdf5_drv/H5FDsilo.c

@@ -1647,42 +1647,42 @@ H5FD_silo_close(H5FD_t *_file)
         hsize_t tot_raw_count, tot_raw_bytes, tot_md_count, tot_md_bytes;
         FILE* logf = fopen(file->log_name, "w");
         fprintf(logf, "======== Interactions between the VFD and the filesystem ========\n");
-        fprintf(logf, "block size = %llu\n", file->block_size);
+        fprintf(logf, "block size = %llu\n", (long long unsigned) file->block_size);
         fprintf(logf, "block count = %d\n", file->max_blocks);
         fprintf(logf, "\n");
-        fprintf(logf, "max block id = %llu\n", file->stats.max_block_id);
-        fprintf(logf, "max blocks in mem = %llu\n", file->stats.max_blocks_in_mem);
+        fprintf(logf, "max block id = %llu\n", (long long unsigned) file->stats.max_block_id);
+        fprintf(logf, "max blocks in mem = %llu\n", (long long unsigned) file->stats.max_blocks_in_mem);
         fprintf(logf, "\n");
-        fprintf(logf, "total seeks = %llu\n", file->stats.total_seeks);
+        fprintf(logf, "total seeks = %llu\n", (long long unsigned) file->stats.total_seeks);
         fprintf(logf, "\n");
-        fprintf(logf, "number of multi-block writes = %llu\n", file->stats.num_multiblock_writes);
-        fprintf(logf, "number of multi-block reads = %llu\n", file->stats.num_multiblock_reads);
+        fprintf(logf, "number of multi-block writes = %llu\n", (long long unsigned) file->stats.num_multiblock_writes);
+        fprintf(logf, "number of multi-block reads = %llu\n", (long long unsigned) file->stats.num_multiblock_reads);
         fprintf(logf, "\n");
-        fprintf(logf, "number of blocks majority md = %llu\n", file->stats.num_blocks_majority_md);
-        fprintf(logf, "number of blocks majority raw = %llu\n", file->stats.num_blocks_majority_raw);
+        fprintf(logf, "number of blocks majority md = %llu\n", (long long unsigned) file->stats.num_blocks_majority_md);
+        fprintf(logf, "number of blocks majority raw = %llu\n", (long long unsigned) file->stats.num_blocks_majority_raw);
         fprintf(logf, "\n");
-        fprintf(logf, "number of writes = %llu\n", file->stats.total_write_count);
-        fprintf(logf, "number of bytes written = %llu\n", file->stats.total_write_bytes);
+        fprintf(logf, "number of writes = %llu\n", (long long unsigned) file->stats.total_write_count);
+        fprintf(logf, "number of bytes written = %llu\n", (long long unsigned) file->stats.total_write_bytes);
         fprintf(logf, "\n");
-        fprintf(logf, "number of times a raw block was written = %llu\n", file->stats.total_block_raw_writes);
-        fprintf(logf, "number of times a raw block was written more than once = %llu\n", file->stats.total_block_raw_re_writes);
+        fprintf(logf, "number of times a raw block was written = %llu\n", (long long unsigned) file->stats.total_block_raw_writes);
+        fprintf(logf, "number of times a raw block was written more than once = %llu\n", (long long unsigned) file->stats.total_block_raw_re_writes);
         fprintf(logf, "\n");
-        fprintf(logf, "number of times an md block was written = %llu\n", file->stats.total_block_md_writes);
-        fprintf(logf, "number of times an md block was written more than once = %llu\n", file->stats.total_block_md_re_writes);
+        fprintf(logf, "number of times an md block was written = %llu\n", (long long unsigned) file->stats.total_block_md_writes);
+        fprintf(logf, "number of times an md block was written more than once = %llu\n", (long long unsigned) file->stats.total_block_md_re_writes);
         fprintf(logf, "\n");
-        fprintf(logf, "number of reads = %llu\n", file->stats.total_read_count);
-        fprintf(logf, "number of bytes read = %llu\n", file->stats.total_read_bytes);
+        fprintf(logf, "number of reads = %llu\n", (long long unsigned) file->stats.total_read_count);
+        fprintf(logf, "number of bytes read = %llu\n", (long long unsigned) file->stats.total_read_bytes);
         fprintf(logf, "\n");
-        fprintf(logf, "number of times a block was read = %llu\n", file->stats.total_block_reads);
-        fprintf(logf, "number of times a block was read more than once = %llu\n", file->stats.total_block_re_reads);
+        fprintf(logf, "number of times a block was read = %llu\n", (long long unsigned) file->stats.total_block_reads);
+        fprintf(logf, "number of times a block was read more than once = %llu\n", (long long unsigned) file->stats.total_block_re_reads);
         fprintf(logf, "\n");
         fprintf(logf, "number of hot blocks %d\n", file->stats.num_hot_blocks);
         fprintf(logf, "hot blocks...\n");
         for (i = 0; i < file->stats.num_hot_blocks; i++)
         {
             silo_vfd_hot_block_stats_t *hb = &(file->stats.hot_block_list[i]); 
             fprintf(logf,"    %8llu: %4s (%f), #writes=%8llu, #reads=%8llu\n",
-                hb->id, (hb->raw_frac>0.5?"raw":"meta"), hb->raw_frac, hb->num_block_writes+1, hb->num_block_reads+1);
+                (long long unsigned) hb->id, (hb->raw_frac>0.5?"raw":"meta"), hb->raw_frac, (long long unsigned) hb->num_block_writes+1, (long long unsigned) hb->num_block_reads+1);
         }
         if (file->stats.hot_block_list) free(file->stats.hot_block_list);
         if (file->was_written_map.bitmap) free(file->was_written_map.bitmap);
@@ -1691,10 +1691,10 @@ H5FD_silo_close(H5FD_t *_file)
         fprintf(logf, "\n");
         fprintf(logf, "\n");
         fprintf(logf, "======== Interactions between HDF5 library and the VFD ========\n");
-        fprintf(logf, "number raw writes = %llu\n", file->stats.total_vfd_raw_write_count);
-        fprintf(logf, "number raw bytes written = %llu\n", file->stats.total_vfd_raw_write_bytes);
-        fprintf(logf, "number md writes = %llu\n", file->stats.total_vfd_md_write_count);
-        fprintf(logf, "number md bytes written = %llu\n", file->stats.total_vfd_md_write_bytes);
+        fprintf(logf, "number raw writes = %llu\n", (long long unsigned) file->stats.total_vfd_raw_write_count);
+        fprintf(logf, "number raw bytes written = %llu\n", (long long unsigned) file->stats.total_vfd_raw_write_bytes);
+        fprintf(logf, "number md writes = %llu\n", (long long unsigned) file->stats.total_vfd_md_write_count);
+        fprintf(logf, "number md bytes written = %llu\n", (long long unsigned) file->stats.total_vfd_md_write_bytes);
         fprintf(logf, "histogram...\n");
         cum_raw_count = 0;
         cum_raw_bytes = 0;
@@ -1730,16 +1730,16 @@ H5FD_silo_close(H5FD_t *_file)
 
             fprintf(logf,"%2d: %8llu (%3d%%, %3d%%) %8llu (%3d%%, %3d%%) | "
                               "%8llu (%3d%%, %3d%%) %8llu (%3d%%, %3d%%)\n", i,
-                file->stats.vfd_raw_write_count_hist[i],
+                (long long unsigned) file->stats.vfd_raw_write_count_hist[i],
                 (int) (100.0 * file->stats.vfd_raw_write_count_hist[i] / tot_raw_count),
                 (int) (100.0 * cum_raw_count / tot_raw_count),
-                file->stats.vfd_raw_write_bytes_hist[i],
+                (long long unsigned) file->stats.vfd_raw_write_bytes_hist[i],
                 (int) (100.0 * file->stats.vfd_raw_write_bytes_hist[i] / tot_raw_bytes),
                 (int) (100.0 * cum_raw_bytes / tot_raw_bytes),
-                file->stats.vfd_md_write_count_hist[i],
+                (long long unsigned) file->stats.vfd_md_write_count_hist[i],
                 (int) (100.0 * file->stats.vfd_md_write_count_hist[i] / tot_md_count),
                 (int) (100.0 * cum_md_count / tot_md_count),
-                file->stats.vfd_md_write_bytes_hist[i],
+                (long long unsigned) file->stats.vfd_md_write_bytes_hist[i],
                 (int) (100.0 * file->stats.vfd_md_write_bytes_hist[i] / tot_md_bytes),
                 (int) (100.0 * cum_md_bytes / tot_md_bytes));
         }
@@ -1777,16 +1777,16 @@ H5FD_silo_close(H5FD_t *_file)
 
             fprintf(logf,"%2d: %8llu (%3d%%, %3d%%) %8llu (%3d%%, %3d%%) | "
                               "%8llu (%3d%%, %3d%%) %8llu (%3d%%, %3d%%)\n", i,
-                file->stats.vfd_raw_read_count_hist[i],
+                (long long unsigned) file->stats.vfd_raw_read_count_hist[i],
                 (int) (100.0 * file->stats.vfd_raw_read_count_hist[i] / tot_raw_count),
                 (int) (100.0 * cum_raw_count / tot_raw_count),
-                file->stats.vfd_raw_read_bytes_hist[i],
+                (long long unsigned) file->stats.vfd_raw_read_bytes_hist[i],
                 (int) (100.0 * file->stats.vfd_raw_read_bytes_hist[i] / tot_raw_bytes),
                 (int) (100.0 * cum_raw_bytes / tot_raw_bytes),
-                file->stats.vfd_md_read_count_hist[i],
+                (long long unsigned) file->stats.vfd_md_read_count_hist[i],
                 (int) (100.0 * file->stats.vfd_md_read_count_hist[i] / tot_md_count),
                 (int) (100.0 * cum_md_count / tot_md_count),
-                file->stats.vfd_md_read_bytes_hist[i],
+                (long long unsigned) file->stats.vfd_md_read_bytes_hist[i],
                 (int) (100.0 * file->stats.vfd_md_read_bytes_hist[i] / tot_md_bytes),
                 (int) (100.0 * cum_md_bytes / tot_md_bytes));
         }