update to silo 4.12.0 and hdf5 2.0.0

.github/workflows/build_conduit_gcc.yml

@@ -153,6 +153,11 @@ jobs:
       run: |
         echo "**** Building Conduit"
         cmake --build build -j2
+    - name: Run Conduit Unit Tests
+      run: |
+        echo "**** Conduit Unit Tests"
+        export CTEST_OUTPUT_ON_FAILURE=1
+        ctest --test-dir build
     - name: Install Conduit
       run: |
         echo "**** Installing Conduit"

CHANGELOG.md

@@ -19,6 +19,12 @@ and this project aspires to adhere to [Semantic Versioning](https://semver.org/s
 - Sped up `conduit::blueprint::mesh::topology::unstructured::to_polygonal()` algorithm and added support for mixed element types.
 - Improved support for "mixed" element types in  `conduit::blueprint::mesh::utils::ShapeType` and also removed a string member to speed up construction.
 
+### Changed
+
+#### Relay
+- Updates to use Silo 4.12 and HDF5 2.0.0.
+- Reworked HDF5 handle managment to avoid resource leaks with exceptions.
+
 ## [0.9.5] - Released 2025-09-10
 
 ### Added

scripts/build_conduit/2025_12_08_h5zzfp-hdf5-cmake-fix.patch

@@ -0,0 +1,32 @@
+From e3caf7354f1cfb4bd56073cd9d145bb4fff32f1b Mon Sep 17 00:00:00 2001
+From: Cyrus Harrison <[email protected]>
+Date: Mon, 8 Dec 2025 15:26:12 -0800
+Subject: [PATCH] hdf5 cmake logic fix
+
+---
+ cmake/HDFMacros.cmake | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/cmake/HDFMacros.cmake b/cmake/HDFMacros.cmake
+index 5aaacd3..bfe1932 100644
+--- a/cmake/HDFMacros.cmake
++++ b/cmake/HDFMacros.cmake
+@@ -97,7 +97,7 @@ macro (HDF5_SUPPORT)
+         else ()
+           add_definitions (-DH5_BUILT_AS_STATIC_LIB)
+         endif ()
+-        if (FORTRAN_INTERFACE AND ${HDF5_BUILD_FORTRAN})
++        if (FORTRAN_INTERFACE)
+           if (HDF5_shared_Fortran_FOUND)
+             set (HDF5_FORTRAN_INCLUDE_DIRS ${HDF5_INCLUDE_DIR_FORTRAN})
+             set (HDF5_FORTRAN_LIBRARIES ${HDF5_FORTRAN_SHARED_LIBRARY})
+@@ -125,7 +125,7 @@ macro (HDF5_SUPPORT)
+         else ()
+           set (HDF5_FOUND 0)
+         endif ()
+-        if (FORTRAN_INTERFACE AND ${HDF5_BUILD_FORTRAN})
++        if (FORTRAN_INTERFACE)
+           if (HDF5_shared_Fortran_FOUND)
+             set (HDF5_FORTRAN_INCLUDE_DIRS ${HDF5_INCLUDE_DIR_FORTRAN})
+             set (HDF5_FORTRAN_LIBRARIES ${HDF5_FORTRAN_SHARED_LIBRARY})
+-- 

scripts/build_conduit/build_conduit.sh

@@ -196,10 +196,9 @@ fi # build_zlib
 ################
 # HDF5
 ################
-# release 1-2 GAH!
-hdf5_version=1.14.1-2
-hdf5_middle_version=1.14.1
-hdf5_short_version=1.14
+hdf5_version=2.0.0
+hdf5_middle_version=2_0_0
+hdf5_short_version=2_0
 hdf5_src_dir=$(ospath ${source_dir}/hdf5-${hdf5_version})
 hdf5_build_dir=$(ospath ${build_dir}/hdf5-${hdf5_version}/)
 hdf5_install_dir=$(ospath ${install_dir}/hdf5-${hdf5_version}/)
@@ -210,13 +209,14 @@ if [ ! -d ${hdf5_install_dir} ]; then
 if ${build_hdf5}; then
 if [ ! -d ${hdf5_src_dir} ]; then
   echo "**** Downloading ${hdf5_tarball}"
-  curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${hdf5_short_version}/hdf5-${hdf5_middle_version}/src/hdf5-${hdf5_version}.tar.gz -o ${hdf5_tarball}
+  curl -L https://support.hdfgroup.org/releases/hdf5/v${hdf5_short_version}/v${hdf5_middle_version}/downloads/hdf5-${hdf5_version}.tar.gz -o ${hdf5_tarball}
   tar ${tar_extra_args} -xzf ${hdf5_tarball} -C ${source_dir}
 fi
 
+
 #################
 #
-# hdf5 1.14.x CMake recipe for using zlib
+# hdf5 CMake recipe for using zlib
 #
 # -DHDF5_ENABLE_Z_LIB_SUPPORT=ON
 # Add zlib install dir to CMAKE_PREFIX_PATH
@@ -227,7 +227,7 @@ echo "**** Configuring HDF5 ${hdf5_version}"
 cmake -S ${hdf5_src_dir} -B ${hdf5_build_dir} ${cmake_compiler_settings} \
   -DCMAKE_VERBOSE_MAKEFILE:BOOL=${enable_verbose} \
   -DCMAKE_BUILD_TYPE=${build_config} \
-  -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
+  -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=ON \
   -DCMAKE_PREFIX_PATH=${zlib_install_dir} \
   -DCMAKE_INSTALL_PREFIX=${hdf5_install_dir}
 
@@ -245,7 +245,7 @@ fi # build_hdf5
 ################
 # Silo
 ################
-silo_version=4.11.1
+silo_version=4.12.0
 silo_src_dir=$(ospath ${source_dir}/Silo-${silo_version})
 silo_build_dir=$(ospath ${build_dir}/silo-${silo_version}/)
 silo_install_dir=$(ospath ${install_dir}/silo-${silo_version}/)
@@ -260,17 +260,8 @@ if [ ! -d ${silo_src_dir} ]; then
   # untar and avoid symlinks (which windows despises)
   tar ${tar_extra_args} -xzf ${silo_tarball} -C ${source_dir} \
       --exclude="Silo-${silo_version}/config-site/*" \
-      --exclude="Silo-${silo_version}/README.md"
-  # apply silo patches
-  cd  ${silo_src_dir}
-  patch -p1 < ${script_dir}/2024_07_25_silo_4_11_cmake_fix.patch
-
-  # windows specifc patch
-  if [[ "$build_windows" == "ON" ]]; then
-    patch -p1 < ${script_dir}/2024_07_29_silo-pr389-win32-bugfix.patch
-  fi
-
-  cd ${root_dir}
+      --exclude="Silo-${silo_version}/LICENSE.md" \
+      --exclude="Silo-${silo_version}/silo_objects.png"
 fi
 
 
@@ -471,6 +462,11 @@ if [ ! -d ${h5zzfp_src_dir} ]; then
   echo "**** Downloading ${h5zzfp_tarball}"
   curl -L "https://github.com/LLNL/H5Z-ZFP/archive/refs/tags/v${h5zzfp_version}.tar.gz"  -o ${h5zzfp_tarball}
   tar ${tar_extra_args} -xzf ${h5zzfp_tarball} -C ${source_dir}
+
+  # apply patches
+  cd ${h5zzfp_src_dir}
+  patch -p1 < ${script_dir}/2025_12_08_h5zzfp-hdf5-cmake-fix.patch
+  cd ${root_dir}
 fi
 
 echo "**** Configuring H5Z-ZFP ${h5zzfp_version}"

scripts/uberenv_configs/packages/hdf5/find_package_zlib.patch

@@ -0,0 +1,12 @@
+diff --git a/CMakeFilters.cmake b/CMakeFilters.cmake
+index dbd68fd110..3d06b13d57 100644
+--- a/CMakeFilters.cmake
++++ b/CMakeFilters.cmake
+@@ -70,7 +70,6 @@ option (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON)
+ if (HDF5_ENABLE_Z_LIB_SUPPORT)
+   if (NOT H5_ZLIB_HEADER)
+     if (NOT ZLIB_USE_EXTERNAL)
+-      find_package (ZLIB NAMES ${ZLIB_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static shared)
+       if (NOT ZLIB_FOUND)
+         find_package (ZLIB) # Legacy find
+       endif ()

scripts/uberenv_configs/packages/hdf5/fortran-kinds-2.patch

@@ -0,0 +1,24 @@
+From 598df49b738fd99df9f2671e4e967fd9c33ae8a9 Mon Sep 17 00:00:00 2001
+From: Seth R Johnson <[email protected]>
+Date: Wed, 16 Feb 2022 20:38:03 -0500
+Subject: [PATCH] Close file to work around GCC11.2/macOS12 bug
+
+---
+ m4/aclocal_fc.f90 | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/m4/aclocal_fc.f90 b/m4/aclocal_fc.f90
+index e9a11c0ab5..bfda49aa40 100644
+--- a/m4/aclocal_fc.f90
++++ b/m4/aclocal_fc.f90
+@@ -151,6 +151,7 @@ PROGRAM FC_AVAIL_KINDS
+      WRITE(8,'(I0)') max_decimal_prec
+      WRITE(8,'(I0)') num_ikinds
+      WRITE(8,'(I0)') num_rkinds
++     CLOSE(8)
+ END PROGRAM FC_AVAIL_KINDS
+ !---- END ----- Determine the available KINDs for REALs and INTEGERs
+
+-- 
+2.32.0
+

scripts/uberenv_configs/packages/hdf5/fortran-kinds.patch

@@ -0,0 +1,20 @@
+--- a/config/cmake/HDF5UseFortran.cmake
++++ a/config/cmake/HDF5UseFortran.cmake
+@@ -181,6 +181,7 @@
+          WRITE(8,'(I0)') max_decimal_prec
+          WRITE(8,'(I0)') num_ikinds
+          WRITE(8,'(I0)') num_rkinds
++         CLOSE(8)
+       END PROGRAM FC_AVAIL_KINDS
+   "
+ )
+--- a/m4/aclocal_fc.f90
++++ b/m4/aclocal_fc.f90
+@@ -151,6 +151,7 @@
+      WRITE(8,'(I0)') max_decimal_prec
+      WRITE(8,'(I0)') num_ikinds
+      WRITE(8,'(I0)') num_rkinds
++     CLOSE(8)
+ END PROGRAM FC_AVAIL_KINDS
+ !---- END ----- Determine the available KINDs for REALs and INTEGERs
+

scripts/uberenv_configs/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch

@@ -0,0 +1,16 @@
+diff --git a/fortran/src/H5f90global.F90 b/fortran/src/H5f90global.F90
+index dd2b171..629418a 100644
+--- a/fortran/src/H5f90global.F90
++++ b/fortran/src/H5f90global.F90
+@@ -142,10 +142,7 @@ MODULE H5GLOBAL
+
+   INTEGER(HID_T), DIMENSION(PREDEF_TYPES_LEN) :: predef_types
+   EQUIVALENCE (predef_types(1), H5T_NATIVE_INTEGER_KIND(1))
+-  EQUIVALENCE (predef_types(2), H5T_NATIVE_INTEGER_KIND(2))
+-  EQUIVALENCE (predef_types(3), H5T_NATIVE_INTEGER_KIND(3))
+-  EQUIVALENCE (predef_types(4), H5T_NATIVE_INTEGER_KIND(4))
+-  EQUIVALENCE (predef_types(5), H5T_NATIVE_INTEGER_KIND(5))
++  ! EQUIVALENCE predef_types(2:5) are unnecessary and violate the standard
+   EQUIVALENCE (predef_types(6), H5T_NATIVE_INTEGER)
+   EQUIVALENCE (predef_types(7), H5T_NATIVE_REAL)
+   EQUIVALENCE (predef_types(8), H5T_NATIVE_DOUBLE)

scripts/uberenv_configs/packages/hdf5/h5public-skip-mpicxx.patch

@@ -0,0 +1,11 @@
+--- a/src/H5public.h	2019-08-28 18:51:39.393781356 -0400
++++ b/src/H5public.h	2019-08-28 20:59:50.315181711 -0400
+@@ -57,6 +57,8 @@
+ #   include <stddef.h>
+ #endif
+ #ifdef H5_HAVE_PARALLEL
++#   define MPICH_SKIP_MPICXX 1
++#   define OMPI_SKIP_MPICXX 1
+ #   include <mpi.h>
+ #ifndef MPI_FILE_NULL		/*MPIO may be defined in mpi.h already       */
+ #   include <mpio.h>

scripts/uberenv_configs/packages/hdf5/hdf5_1.8_gcc10.patch

@@ -0,0 +1,12 @@
+diff -Naur hdf5.orig/fortran/test/tH5T_F03.f90 hdf5/fortran/test/tH5T_F03.f90
+--- hdf5.orig/fortran/test/tH5T_F03.f90	2021-01-19 13:23:11.298000000 +0100
++++ hdf5/fortran/test/tH5T_F03.f90	2021-01-19 13:19:17.637000000 +0100
+@@ -1541,7 +1541,7 @@
+   INTEGER :: A, B, C, D
+   INTEGER :: Aw, Bw, Cw, Dw
+   INTEGER :: i, j
+-  INTEGER, PARAMETER :: hex =  Z'00000003'
++  INTEGER, PARAMETER :: hex =  INT(Z'00000003')
+   TYPE(C_PTR) :: f_ptr
+   INTEGER :: error     ! Error flag
+   !

scripts/uberenv_configs/packages/hdf5/hdf5_1_14_0_config_find_mpi.patch

@@ -0,0 +1,13 @@
+diff --git a/config/cmake/hdf5-config.cmake.in b/config/cmake/hdf5-config.cmake.in
+index 35cee4f..b336377 100644
+--- a/config/cmake/hdf5-config.cmake.in
++++ b/config/cmake/hdf5-config.cmake.in
+@@ -63,6 +63,8 @@ if (${HDF5_PACKAGE_NAME}_ENABLE_PARALLEL)
+     set (${HDF5_PACKAGE_NAME}_MPI_Fortran_INCLUDE_PATH "@MPI_Fortran_INCLUDE_DIRS@")
+     set (${HDF5_PACKAGE_NAME}_MPI_Fortran_LIBRARIES    "@MPI_Fortran_LIBRARIES@")
+   endif ()
++
++    find_package(MPI QUIET REQUIRED)
+ endif ()
+
+ if (${HDF5_PACKAGE_NAME}_BUILD_JAVA)