fix errors in apple-clang 17

CMakeLists.txt

@@ -565,7 +565,7 @@ list(APPEND build_list pugixml )
 ################################
 if (ENABLE_TRILINOS)
     set(TRILINOS_DIR "${CMAKE_INSTALL_PREFIX}/trilinos")
-    set(TRILINOS_URL "${TPL_MIRROR_DIR}/trilinos-release-16-0-0.tar.gz")
+    set(TRILINOS_URL "${TPL_MIRROR_DIR}/trilinos-release-16-1-0.tar.gz")
 
     message(STATUS "Building TRILINOS found at ${TRILINOS_URL}")
 
@@ -1136,7 +1136,7 @@ endif()
 ################################
 if( ENABLE_VTK )
     set( VTK_DIR "${CMAKE_INSTALL_PREFIX}/vtk" )
-    set( VTK_URL "${TPL_MIRROR_DIR}/VTK-9.3.1.tar.gz" )
+    set( VTK_URL "${TPL_MIRROR_DIR}/VTK-9.4.2.tar.gz" )
 
     message( STATUS "Building VTK found at ${VTK_URL}" )
 
@@ -1164,6 +1164,9 @@ endif( ENABLE_MPI )
                          PREFIX ${PROJECT_BINARY_DIR}/vtk
                          URL ${VTK_URL}
                          INSTALL_DIR ${VTK_DIR}
+                         PATCH_COMMAND patch --forward -p0 < ${CMAKE_SOURCE_DIR}/patch/vtkCellGridReader.cxx.patch &&
+                                       patch --forward -p0 < ${CMAKE_SOURCE_DIR}/patch/vtkLegacyCellGridReader.cxx.patch &&
+                                       patch --forward -p0 < ${CMAKE_SOURCE_DIR}/patch/vtkformat.h.patch
                          BUILD_COMMAND ${TPL_BUILD_COMMAND}
                          INSTALL_COMMAND "${TPL_INSTALL_COMMAND}"
                          CMAKE_GENERATOR ${TPL_GENERATOR}

patch/vtkCellGridReader.cxx.patch

@@ -0,0 +1,14 @@
+--- IO/CellGrid/vtkCellGridReader.cxx	2025-03-27 23:59:55
++++ IO/CellGrid/vtkCellGridReader.cxx.modified	2025-04-15 13:17:03
+@@ -409,7 +409,10 @@
+       // The final "false" below allows the data to not be fully consumed,
+       // which may happen if sizeof(istream::char_type) > 1. In the future,
+       // it may also happen that a file contains multiple JSON streams.
+-      jj = nlohmann::json::from_msgpack(data.begin(), data.end(), false);
++
++      char const * const begin = reinterpret_cast<const char*>(data.data());
++      char const * const end = begin + data.size();
++      jj = nlohmann::json::from_msgpack(begin, end, false);
+     }
+     catch (...)
+     {

patch/vtkLegacyCellGridReader.cxx.patch

@@ -0,0 +1,14 @@
+--- IO/Legacy/vtkLegacyCellGridReader.cxx	2025-03-27 23:59:55
++++ IO/Legacy/vtkLegacyCellGridReader.cxx.modified	2025-04-15 13:28:24
+@@ -115,7 +115,10 @@
+       // The final argument (false) indicates that the decoder should allow
+       // partial consumption of raw.data() (meaning the trailing newline will
+       // not cause an exception):
+-      jdata = nlohmann::json::from_msgpack(raw.data(), raw.data() + contentLength, false);
++
++      char const * const begin = reinterpret_cast<const char*>(raw.data());
++      char const * const end = begin + contentLength;
++      jdata = nlohmann::json::from_msgpack(begin, end, false);
+     }
+     catch (nlohmann::json::exception& e)
+     {

patch/vtkfmt.patch

@@ -0,0 +1,18 @@
+--- ThirdParty/diy2/vtkdiy2/include/vtkdiy2/fmt/format.h	2025-04-15 14:30:09
++++ ThirdParty/diy2/vtkdiy2/include/vtkdiy2/fmt/format.h.patched	2025-04-15 14:29:55
+@@ -481,12 +481,12 @@
+ }  // namespace internal
+
+ // A UTF-8 string view.
+-class u8string_view : public basic_string_view<char8_t> {
++class u8string_view : public basic_string_view<char> {
+  public:
+   u8string_view(const char* s)
+-      : basic_string_view<char8_t>(reinterpret_cast<const char8_t*>(s)) {}
++      : basic_string_view<char>( s ) {}
+   u8string_view(const char* s, size_t count) FMT_NOEXCEPT
+-      : basic_string_view<char8_t>(reinterpret_cast<const char8_t*>(s), count) {
++      : basic_string_view<char>( s, count) {
+   }
+ };
+

patch/vtkformat.h.patch

@@ -0,0 +1,18 @@
+--- ThirdParty/diy2/vtkdiy2/include/vtkdiy2/fmt/format.h	2025-04-15 14:30:09
++++ ThirdParty/diy2/vtkdiy2/include/vtkdiy2/fmt/format.h.patched	2025-04-15 14:29:55
+@@ -481,12 +481,12 @@
+ }  // namespace internal
+
+ // A UTF-8 string view.
+-class u8string_view : public basic_string_view<char8_t> {
++class u8string_view : public basic_string_view<char> {
+  public:
+   u8string_view(const char* s)
+-      : basic_string_view<char8_t>(reinterpret_cast<const char8_t*>(s)) {}
++      : basic_string_view<char>( s ) {}
+   u8string_view(const char* s, size_t count) FMT_NOEXCEPT
+-      : basic_string_view<char8_t>(reinterpret_cast<const char8_t*>(s), count) {
++      : basic_string_view<char>( s, count) {
+   }
+ };
+

scripts/setupLC-TPL-uberenv.bash

@@ -46,9 +46,10 @@ echo "Building all LC TPLs from $GEOS_BRANCH to be installed at $INSTALL_DIR..."
 ./scripts/setupLC-TPL-uberenv-helper.bash $INSTALL_DIR ruby gcc-12noAVX "%gcc@12noAVX +docs" "salloc -N 1 -n 1 -t 150 -A vortex" $@ &
 ./scripts/setupLC-TPL-uberenv-helper.bash $INSTALL_DIR dane gcc-12 "%gcc@12.1.1 +docs" "salloc -N 1 -n 1 -t 150 -A vortex" $@ &
 ./scripts/setupLC-TPL-uberenv-helper.bash $INSTALL_DIR lassen gcc-8-cuda-11 "%gcc@8.3.1+cuda~uncrustify cuda_arch=70 ^cuda@11.8.0+allow-unsupported-compilers" "lalloc 1 -W 150" $@ &
+./scripts/setupLC-TPL-uberenv-helper.bash $INSTALL_DIR lassen gcc-12-cuda-11 "%gcc@12.2.1+cuda~uncrustify cuda_arch=70 ^cuda@11.8.0+allow-unsupported-compilers" "lalloc 1 -W 150" $@ &
 ./scripts/setupLC-TPL-uberenv-helper.bash $INSTALL_DIR lassen clang-13-cuda-11 "%clang@13.0.1+cuda~uncrustify cuda_arch=70 ^cuda@11.8.0+allow-unsupported-compilers" "lalloc 1 -W 150" $@ &
 ./scripts/setupLC-TPL-uberenv-helper.bash $INSTALL_DIR lassen clang-10-cuda-11 "%clang@10.0.1+cuda~uncrustify cuda_arch=70 ^cuda@11.8.0+allow-unsupported-compilers" "lalloc 1 -W 150" $@ &
-./scripts/setupLC-TPL-uberenv-helper.bash $INSTALL_DIR lassen clang-13-cuda-12 "%clang@13.0.1+cuda~uncrustify cuda_arch=70 ^cuda@12.0.0+allow-unsupported-compilers" "lalloc 1 -W 150" $@ &
+./scripts/setupLC-TPL-uberenv-helper.bash $INSTALL_DIR lassen clang-13-cuda-12 "%clang@13.0.1+cuda~uncrustify cuda_arch=70 ^cuda@12.2.2+allow-unsupported-compilers" "lalloc 1 -W 150" $@ &
 
 # Note: Estimated completion time is ~90 minutes.
 # Check log files for unreported completion of jobs.

scripts/spack_configs/blueos_3_ppc64le_ib_p9/spack.yaml

@@ -13,7 +13,7 @@
 # geosx@develop%clang@10.0.1+cuda cuda_arch=70 ^cuda@11.8.0+allow-unsupported-compilers
 # geosx@develop%gcc@8.3.1+cuda cuda_arch=70 ^cuda@11.8.0+allow-unsupported-compilers
 # geosx@develop%clang@13.0.1+cuda cuda_arch=70 ^cuda@11.8.0+allow-unsupported-compilers
-# geosx@develop%clang@13.0.1+cuda cuda_arch=70 ^cuda@12.0.0+allow-unsupported-compilers
+# geosx@develop%clang@13.0.1+cuda cuda_arch=70 ^cuda@12.2.2+allow-unsupported-compilers
 #
 # Uberenv command to build geos dependencies:
 # python3 ./scripts/uberenv/uberenv.py --spec="%clang@10.0.1+cuda~uncrustify cuda_arch=70 ^cuda@11.8.0+allow-unsupported-compilers"
@@ -22,7 +22,7 @@
 #
 # python3 ./scripts/uberenv/uberenv.py --spec="%clang@13.0.1+cuda~uncrustify cuda_arch=70 ^cuda@11.8.0+allow-unsupported-compilers"
 #
-# python3 ./scripts/uberenv/uberenv.py --spec="%clang@13.0.1+cuda~openmp~uncrustify cuda_arch=70 ^cuda@12.0.0+allow-unsupported-compilers"
+# python3 ./scripts/uberenv/uberenv.py --spec="%clang@13.0.1+cuda~openmp~uncrustify cuda_arch=70 ^cuda@12.2.2+allow-unsupported-compilers"
 
 
 spack:
@@ -90,6 +90,24 @@ spack:
           BISON: bison
           FLEX: flex
       extra_rpaths: []
+  - compiler:
+      spec: gcc@12.2.1
+      paths:
+        cc: /usr/tce/packages/gcc/gcc-12.2.1/bin/gcc
+        cxx: /usr/tce/packages/gcc/gcc-12.2.1/bin/g++
+        f77: /usr/tce/packages/gcc/gcc-12.2.1/bin/gfortran
+        fc: /usr/tce/packages/gcc/gcc-12.2.1/bin/gfortran
+      flags:
+        # Fix for "undefined reference to `_gfortran_transfer_integer_write'"
+        ldlibs: -lgfortran
+      operating_system: rhel7
+      target: ppc64le
+      modules: []
+      environment:
+        set: # Needed for scotch
+          BISON: bison
+          FLEX: flex
+      extra_rpaths: []
 
   packages:
     all:
@@ -141,6 +159,8 @@ spack:
       externals:
         - spec: spectrum-mpi@release%gcc@8.3.1
           prefix: /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-8.3.1
+        - spec: spectrum-mpi@release%gcc@12.2.1
+          prefix: /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-12.2.1
         # Previously clang@upstream - clingo doesn't like "upstream" version
         - spec: spectrum-mpi@release%clang@10.0.1
           prefix: /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-clang-10.0.1-gcc-8.3.1
@@ -158,8 +178,8 @@ spack:
       externals:
       - spec: cuda@11.8.0 +allow-unsupported-compilers
         prefix: /usr/tce/packages/cuda/cuda-11.8.0
-      - spec: cuda@12.0.0 +allow-unsupported-compilers
-        prefix: /usr/tce/packages/cuda/cuda-12.0.0
+      - spec: cuda@12.2.2 +allow-unsupported-compilers
+        prefix: /usr/tce/packages/cuda/cuda-12.2.2
 
   # System level packages to not build
     cmake:

scripts/spack_configs/macOS/spack.yaml

@@ -24,6 +24,29 @@ spack:
           cflags:
           cxxflags:
           fflags:
+          cppflags: -I/opt/homebrew/opt/openblas/include
+          ldflags: -L/opt/homebrew/opt/openblas/lib
+        operating_system: sequoia
+        target: aarch64
+        modules: []
+        environment:
+          set: # Needed for scotch
+            BISON: bison
+            FLEX: flex
+        extra_rpaths: []
+    - compiler:
+        spec: apple-clang@17.0.0
+        paths:
+          cc: /usr/bin/clang
+          cxx: /usr/bin/clang++
+          f77: /opt/homebrew/bin/gfortran 
+          fc: /opt/homebrew/bin/gfortran  
+        flags:
+          cppflags: -I/opt/homebrew/opt/openblas/include
+          ldflags: -L/opt/homebrew/opt/openblas/lib
+          cflags:
+          cxxflags:
+          fflags:
         operating_system: sequoia
         target: aarch64
         modules: []
@@ -39,8 +62,14 @@ spack:
       compiler: [apple-clang]
       providers:
         mpi: [openmpi]
-        blas: [netlib-lapack]
-        lapack: [netlib-lapack]
+        blas: [openblas]
+        lapack: [openblas]
+
+    openblas:
+      buildable: False
+      externals:
+        - spec: openblas@0.3.29
+          prefix: /opt/homebrew/opt/openblas
 
     # v0.6.2
     blt:
@@ -151,4 +180,16 @@ spack:
       buildable: False
       externals:
         - spec: addr2line@2.43.1
-          prefix: /opt/homebrew/opt/binutils     
+          prefix: /opt/homebrew/opt/binutils     
+
+    zlib:
+      buildable: False
+      externals:
+        - spec: zlib@1.3.1
+          prefix: /opt/homebrew/opt/zlib 
+
+    python:
+      buildable: false
+      externals:
+        - spec: python@3.13.2
+          prefix: /opt/homebrew/opt/python@3.13

scripts/spack_packages/packages/geosx/package.py

@@ -125,7 +125,7 @@ class Geosx(CMakePackage, CudaPackage):
     # IO
     #
     depends_on('hdf5@1.12.1')
-    depends_on('silo@4.11.1-bsd~fortran~shared')
+    depends_on('silo@4.11.1-bsd~fortran~shared~python')
 
     depends_on('conduit~test~fortran~hdf5_compat~shared')
 
@@ -135,7 +135,7 @@ class Geosx(CMakePackage, CudaPackage):
     depends_on('pugixml@1.13 ~shared')
 
     depends_on('fmt@10.0.0 cxxstd=14')
-    depends_on('vtk@9.3.1', when='+vtk')
+    depends_on('vtk@9.4.2', when='+vtk')
 
     #
     # Math
@@ -156,7 +156,7 @@ class Geosx(CMakePackage, CudaPackage):
 
     with when("+trilinos"):
         trilinos_packages = '+aztec+stratimikos~amesos2~anasazi~belos~ifpack2~muelu~sacado+thyra+zoltan'
-        depends_on("trilinos@16.0.0 cflags='-fPIC' cxxflags='-fPIC -include cstdint' fflags='-fPIC'" + trilinos_packages)
+        depends_on("trilinos@16.1.0 cflags='-fPIC' cxxflags='-fPIC -include cstdint' fflags='-fPIC'" + trilinos_packages)
         depends_on("trilinos~openmp", when="~openmp")
         depends_on("trilinos+openmp", when="+openmp")
 
@@ -462,6 +462,7 @@ def geos_hostconfig(self, spec, prefix, py_site_pkgs_dir=None):
 
             # yapf: disable
             io_tpls = (
+                ('zlib', 'ZLIB', True),
                 ('hdf5', 'HDF5', True),
                 ('conduit', 'CONDUIT', True),
                 ('silo', 'SILO', True),

scripts/spack_packages/packages/trilinos/package.py

@@ -47,6 +47,7 @@ class Trilinos(CMakePackage, CudaPackage, ROCmPackage):
     version('master', branch='master')
     version('develop', branch='develop')
     # GEOS Added
+    version("16.1.0", sha256="e9651c88f581049457036cfc01b527a9d3903c257338eeeab942befd7452f23a")
     version("16.0.0", sha256="46bfc40419ed2aa2db38c144fb8e61d4aa8170eaa654a88d833ba6b92903f309")
 
     version("13.4.1", sha256="5465cbff3de7ef4ac7d40eeff9d99342c00d9d20eee0a5f64f0a523093f5f1b3")

scripts/spack_packages/packages/vtk/9.4.2-patch/vtkCellGridReader.cxx.patch

@@ -0,0 +1,14 @@
+--- a/IO/CellGrid/vtkCellGridReader.cxx	2025-03-27 23:59:55
++++ b/IO/CellGrid/vtkCellGridReader.cxx	2025-04-15 13:17:03
+@@ -409,7 +409,10 @@
+       // The final "false" below allows the data to not be fully consumed,
+       // which may happen if sizeof(istream::char_type) > 1. In the future,
+       // it may also happen that a file contains multiple JSON streams.
+-      jj = nlohmann::json::from_msgpack(data.begin(), data.end(), false);
++
++      char const * const begin = reinterpret_cast<const char*>(data.data());
++      char const * const end = begin + data.size();
++      jj = nlohmann::json::from_msgpack(begin, end, false);
+     }
+     catch (...)
+     {

scripts/spack_packages/packages/vtk/9.4.2-patch/vtkLegacyCellGridReader.cxx.patch

@@ -0,0 +1,14 @@
+--- a/IO/Legacy/vtkLegacyCellGridReader.cxx	2025-03-27 23:59:55
++++ b/IO/Legacy/vtkLegacyCellGridReader.cxx	2025-04-15 13:28:24
+@@ -115,7 +115,10 @@
+       // The final argument (false) indicates that the decoder should allow
+       // partial consumption of raw.data() (meaning the trailing newline will
+       // not cause an exception):
+-      jdata = nlohmann::json::from_msgpack(raw.data(), raw.data() + contentLength, false);
++
++      char const * const begin = reinterpret_cast<const char*>(raw.data());
++      char const * const end = begin + contentLength;
++      jdata = nlohmann::json::from_msgpack(begin, end, false);
+     }
+     catch (nlohmann::json::exception& e)
+     {

scripts/spack_packages/packages/vtk/9.4.2-patch/vtkfmt.patch

@@ -0,0 +1,18 @@
+--- a/ThirdParty/diy2/vtkdiy2/include/vtkdiy2/fmt/format.h	2025-04-15 14:30:09
++++ b/ThirdParty/diy2/vtkdiy2/include/vtkdiy2/fmt/format.h	2025-04-15 14:29:55
+@@ -481,12 +481,12 @@
+ }  // namespace internal
+
+ // A UTF-8 string view.
+-class u8string_view : public basic_string_view<char8_t> {
++class u8string_view : public basic_string_view<char> {
+  public:
+   u8string_view(const char* s)
+-      : basic_string_view<char8_t>(reinterpret_cast<const char8_t*>(s)) {}
++      : basic_string_view<char>( s ) {}
+   u8string_view(const char* s, size_t count) FMT_NOEXCEPT
+-      : basic_string_view<char8_t>(reinterpret_cast<const char8_t*>(s), count) {
++      : basic_string_view<char>( s, count) {
+   }
+ };
+

scripts/spack_packages/packages/vtk/package.py

@@ -15,11 +15,12 @@ class Vtk(CMakePackage):
     processing and visualization. """
 
     homepage = "http://www.vtk.org"
-    url = "https://www.vtk.org/files/release/9.0/VTK-9.0.0.tar.gz"
+    url = "https://www.vtk.org/files/release/9.4/VTK-9.4.2.tar.gz"
     list_url = "http://www.vtk.org/download/"
 
     maintainers = ['chuckatkins', 'danlipsa']
-
+
+    version("9.4.2", sha256="36c98e0da96bb12a30fe53708097aa9492e7b66d5c3b366e1c8dc251e2856a02", preferred=True)
     version("9.3.1", sha256="8354ec084ea0d2dc3d23dbe4243823c4bfc270382d0ce8d658939fd50061cab8")
     version("9.2.6", sha256="06fc8d49c4e56f498c40fcb38a563ed8d4ec31358d0101e8988f0bb4d539dd12")
     version('9.1.0', sha256='8fed42f4f8f1eb8083107b68eaa9ad71da07110161a3116ad807f43e5ca5ce96')
@@ -52,6 +53,13 @@ class Vtk(CMakePackage):
     depends_on('py-mpi4py', when='+python+mpi', type='run')
 
     depends_on('mpi', when='+mpi')
+
+    patch_dir = os.path.join(os.path.dirname(__file__), '9.4.2-patch')
+    if os.path.isdir(patch_dir):
+        for fname in sorted(os.listdir(patch_dir)):
+               full_path = os.path.join(patch_dir, fname)
+               if fname.endswith('.patch') and os.path.isfile(full_path):
+                   patch(os.path.join('9.4.2-patch', fname), when='@9.4.2')
 
     def cmake_args(self):
         spec = self.spec