ParaView/VTK: Patch xdmf2 for HDF5 1.13 (#33930)

* ParaView/VTK: Patch xdmf2 for HDF5 1.13

* Meson: update meson build system for 0.64

* ParaView: Change HDF5 1.13 patch to 1.13.1/2 patchs

* Mesa: Remove legacy mesa option from meson_args

* Use append to assemble meson args

lib/spack/spack/build_systems/meson.py

@@ -120,6 +120,7 @@ def std_meson_args(self):
         of package writers.
         """
         # standard Meson arguments
+
         std_meson_args = MesonBuilder.std_args(self.pkg)
         std_meson_args += getattr(self, "meson_flag_args", [])
         return std_meson_args
@@ -182,7 +183,10 @@ def meson_args(self):
 
     def meson(self, pkg, spec, prefix):
         """Run ``meson`` in the build directory"""
-        options = [os.path.abspath(self.root_mesonlists_dir)]
+        options = []
+        if self.spec["meson"].satisfies("@0.64:"):
+            options.append("setup")
+        options.append(os.path.abspath(self.root_mesonlists_dir))
         options += self.std_meson_args
         options += self.meson_args()
         with fs.working_dir(self.build_directory, create=True):

var/spack/repos/builtin/packages/mesa/package.py

@@ -118,6 +118,7 @@ class Mesa(MesonPackage):
         depends_on("libllvm@6:")
         depends_on("libllvm@:11", when="@:20")
         depends_on("libllvm@:12", when="@:21")
+
     depends_on("libx11", when="+glx")
     depends_on("libxcb", when="+glx")
     depends_on("libxext", when="+glx")
@@ -202,8 +203,10 @@ def meson_args(self):
             "-Dbuild-tests=false",
             "-Dglvnd=false",
         ]
-        if spec.satisfies("@:22.2"):
+        # gallium-xvmc was removed in @main and @2.23:
+        if self.spec.satisfies("@:22.2"):
             args.append("-Dgallium-xvmc=disabled")
+
         args_platforms = []
         args_gallium_drivers = ["swrast"]
         args_dri_drivers = []

var/spack/repos/builtin/packages/paraview/package.py

@@ -268,6 +268,11 @@ class Paraview(CMakePackage, CudaPackage, ROCmPackage):
     # intel oneapi doesn't compile some code in catalyst
     patch("catalyst-etc_oneapi_fix.patch", when="@5.10.0:5.10.1%oneapi")
 
+    # Patch for paraview 5.10: +hdf5 ^hdf5@1.13.2:
+    # https://gitlab.kitware.com/vtk/vtk/-/merge_requests/9690
+    patch("vtk-xdmf2-hdf51.13.1.patch", when="@5.10.0:5.10 +hdf5")
+    patch("vtk-xdmf2-hdf51.13.2.patch", when="@5.10: +hdf5")
+
     @property
     def generator(self):
         # https://gitlab.kitware.com/paraview/paraview/-/issues/21223

var/spack/repos/builtin/packages/paraview/vtk-xdmf2-hdf51.13.1.patch

@@ -0,0 +1,61 @@
+From 3a536a3c6b949cb1c9dd147c3a395c3ff31856e8 Mon Sep 17 00:00:00 2001
+From: Ben Boeckel <ben.boeckel@kitware.com>
+Date: Thu, 14 Apr 2022 12:53:36 -0400
+Subject: [PATCH 1/6] xdmf2: install `XdmfExport.h`
+
+---
+ VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/CMakeLists.txt | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/CMakeLists.txt b/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/CMakeLists.txt
+index 274dbc4423c..a47bf4ee4d9 100644
+--- a/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/CMakeLists.txt
++++ b/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/CMakeLists.txt
+@@ -276,6 +276,7 @@ vtk_module_add_module(VTK::xdmf2
+           ${XdmfModelSource}
+   SOURCES ${XdmfExtraSource}
+   HEADERS Xdmf.h
++          XdmfExport.h
+           "${CMAKE_CURRENT_BINARY_DIR}/XdmfConfig.h"
+   HEADERS_SUBDIR "vtkxdmf2/libsrc")
+ set_target_properties(xdmf2
+-- 
+GitLab
+
+
+From 1456c9e6ab2b244d225dcfc0a7f985933c09d5f3 Mon Sep 17 00:00:00 2001
+From: Ben Boeckel <ben.boeckel@kitware.com>
+Date: Thu, 14 Apr 2022 15:20:13 -0400
+Subject: [PATCH 6/6] xdmf2: support HDF5 1.13.1
+
+---
+ VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx | 7 +++++++
+ 1 file changed, 7 insertions(+)
+
+diff --git a/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx b/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx
+index 6a4966bb231..1a412b56d02 100644
+--- a/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx
++++ b/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx
+@@ -156,6 +156,9 @@ static herr_t H5FD_dsm_write(H5FD_t *_file, H5FD_mem_t type, hid_t fapl_id, hadd
+ }
+ 
+ static const H5FD_class_t H5FD_dsm_g = {
++#if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=13))
++    H5_VFD_RESERVED + 0xd3f2,   /*value         */
++#endif
+     "dsm",                      /*name          */
+     MAXADDR,                    /*maxaddr       */
+     H5F_CLOSE_WEAK,             /*fc_degree     */
+@@ -193,6 +196,10 @@ static const H5FD_class_t H5FD_dsm_g = {
+ #endif
+     NULL,                       /*lock          */
+     NULL,                       /*unlock        */
++#if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=13))
++    NULL,                       /*del           */
++    NULL,                       /*ctl           */
++#endif
+     H5FD_FLMAP_SINGLE           /*fl_map        */
+ };
+ 
+-- 
+GitLab

var/spack/repos/builtin/packages/paraview/vtk-xdmf2-hdf51.13.2.patch

@@ -0,0 +1,36 @@
+From 2cc0d020359f714587d14b2f25a2c5f235f829c9 Mon Sep 17 00:00:00 2001
+From: Ryan Krattiger <ryan.krattiger@kitware.com>
+Date: Tue, 15 Nov 2022 15:00:36 -0600
+Subject: [PATCH] Xdmf2: Update HDF5 driver for 1.13.2
+
+---
+ VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx | 7 +++++++
+ 1 file changed, 7 insertions(+)
+
+diff --git a/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx b/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx
+index 1a412b56d02..ff4427d0265 100644
+--- a/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx
++++ b/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx
+@@ -157,6 +157,7 @@ static herr_t H5FD_dsm_write(H5FD_t *_file, H5FD_mem_t type, hid_t fapl_id, hadd
+ 
+ static const H5FD_class_t H5FD_dsm_g = {
+ #if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=13))
++    0,                          /*version       */
+     H5_VFD_RESERVED + 0xd3f2,   /*value         */
+ #endif
+     "dsm",                      /*name          */
+@@ -190,6 +191,12 @@ static const H5FD_class_t H5FD_dsm_g = {
+     NULL,                       /*get_handle    */
+     H5FD_dsm_read,              /*read          */
+     H5FD_dsm_write,             /*write         */
++#if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=13))
++    NULL,                       /*read_vector     */
++    NULL,                       /*write_vector    */
++    NULL,                       /*read_selection  */
++    NULL,                       /*write_selection */
++#endif
+     NULL,                       /*flush         */
+ #if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=8))
+     NULL,                       /* truncate     */
+-- 
+GitLab

var/spack/repos/builtin/packages/vtk/package.py

@@ -55,6 +55,10 @@ class Vtk(CMakePackage):
         sha256="0546696bd02f3a99fccb9b7c49533377bf8179df16d901cefe5abf251173716d",
     )
 
+    # Patch for paraview 5.10: +hdf5 ^hdf5@1.13.2:
+    # https://gitlab.kitware.com/vtk/vtk/-/merge_requests/9690
+    patch("xdmf2-hdf51.13.2.patch", when="@9:9.2 +xdmf")
+
     # We cannot build with both osmesa and qt in spack
     conflicts("+osmesa", when="+qt")
 

var/spack/repos/builtin/packages/vtk/xdmf2-hdf51.13.2.patch

@@ -0,0 +1,36 @@
+--- a/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx   2022-11-15 15:37:37.242113202 -0600
++++ b/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx	  2022-11-15 14:51:30.849230122 -0600
+@@ -156,6 +156,10 @@
+ }
+ 
+ static const H5FD_class_t H5FD_dsm_g = {
++#if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=13))
++    0,                          /*version       */
++    H5_VFD_RESERVED + 0xd3f2,   /*value         */
++#endif
+     "dsm",                      /*name          */
+     MAXADDR,                    /*maxaddr       */
+     H5F_CLOSE_WEAK,             /*fc_degree     */
+@@ -187,12 +191,22 @@
+     NULL,                       /*get_handle    */
+     H5FD_dsm_read,              /*read          */
+     H5FD_dsm_write,             /*write         */
++#if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=13))
++    NULL,                       /*read_vector     */
++    NULL,                       /*write_vector    */
++    NULL,                       /*read_selection  */
++    NULL,                       /*write_selection */
++#endif
+     NULL,                       /*flush         */
+ #if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=8))
+     NULL,                       /* truncate     */
+ #endif
+     NULL,                       /*lock          */
+     NULL,                       /*unlock        */
++#if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=13))
++    NULL,                       /*del           */
++    NULL,                       /*ctl           */
++#endif
+     H5FD_FLMAP_SINGLE           /*fl_map        */
+ };
+