Patch VTK 9.4 build on resolute

scripts/custom/install_boost.sh

@@ -100,7 +100,7 @@ install_dir=${base_dir}/opt/boost/${version}
 mkdir -p ${install_dir}
 
 cd ${src_dir}
-./bootstrap.sh --prefix=${install_dir} && \
+./bootstrap.sh --prefix=${install_dir}
 ./b2 -j ${parallel} toolset=gcc cxxflags=-w install
 
 # Add modulefile

scripts/custom/install_cmake.sh

@@ -67,8 +67,8 @@ mkdir -p ${install_dir}
 cd cmake-${version}
 ./bootstrap \
     --prefix=${install_dir} \
-    --parallel=${parallel} && \
-make -j ${parallel} && \
+    --parallel=${parallel}
+make -j ${parallel}
 make install
 
 # Add modulefile

scripts/custom/install_hdf5.sh

@@ -115,24 +115,25 @@ if version_lt "${version}" '2.0.0'; then # HDF5 < 2.0.0
         CPPFLAGS=-fPIC \
         CXXFLAGS=-fPIC \
         CC=mpicc \
-        CXX=mpic++ &&
-        make -j ${parallel} all &&
-        make install
+        CXX=mpic++
+    make -j ${parallel} all
+    make install
 
 else # HDF5 >= 2.0.0
     # Check cmake version (HDF5 2.0+ requires cmake >= 3.26)
     cmake --version
 
-    mkdir -p build && cd build
+    mkdir -p build
+    cd build
     CC=mpicc CXX=mpic++ cmake \
         -DBUILD_SHARED_LIBS=ON \
         -DCMAKE_BUILD_TYPE=Release \
         -DCMAKE_INSTALL_PREFIX=${install_dir} \
         -DHDF5_BUILD_HL_LIB=ON \
         -DHDF5_BUILD_TOOLS=ON \
-        -DHDF5_ENABLE_PARALLEL=ON .. &&
-        make -j ${parallel} &&
-        make install
+        -DHDF5_ENABLE_PARALLEL=ON ..
+    make -j ${parallel}
+    make install
 fi
 
 # Add modulefile

scripts/custom/install_petsc.sh

@@ -115,7 +115,7 @@ case ${arch} in
             --with-fc=0 \
             --with-shared-libraries \
             --with-ssl=false \
-            --with-x=false && \
+            --with-x=false
         make -j ${parallel} all
         ;;
 
@@ -132,7 +132,7 @@ case ${arch} in
             --with-fc=0 \
             --with-shared-libraries \
             --with-ssl=false \
-            --with-x=false && \
+            --with-x=false
         make -j ${parallel} all
         ;;
     *)

scripts/custom/install_python.sh

@@ -58,8 +58,8 @@ mkdir -p ${install_dir}
 cd Python-${version}
 ./configure \
      --enable-optimizations \
-     --prefix=${install_dir} && \
-make -j ${parallel} && \
+     --prefix=${install_dir}
+make -j ${parallel}
 make install
 
 # Add symbolic links

scripts/custom/install_sundials.sh

@@ -75,8 +75,8 @@ cmake \
     -DBUILD_SHARED_LIBS=ON \
     -DCMAKE_BUILD_TYPE=Release \
     -DENABLE_MPI=ON \
-    -DEXAMPLES_ENABLE=OFF .. && \
-make -j ${parallel} && \
+    -DEXAMPLES_ENABLE=OFF ..
+make -j ${parallel}
 make install
 
 # Add modulefile

scripts/custom/install_vtk.sh

@@ -193,6 +193,17 @@ if version_eq "${major}.${minor}" '9.2'; then  # VTK == 9.2.x
     patch -t -p1 < ${patch_dir}/9.2/gcc-13.patch
 fi
 
+# VTK 9.4.x patches
+if version_eq "${major}.${minor}" '9.4'; then  # VTK == 9.4.x
+    # netCDF 4.9.3 replaced the _FillValue macro with NC_FillValue, which the
+    # bundled exodusII on VTK < 9.5 still uses, so do a rename if applicable.
+    netcdf_version="$(pkg-config --modversion netcdf 2>/dev/null || true)"
+    if [ -n "${netcdf_version}" ] && version_ge "${netcdf_version}" '4.9.3'; then
+        cd ${src_dir}
+        patch -t -p1 < ${patch_dir}/9.4/netcdf-fillvalue.patch
+    fi
+fi
+
 # Build and install
 install_dir=${base_dir}/opt/vtk/${version}
 mkdir -p ${install_dir}
@@ -231,8 +242,8 @@ cmake \
     -DVTK_MODULE_USE_EXTERNAL_VTK_utf8=ON \
     -DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON \
     -DHDF5_IS_PARALLEL=ON \
-    ${src_dir} && \
-make -j ${parallel} && \
+    ${src_dir}
+make -j ${parallel}
 make install
 
 # Add modulefile

scripts/custom/install_xercesc.sh

@@ -69,15 +69,15 @@ if [ ${major} -le 2 ]; then
     cd xerces-c-src_${ver_si_on}
     export XERCESCROOT=$(pwd)
     cd src/xercesc
-    ./runConfigure -plinux -cgcc -xg++ -P${install_dir} && \
-    make -j ${parallel} && \
+    ./runConfigure -plinux -cgcc -xg++ -P${install_dir}
+    make -j ${parallel}
     make install
 else
     wget -nc https://archive.apache.org/dist/xerces/c/${major}/sources/xerces-c-${version}.tar.gz
     tar -xzf xerces-c-${version}.tar.gz
     cd xerces-c-${version}
-    ./configure --enable-netaccessor-socket --prefix=${install_dir} && \
-    make -j ${parallel} && \
+    ./configure --enable-netaccessor-socket --prefix=${install_dir}
+    make -j ${parallel}
     make install
 fi
 

scripts/custom/patches/vtk/9.4/netcdf-fillvalue.patch

@@ -0,0 +1,39 @@
+Subject: Use NC_FillValue instead of _FillValue in bundled exodusII
+Origin: vendor, https://github.com/Unidata/netcdf-c/blob/main/include/netcdf.h
+
+netCDF 4.9.3 removed the _FillValue macro, which used a reserved identifier,
+and replaced it with NC_FillValue. VTK's bundled exodusII still refers to
+_FillValue, so it fails to compile against netCDF >= 4.9.3 when VTK is built
+with VTK_MODULE_USE_EXTERNAL_VTK_netcdf=ON:
+
+    ex_put_prop.c:246:54: error: '_FillValue' undeclared (first use in this
+    function); did you mean 'NC_FillValue'?
+
+Both macros expand to the string "_FillValue", so the attribute name written
+to file is unchanged.
+
+This patch is only applied when building against netCDF >= 4.9.3;
+see install_vtk.sh.
+---
+--- vtk9.orig/ThirdParty/exodusII/vtkexodusII/src/ex_put_prop.c
++++ vtk9/ThirdParty/exodusII/vtkexodusII/src/ex_put_prop.c
+@@ -243,7 +243,7 @@
+     vals[0] = 0; /* fill value */
+     /*   create attribute to cause variable to fill with zeros per routine spec
+      */
+-    if ((status = nc_put_att_longlong(exoid, propid, _FillValue, int_type, 1, vals)) != NC_NOERR) {
++    if ((status = nc_put_att_longlong(exoid, propid, NC_FillValue, int_type, 1, vals)) != NC_NOERR) {
+       snprintf(errmsg, MAX_ERR_LENGTH,
+                "ERROR: failed to create property name fill attribute in file id %d", exoid);
+       ex_err_fn(exoid, __func__, errmsg, status);
+--- vtk9.orig/ThirdParty/exodusII/vtkexodusII/src/ex_put_prop_names.c
++++ vtk9/ThirdParty/exodusII/vtkexodusII/src/ex_put_prop_names.c
+@@ -172,7 +172,7 @@
+
+     /*   create attribute to cause variable to fill with zeros per routine spec
+      */
+-    if ((status = nc_put_att_longlong(exoid, propid, _FillValue, int_type, 1, vals)) != NC_NOERR) {
++    if ((status = nc_put_att_longlong(exoid, propid, NC_FillValue, int_type, 1, vals)) != NC_NOERR) {
+       snprintf(errmsg, MAX_ERR_LENGTH,
+                "ERROR: failed to create property name fill attribute in file id %d", exoid);
+       ex_err_fn(exoid, __func__, errmsg, status);

scripts/custom/setup_ubuntu_2204.sh

@@ -24,6 +24,8 @@ apt-get install -y --no-install-recommends \
   doxygen \
   git \
   lcov \
+  patch \
+  pkg-config \
   python-is-python3 \
   python3 \
   python3-dev \

scripts/custom/setup_ubuntu_2404.sh

@@ -26,6 +26,8 @@ apt-get install -y --no-install-recommends \
   doxygen \
   git \
   lcov \
+  patch \
+  pkg-config \
   python-is-python3 \
   python3 \
   python3-dev \

scripts/custom/setup_ubuntu_2604.sh

@@ -26,6 +26,8 @@ apt-get install -y --no-install-recommends \
   doxygen \
   git \
   lcov \
+  patch \
+  pkg-config \
   python-is-python3 \
   python3 \
   python3-dev \