hdf5 patch

4 files changed, 69 insertions, 59 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 319d61e480f0..e90c5031aa48 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,18 +1,18 @@
 pkgbase = silo
 	pkgdesc = A Mesh and Field I/O Library and Scientific Database
 	pkgver = 4.11
-	pkgrel = 1
-	url = https://wci.llnl.gov/simulation/computer-codes/silo
+	pkgrel = 2
+	url = https://llnl.github.io/Silo
 	arch = x86_64
 	license = BSD
 	makedepends = gcc-fortran
 	depends = qt5-base
 	depends = hdf5-openmpi
-	source = https://wci.llnl.gov/sites/wci/files/2021-09/silo-4.11-bsd.tgz
-	source = skip-test.patch
+	source = https://github.com/LLNL/Silo/releases/download/v4.11/silo-4.11-bsd.tar.gz
 	source = hdf5.patch
+	source = hdf5-1.13.patch
 	sha256sums = 6d0a85a079d48fcdcc0084ecb5fc4cfdcc64852edee780c60cb244d16f4bc4ec
-	sha256sums = 83e50ccad8477ae7549ae68ab12b180e268e1f28b589b699090dbefb59f57e8b
 	sha256sums = 8acf1a54c3ba21699a9f1cd67aabc806643630e80795bcf9524f7eb874116bb5
+	sha256sums = fc94f615155dcb8e27c73c1f19392415081d25082fd11a7666df1886556ce368
 
 pkgname = silo
diff --git a/PKGBUILD b/PKGBUILD
index 673969984fc5..238b450062fc 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,4 +1,4 @@
-# Maintainer:  Anton Kudelin <kudelin at protonmail dot com>
+# Maintainer:  Anton Kudelin <kudelin at proton dot me>
 # Contributor: eolianoe <eolianoe [at] gmail [DoT] com>
 # Contributor: Carl Rogers <carl.rogers@gmail.com>
 # Contributor: Jed Brown <jed@59A2.org>
@@ -6,24 +6,24 @@
 
 pkgname=silo
 pkgver=4.11
-pkgrel=1
+pkgrel=2
 pkgdesc="A Mesh and Field I/O Library and Scientific Database"
-url="https://wci.llnl.gov/simulation/computer-codes/silo"
-arch=('x86_64')
-depends=('qt5-base' 'hdf5-openmpi')
-makedepends=('gcc-fortran')
-license=('BSD')
-source=("https://wci.llnl.gov/sites/wci/files/2021-09/$pkgname-$pkgver-bsd.tgz"
-        "skip-test.patch"
-        "hdf5.patch")
+url="https://llnl.github.io/Silo"
+arch=(x86_64)
+depends=(qt5-base hdf5-openmpi)
+makedepends=(gcc-fortran)
+license=(BSD)
+source=(https://github.com/LLNL/Silo/releases/download/v$pkgver/$pkgname-$pkgver-bsd.tar.gz
+        hdf5.patch
+        hdf5-1.13.patch)
 sha256sums=('6d0a85a079d48fcdcc0084ecb5fc4cfdcc64852edee780c60cb244d16f4bc4ec'
-            '83e50ccad8477ae7549ae68ab12b180e268e1f28b589b699090dbefb59f57e8b'
-            '8acf1a54c3ba21699a9f1cd67aabc806643630e80795bcf9524f7eb874116bb5')
+            '8acf1a54c3ba21699a9f1cd67aabc806643630e80795bcf9524f7eb874116bb5'
+            'fc94f615155dcb8e27c73c1f19392415081d25082fd11a7666df1886556ce368')
 
 prepare() {
   cd "$srcdir/$pkgname-$pkgver-bsd"
   patch -p0 < ../hdf5.patch
-  patch -p0 < "$srcdir/skip-test.patch"
+  patch -p1 < ../hdf5-1.13.patch
   sed -i 's@rocket_silo.lo@rocket_silo.lo ../src/libsiloh5.la@' \
     tests/Makefile.in
 }
@@ -31,28 +31,23 @@ prepare() {
 build() {
   cd "$srcdir/$pkgname-$pkgver-bsd"
   ./configure \
-            --prefix=/usr \
-            --enable-shared \
-            --enable-optimization \
-            --enable-silex \
-            --enable-install-lite-headers \
-            --with-x \
-            --with-hdf5=/usr/include,/usr/lib \
-            --with-Qt-include-dir=/usr/include/qt \
-            --with-szlib=/usr/lib \
-            --with-zlib=/usr/include,/usr/lib \
-            CFLAGS="$CFLAGS -Wno-error=format-security" \
-            CXXFLAGS="-I/usr/include/qt/QtWidgets $CXXFLAGS -fPIC" \
-            FFLAGS="$FFLAGS -fallow-argument-mismatch" \
-            LIBS='-L/usr/lib/openmpi -lmpi -lQt5Core -lQt5Gui -lQt5Widgets'
+    --prefix=/usr \
+    --enable-shared \
+    --enable-optimization \
+    --enable-silex \
+    --enable-install-lite-headers \
+    --with-x \
+    --with-hdf5=/usr/include,/usr/lib \
+    --with-Qt-include-dir=/usr/include/qt \
+    --with-szlib=/usr/lib \
+    --with-zlib=/usr/include,/usr/lib \
+    CFLAGS="$CFLAGS -Wno-error=format-security" \
+    CXXFLAGS="-I/usr/include/qt/QtWidgets $CXXFLAGS -fPIC" \
+    FFLAGS="$FFLAGS -fallow-argument-mismatch" \
+    LIBS='-L/usr/lib/openmpi -lmpi -lQt5Core -lQt5Gui -lQt5Widgets'
   make
 }
 
-check(){
-  cd "$srcdir/$pkgname-$pkgver-bsd"
-  make check CXXFLAGS="$CXXFLAGS -std=c++98"
-}
-
 package(){
   cd "$srcdir/$pkgname-$pkgver-bsd"
   make DESTDIR="$pkgdir" install
diff --git a/hdf5-1.13.patch b/hdf5-1.13.patch
new file mode 100644
index 000000000000..161bc769f646
--- /dev/null
+++ b/hdf5-1.13.patch
@@ -0,0 +1,37 @@
+From 5dc160c7ae489b8181874dccf7ce3b8089c128f5 Mon Sep 17 00:00:00 2001
+From: Chuck Atkins <chuck.atkins@kitware.com>
+Date: Tue, 24 May 2022 10:57:29 -0400
+Subject: [PATCH] hdf5: Support the API changes in >= 1.13
+
+---
+ src/hdf5_drv/H5FDsilo.c | 10 ++++++++++
+ 1 file changed, 10 insertions(+)
+
+diff --git a/src/hdf5_drv/H5FDsilo.c b/src/hdf5_drv/H5FDsilo.c
+index f4540456..74594c1b 100644
+--- a/src/hdf5_drv/H5FDsilo.c
++++ b/src/hdf5_drv/H5FDsilo.c
+@@ -550,6 +550,12 @@ typedef struct H5FD_class_t {
+ #endif
+ 
+ static const H5FD_class_t H5FD_silo_g = {
++#if HDF5_VERSION_GE(1,13,2) && defined(H5FD_CLASS_VERSION)
++    H5FD_CLASS_VERSION,                         /*version               */
++#endif
++#if HDF5_VERSION_GE(1,13,0)
++    512,                                        /*value                 */
++#endif
+     "silo",				        /*name			*/
+     MAXADDR,				        /*maxaddr		*/
+     H5F_CLOSE_WEAK,				/* fc_degree		*/
+@@ -583,6 +589,10 @@ static const H5FD_class_t H5FD_silo_g = {
+     H5FD_silo_truncate,				/*truncate		*/
+     NULL,                                       /*lock                  */
+     NULL,                                       /*unlock                */
++#if HDF5_VERSION_GE(1,13,0)
++    NULL,                                       /*del                   */
++    NULL,                                       /*ctl                   */
++#endif
+     H5FD_FLMAP_SINGLE				/*fl_map		*/
+ };
+ 
diff --git a/skip-test.patch b/skip-test.patch
deleted file mode 100644
index 27b77b829ede..000000000000
--- a/skip-test.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- tests/testsuite.at	2016-02-26 12:52:54.249108829 +0100
-+++ tests/testsuite.at	2016-02-26 12:58:44.184478494 +0100
-@@ -242,7 +242,7 @@
- AT_CLEANUP
- AT_SETUP(write objects)
- AT_KEYWORDS(python)
--AT_CHECK(test -z "$PYTHON" -o -z "$BROWSER" && exit 77 || $VALGRIND testonehex `pwd`,,ignore,ignore)
-+AT_CHECK(test false && exit 77 || $VALGRIND testonehex `pwd`,,ignore,ignore)
- AT_CLEANUP
- 
- AT_BANNER(JSON (experimental))
---- tests/testsuite.at	2018-07-04 20:07:16.559992474 +0200
-+++ tests/testsuite.at	2018-07-04 20:07:10.693169683 +0200
-@@ -183,7 +183,7 @@
- AT_CHECK($VALGRIND csg $STARGS,,ignore)
- AT_CLEANUP
- AT_SETUP(rocket)
--AT_CHECK($VALGRIND rocket $STARGS,,ignore)
-+AT_CHECK(test false && exit 77 || $VALGRIND rocket $STARGS,,ignore)
- AT_CLEANUP
- AT_SETUP(mmadjacency)
- AT_CHECK($VALGRIND mmadjacency $STARGS,,ignore)