updpkg: 4.11

5 files changed, 59 insertions, 198 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 9fe7596e0390..319d61e480f0 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,21 +1,18 @@
 pkgbase = silo
 	pkgdesc = A Mesh and Field I/O Library and Scientific Database
-	pkgver = 4.10.2
-	pkgrel = 10
+	pkgver = 4.11
+	pkgrel = 1
 	url = https://wci.llnl.gov/simulation/computer-codes/silo
 	arch = x86_64
 	license = BSD
 	makedepends = gcc-fortran
 	depends = qt5-base
 	depends = hdf5-openmpi
-	source = https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.10.2/silo-4.10.2-bsd.tar.gz
-	source = remove-mpiposix.patch
+	source = https://wci.llnl.gov/sites/wci/files/2021-09/silo-4.11-bsd.tgz
 	source = skip-test.patch
-	source = qt5.patch
-	sha256sums = 4b901dfc1eb4656e83419a6fde15a2f6c6a31df84edfad7f1dc296e01b20140e
-	sha256sums = 824be92ba71e8d797c5836545c58c2c67de0f296b69e8efd9cb9e8ae206837b8
+	source = hdf5.patch
+	sha256sums = 6d0a85a079d48fcdcc0084ecb5fc4cfdcc64852edee780c60cb244d16f4bc4ec
 	sha256sums = 83e50ccad8477ae7549ae68ab12b180e268e1f28b589b699090dbefb59f57e8b
-	sha256sums = 7928c311e238f4d53176f69b75d8099d786b4526fa81fc6c6f565b04c80d5915
+	sha256sums = 8acf1a54c3ba21699a9f1cd67aabc806643630e80795bcf9524f7eb874116bb5
 
 pkgname = silo
-
diff --git a/PKGBUILD b/PKGBUILD
index f60cfac5b6ed..d16b824c5d78 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,32 +1,29 @@
-# Maintainer: Anton Kudelin <kudelin at protonmail dot com>
+# Maintainer:  Anton Kudelin <kudelin at protonmail dot com>
 # Contributor: eolianoe <eolianoe [at] gmail [DoT] com>
 # Contributor: Carl Rogers <carl.rogers@gmail.com>
 # Contributor: Jed Brown <jed@59A2.org>
 # Contributor: Brenden Mervin <bmervin@utk.edu>
 
 pkgname=silo
-pkgver=4.10.2
-pkgrel=10
+pkgver=4.11
+pkgrel=1
 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/content/assets/docs/simulation/computer-codes/$pkgname/$pkgname-$pkgver/$pkgname-$pkgver-bsd.tar.gz"
-        "remove-mpiposix.patch"
+source=("https://wci.llnl.gov/sites/wci/files/2021-09/$pkgname-$pkgver-bsd.tgz"
         "skip-test.patch"
-        "qt5.patch")
-sha256sums=('4b901dfc1eb4656e83419a6fde15a2f6c6a31df84edfad7f1dc296e01b20140e'
-            '824be92ba71e8d797c5836545c58c2c67de0f296b69e8efd9cb9e8ae206837b8'
+        "hdf5.patch")
+sha256sums=('6d0a85a079d48fcdcc0084ecb5fc4cfdcc64852edee780c60cb244d16f4bc4ec'
             '83e50ccad8477ae7549ae68ab12b180e268e1f28b589b699090dbefb59f57e8b'
-            '7928c311e238f4d53176f69b75d8099d786b4526fa81fc6c6f565b04c80d5915')
+            '8acf1a54c3ba21699a9f1cd67aabc806643630e80795bcf9524f7eb874116bb5')
 
 prepare() {
   cd "$srcdir/$pkgname-$pkgver-bsd"
-  patch -p0 < "$srcdir/remove-mpiposix.patch"
+  patch -p0 < ../hdf5.patch
   patch -p0 < "$srcdir/skip-test.patch"
-  patch -p0 < "$srcdir/qt5.patch"
   sed -i 's@rocket_silo.lo@rocket_silo.lo ../src/libsiloh5.la@' tests/Makefile.in
 }
 
@@ -43,6 +40,7 @@ build() {
             --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'
diff --git a/hdf5.patch b/hdf5.patch
new file mode 100644
index 000000000000..3a518475021e
--- /dev/null
+++ b/hdf5.patch
@@ -0,0 +1,44 @@
+--- src/hdf5_drv/H5FDsilo.c	2021-09-11 01:22:52.000000000 +0300
++++ src/hdf5_drv/H5FDsilo.c	2021-11-25 00:37:06.685422949 +0200
+@@ -252,13 +252,13 @@
+         snprintf(msg, sizeof(msg), Msg "(errno=%d, \"%s\")",	\
+             Errno, strerror(Errno));					\
+     ret_value = Ret;							\
+-    H5Epush_ret(Func, Cls, Maj, Min, msg, Ret)				\
++    H5Epush_ret(Func, Cls, Maj, Min, msg, Ret);				\
+ }
+ #else
+ #define H5E_PUSH_HELPER(Func,Cls,Maj,Min,Msg,Ret,Errno)			\
+ {									\
+     ret_value = Ret;							\
+-    H5Epush_ret(Func, Cls, Maj, Min, Msg, Ret)				\
++    H5Epush_ret(Func, Cls, Maj, Min, Msg, Ret);				\
+ }
+ #endif
+ 
+@@ -1355,7 +1355,7 @@
+     assert(sizeof(hsize_t)<=8);
+     memcpy(p, &file->block_size, sizeof(hsize_t));
+     if (H5Tconvert(H5T_NATIVE_HSIZE, H5T_STD_U64LE, 1, buf+8, NULL, H5P_DEFAULT)<0)
+-        H5Epush_ret(func, H5E_ERR_CLS, H5E_DATATYPE, H5E_CANTCONVERT, "can't convert superblock info", -1)
++        H5Epush_ret(func, H5E_ERR_CLS, H5E_DATATYPE, H5E_CANTCONVERT, "can't convert superblock info", -1);
+ 
+     return 0;
+ }
+@@ -1383,14 +1383,14 @@
+ 
+     /* Make sure the name/version number is correct */
+     if (strcmp(name, "LLNLsilo"))
+-        H5Epush_ret(func, H5E_ERR_CLS, H5E_FILE, H5E_BADVALUE, "invalid silo superblock", -1)
++        H5Epush_ret(func, H5E_ERR_CLS, H5E_FILE, H5E_BADVALUE, "invalid silo superblock", -1);
+ 
+     buf += 8;
+     /* Decode block size */
+     assert(sizeof(hsize_t)<=8);
+     memcpy(x, buf, 8);
+     if (H5Tconvert(H5T_STD_U64LE, H5T_NATIVE_HSIZE, 1, x, NULL, H5P_DEFAULT)<0)
+-        H5Epush_ret(func, H5E_ERR_CLS, H5E_DATATYPE, H5E_CANTCONVERT, "can't convert superblock info", -1)
++        H5Epush_ret(func, H5E_ERR_CLS, H5E_DATATYPE, H5E_CANTCONVERT, "can't convert superblock info", -1);
+     ap = (hsize_t*)x;
+     /*file->block_size = *ap; ignore stored value for now */
+ 
diff --git a/qt5.patch b/qt5.patch
deleted file mode 100644
index 8b43520dc39a..000000000000
--- a/qt5.patch
+++ /dev/null
@@ -1,140 +0,0 @@
-diff --color -Naur silex/main.cpp silex/main.cpp
---- tools/silex/main.cpp	2020-12-11 18:03:35.497787357 +0300
-+++ tools/silex/main.cpp	2020-12-11 18:03:50.058496239 +0300
-@@ -58,7 +58,7 @@
- #include <cstdlib>
- 
- #ifndef Q_WS_MACX
--#include "qwindowsstyle.h"
-+#include "qproxystyle.h"
- #endif
- #include "qfiledialog.h"
- #include "qstring.h"
-@@ -91,7 +91,7 @@
-     QApplication::setColorSpec(QApplication::ManyColor);
-     QApplication a(argc, argv);
- #ifndef Q_WS_MACX
--    a.setStyle(new QWindowsStyle);
-+    a.setStyle(new QProxyStyle);
- #endif
-     Explorer *w = 0;
-     if (argc > 1)
-diff --color -Naur silex/SiloFile.cpp silex/SiloFile.cpp
---- tools/silex/SiloFile.cpp	2020-12-11 18:03:35.497787357 +0300
-+++ tools/silex/SiloFile.cpp	2020-12-11 18:03:50.058496239 +0300
-@@ -97,7 +97,7 @@
-     int drt = DBGetDriverType(db);
-     if (canCallFreeCompression[drt] && DBFreeCompressionResources(db,0) == -1)
-         canCallFreeCompression[drt] = false;
--    DBSetDir(db, (const char*)path.toAscii());
-+    DBSetDir(db, (const char*)path.toUtf8());
-     DBtoc *toc = DBGetToc(db);
- 
-     int i;
-@@ -204,7 +204,7 @@
- // ****************************************************************************
- SiloFile::SiloFile(const QString &name)
- {
--    db = DBOpen((const char*)name.toAscii(), DB_UNKNOWN, DB_READ);
-+    db = DBOpen((const char*)name.toUtf8(), DB_UNKNOWN, DB_READ);
-     if (db)
-         root = new SiloDir(db, "/", "/");
-     else
-@@ -247,47 +247,47 @@
- void*
- SiloFile::GetVar(const QString &name)
- {
--    return DBGetVar(db, (const char*)name.toAscii());
-+    return DBGetVar(db, (const char*)name.toUtf8());
- }
- 
- int
- SiloFile::GetVarType(const QString &name)
- {
--    return DBGetVarType(db, (const char*)name.toAscii());
-+    return DBGetVarType(db, (const char*)name.toUtf8());
- }
- 
- int
- SiloFile::GetVarLength(const QString &name)
- {
--    return DBGetVarLength(db, (const char*)name.toAscii());
-+    return DBGetVarLength(db, (const char*)name.toUtf8());
- }
- 
- DBobject*
- SiloFile::GetObject(const QString &name)
- {
--    return DBGetObject(db, (const char*)name.toAscii());
-+    return DBGetObject(db, (const char*)name.toUtf8());
- }
- 
- void*
- SiloFile::GetComponent(const QString &oname, const QString &cname)
- {
--    return DBGetComponent(db, (const char*)oname.toAscii(), (const char*)cname.toAscii());
-+    return DBGetComponent(db, (const char*)oname.toUtf8(), (const char*)cname.toUtf8());
- }
- 
- int
- SiloFile::GetComponentType(const QString &oname, const QString &cname)
- {
--    return DBGetComponentType(db, (const char*)oname.toAscii(), (const char*)cname.toAscii());
-+    return DBGetComponentType(db, (const char*)oname.toUtf8(), (const char*)cname.toUtf8());
- }
- 
- DBObjectType
- SiloFile::InqVarType(const QString &name)
- {
--    return DBInqVarType(db, (const char*)name.toAscii());
-+    return DBInqVarType(db, (const char*)name.toUtf8());
- }
- 
- bool
- SiloFile::InqVarExists(const QString &name)
- {
--    return DBInqVarExists(db, (const char*)name.toAscii());
-+    return DBInqVarExists(db, (const char*)name.toUtf8());
- }
-diff --color -Naur silex/SiloObjectView.cpp silex/SiloObjectView.cpp
---- tools/silex/SiloObjectView.cpp	2020-12-11 18:03:35.497787357 +0300
-+++ tools/silex/SiloObjectView.cpp	2020-12-11 18:03:50.058496239 +0300
-@@ -177,8 +177,8 @@
-         void *comp = silo->GetComponent(name, compname);
-         if (!comp)
-         {
--            const char *asciiname = name.toAscii();
--            const char *asciicomp = compname.toAscii();
-+            const char *asciiname = name.toUtf8();
-+            const char *asciicomp = compname.toUtf8();
-             std::cerr << "ERROR: DBGetComponent failed for object '"
-                       << asciiname
-                       <<"', component '"
-@@ -230,11 +230,11 @@
-             break;
-           default:
-             typestr = "var";
--            std::string valStr = std::string(pdbname.toAscii());
-+            std::string valStr = std::string(pdbname.toUtf8());
-             if (pdbname.indexOf("'<s>") == 0)
-             {
-                 int len = pdbname.length();
--                valStr = std::string((const char*)(pdbname.toAscii()),4,len-5);
-+                valStr = std::string((const char*)(pdbname.toUtf8()),4,len-5);
-             }
-             sprintf(value, "%s", valStr.c_str());
-             break;
-diff --color -Naur silex/SiloView.cpp silex/SiloView.cpp
---- tools/silex/SiloView.cpp	2020-12-11 18:03:35.497787357 +0300
-+++ tools/silex/SiloView.cpp	2020-12-11 18:03:50.058496239 +0300
-@@ -109,8 +109,8 @@
-         dirTreeView->OpenRootDir();
-         dirView->Set(silo->root);
- 
--        dirTreeView->header()->setResizeMode(QHeaderView::Interactive);
--        dirView->header()->setResizeMode(QHeaderView::Interactive);
-+        dirTreeView->header()->setSectionResizeMode(QHeaderView::Interactive);
-+        dirView->header()->setSectionResizeMode(QHeaderView::Interactive);
-     }
- }
- 
diff --git a/remove-mpiposix.patch b/remove-mpiposix.patch
deleted file mode 100644
index ca611e3a335e..000000000000
--- a/remove-mpiposix.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- src/hdf5_drv/silo_hdf5.c
-+++ src/hdf5_drv/silo_hdf5.c
-@@ -4717,16 +4717,7 @@ db_hdf5_process_file_options(opts_set_id
- 
-         /* default HDF5 mpi drivers */
-         case DB_FILE_OPTS_H5_DEFAULT_MPIP:
--        {
--#ifdef H5_HAVE_PARALLEL
--            h5status |= H5Pset_fapl_mpiposix(retval, MPI_COMM_SELF, TRUE);
--#else
--            H5Pclose(retval);
--            return db_perror("HDF5 MPI VFD", E_NOTENABLEDINBUILD, me);
--#endif
--            break;
--        }
--
-+        /* FALLTHROUGH */
-         case DB_FILE_OPTS_H5_DEFAULT_MPIO:
-         {
- #ifdef H5_HAVE_PARALLEL
-@@ -4963,15 +4954,8 @@ db_hdf5_process_file_options(opts_set_id
-                     if (p = DBGetOption(opts, DBOPT_H5_MPIP_NO_GPFS_HINTS))
-                         use_gpfs_hints = FALSE;
- 
--                    if (vfd == DB_H5VFD_MPIO)
--                    {
--                        h5status |= H5Pset_fapl_mpio(retval, mpi_comm, mpi_info);
--                        if (created_info) MPI_Info_free(&mpi_info);
--                    }
--                    else
--                    {
--                        h5status |= H5Pset_fapl_mpiposix(retval, mpi_comm, use_gpfs_hints);
--                    }
-+                    h5status |= H5Pset_fapl_mpio(retval, mpi_comm, mpi_info);
-+                    if (created_info) MPI_Info_free(&mpi_info);
- #else 
-                     H5Pclose(retval);
-                     return db_perror("HDF5 MPI VFD", E_NOTENABLEDINBUILD, me);