upgrade to v1.10.5

3 files changed, 9 insertions, 121 deletions

diff --git a/.SRCINFO b/.SRCINFO
index bcd44dab9ed4..6d6669cb7aad 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
 pkgbase = hdf5-openmpi-java
 	pkgdesc = General purpose library and file format for storing scientific data (openmpi version) (full version including its Java Native Interfaces)
-	pkgver = 1.10.4
-	pkgrel = 3
+	pkgver = 1.10.5
+	pkgrel = 1
 	url = https://portal.hdfgroup.org/display/support
 	arch = x86_64
 	license = custom
@@ -22,12 +22,10 @@ pkgbase = hdf5-openmpi-java
 	conflicts = hdf5-openmpi
 	replaces = hdf5-fortran-openmpi
 	options = staticlibs
-	source = https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.4/src/hdf5-1.10.4.tar.bz2
+	source = https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.bz2
 	source = mpi.patch
-	source = mpi4.patch
-	md5sums = 886148d0cc9ffd3c8e1fce0bd75ed07b
+	md5sums = 7c19d6b81ee2a3ba7d36f6922b2f90d3
 	md5sums = 63b43e3d4a5bbea4bcecc84874e08913
-	md5sums = 5b981fb1c802d5cacd46af23162ff410
 
 pkgname = hdf5-openmpi-java
 
diff --git a/PKGBUILD b/PKGBUILD
index 82d59352ce97..c9e3e9d5b742 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -13,8 +13,8 @@ _pkgname=hdf5
 _mpi=openmpi
 pkgname=${_pkgname}-${_mpi}-java
 _prefix=/usr
-pkgver=1.10.4
-pkgrel=3
+pkgver=1.10.5
+pkgrel=1
 pkgdesc="General purpose library and file format for storing scientific data (${_mpi} version) (full version including its Java Native Interfaces)"
 arch=('x86_64')
 url="https://portal.hdfgroup.org/display/support"
@@ -26,11 +26,9 @@ provides=('hdf5-java' 'hdf5-openmpi' 'hdf5' 'hdf5-cpp-fortran' "hdf5-fortran-${_
 conflicts=('hdf5-java' 'hdf5' 'hdf5-openmpi')
 replaces=("hdf5-fortran-${_mpi}")
 source=("https://support.hdfgroup.org/ftp/HDF5/releases/${_pkgname}-${pkgver:0:4}/${_pkgname}-${pkgver}/src/${_pkgname}-${pkgver}.tar.bz2"
-        'mpi.patch'
-        'mpi4.patch')
-md5sums=('886148d0cc9ffd3c8e1fce0bd75ed07b'
-         '63b43e3d4a5bbea4bcecc84874e08913'
-         '5b981fb1c802d5cacd46af23162ff410')
+        'mpi.patch')
+md5sums=('7c19d6b81ee2a3ba7d36f6922b2f90d3'
+         '63b43e3d4a5bbea4bcecc84874e08913')
 
 prepare() {
     mkdir -p build
@@ -38,9 +36,6 @@ prepare() {
 
     # FS#33343
     patch -p1 -i ../mpi.patch
-
-    # patch for MPI4 compatibility
-    patch -p1 -i ../mpi4.patch
 }
 
 build() {
@@ -106,9 +101,6 @@ package() {
 
     make DESTDIR="${pkgdir}" install
 
-    # Remove leftover test files
-    rm "${pkgdir}${_prefix}"/include/tst{ds,image,lite,table}{,_tests}.mod
-
     # Move examples to a proper place
     install -dm755 "${pkgdir}${_prefix}/share/doc/${_pkgname}"
     mv "${pkgdir}${_prefix}"/share/{hdf5_examples,doc/${_pkgname}/examples}
diff --git a/mpi4.patch b/mpi4.patch
deleted file mode 100644
index a816701222fd..000000000000
--- a/mpi4.patch
+++ /dev/null
@@ -1,102 +0,0 @@
---- A/src/H5Smpio.c	2018-09-04 04:54:44.000000000 +0200
-+++ B/src/H5Smpio.c	2018-11-22 16:58:44.365923064 +0100
-@@ -859,7 +859,7 @@
-           *   (2GB-1)number_of_blocks * the_datatype_extent.
-           */
- 
--            MPI_Aint stride_in_bytes, inner_extent;
-+            MPI_Aint stride_in_bytes, inner_extent, lower_bound;
-             MPI_Datatype block_type;
- 
-             /* create a contiguous datatype inner_type x number of BLOCKS.
-@@ -879,7 +879,7 @@
-                     HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code)
-             }
- 
--            MPI_Type_extent (inner_type, &inner_extent);
-+            MPI_Type_get_extent (inner_type, &lower_bound, &inner_extent);
-             stride_in_bytes = inner_extent * (MPI_Aint)d[i].strid;
- 
-             /* If the element count is larger than what a 32 bit integer can hold,
-@@ -1424,7 +1424,7 @@
-     int           block_len[2];
-     int           mpi_code;               /* MPI return code */
-     MPI_Datatype  inner_type, outer_type, leftover_type, type[2];
--    MPI_Aint      disp[2], old_extent;
-+    MPI_Aint      disp[2], old_extent, lower_bound;
-     herr_t        ret_value = SUCCEED;    /* Return value */
- 
-     FUNC_ENTER_NOAPI_NOINIT
-@@ -1500,9 +1500,9 @@
-             }
-         }
- 
--        MPI_Type_extent (old_type, &old_extent);
-+        MPI_Type_get_extent (old_type, &lower_bound, &old_extent);
- 
--        /* Set up the arguments for MPI_Type_struct constructor */
-+        /* Set up the arguments for MPI_Type_create_struct constructor */
-         type[0] = outer_type;
-         type[1] = leftover_type;
-         block_len[0] = 1;
---- A/src/H5.c	2018-10-05 07:21:51.000000000 +0200
-+++ B/src/H5.c	2018-11-22 16:52:52.353016751 +0100
-@@ -138,7 +138,7 @@
-         if (mpi_initialized && !mpi_finalized) {
-             int key_val;
- 
--            if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_NULL_COPY_FN, 
-+            if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN, 
-                                                                  (MPI_Comm_delete_attr_function *)H5_mpi_delete_cb, 
-                                                                  &key_val, NULL)))
-                 HMPI_GOTO_ERROR(FAIL, "MPI_Comm_create_keyval failed", mpi_code)
---- A/testpar/t_cache.c	2018-09-10 16:43:41.000000000 +0200
-+++ B/testpar/t_cache.c	2018-11-22 16:58:45.405881436 +0100
-@@ -1217,20 +1217,20 @@
-     struct mssg_t sample; /* used to compute displacements */
- 
-     /* setup the displacements array */
--    if ( ( MPI_SUCCESS != MPI_Address(&sample.req, &displs[0]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.src, &displs[1]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.dest, &displs[2]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.mssg_num, &displs[3]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.base_addr, &displs[4]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.len, &displs[5]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.ver, &displs[6]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.count, &displs[7]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.magic, &displs[8]) ) ) {
-+    if ( ( MPI_SUCCESS != MPI_Get_address(&sample.req, &displs[0]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.src, &displs[1]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.dest, &displs[2]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.mssg_num, &displs[3]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.base_addr, &displs[4]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.len, &displs[5]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.ver, &displs[6]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.count, &displs[7]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.magic, &displs[8]) ) ) {
- 
-         nerrors++;
-         success = FALSE;
-         if ( verbose ) {
--            HDfprintf(stdout, "%d:%s: MPI_Address() call failed.\n",
-+            HDfprintf(stdout, "%d:%s: MPI_Get_address() call failed.\n",
-                       world_mpi_rank, FUNC);
-         }
- 
-@@ -1245,14 +1245,14 @@
- 
-     if ( success ) {
- 
--        result = MPI_Type_struct(9, block_len, displs, mpi_types, &mpi_mssg_t);
-+        result = MPI_Type_create_struct(9, block_len, displs, mpi_types, &mpi_mssg_t);
- 
-         if ( result != MPI_SUCCESS ) {
- 
-             nerrors++;
-             success = FALSE;
-             if ( verbose ) {
--                HDfprintf(stdout, "%d:%s: MPI_Type_struct() call failed.\n",
-+                HDfprintf(stdout, "%d:%s: MPI_Type_create_struct() call failed.\n",
-                           world_mpi_rank, FUNC);
-             }
-         }