From 94fea21b214a9111c5c8155bfebdad13114df95f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludovic.courtes@inria.fr>
Date: Fri, 13 Dec 2019 13:44:51 +0100
Subject: gnu: hdf5@1.10: Update to 1.10.5.

* gnu/packages/maths.scm (hdf5-1.10): Update to 1.10.5.  Remove
"hdf5-mpi-deprecations.patch".
* gnu/packages/patches/hdf5-mpi-deprecations.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/packages/maths.scm                           |  7 ++-
 gnu/packages/patches/hdf5-mpi-deprecations.patch | 61 ------------------------
 2 files changed, 3 insertions(+), 65 deletions(-)
 delete mode 100644 gnu/packages/patches/hdf5-mpi-deprecations.patch

(limited to 'gnu/packages')

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 8364d528fd..0ed61ad4a1 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -925,7 +925,7 @@ extremely large and complex data collections.")
 
 (define-public hdf5-1.10
   (package (inherit hdf5)
-    (version "1.10.4")
+    (version "1.10.5")
     (source
      (origin
       (method url-fetch)
@@ -939,9 +939,8 @@ extremely large and complex data collections.")
                                        (take (string-split version #\.) 2))
                                 "/src/hdf5-" version ".tar.bz2")))
       (sha256
-       (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
-      (patches (search-patches "hdf5-config-date.patch"
-                               "hdf5-mpi-deprecations.patch"))))))
+       (base32 "0i3g6v521vigzbx8wpd32ibsiiw92r65ca3qdbn0d8fj8f4fmmk8"))
+      (patches (search-patches "hdf5-config-date.patch"))))))
 
 (define-public hdf-java
   (package
diff --git a/gnu/packages/patches/hdf5-mpi-deprecations.patch b/gnu/packages/patches/hdf5-mpi-deprecations.patch
deleted file mode 100644
index eb5d1cb681..0000000000
--- a/gnu/packages/patches/hdf5-mpi-deprecations.patch
+++ /dev/null
@@ -1,61 +0,0 @@
---- a/src/H5.c
-+++ b/src/H5.c
-@@ -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)
---- hdf5-1.10.4/testpar/t_cache.c
-+++ hdf5-1.10.4/testpar/t_cache.c
-@@ -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);
-             }
-         }
-- 
cgit v1.2.3