gnu: hdf5: Remove use of deprecated MPI1 symbols.

* gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch,
  gnu/packages/patches/hdf5-mpi-deprecations.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/maths.scm (hdf5, hdf5-1.10)[source]: Use them.

1 files changed, 61 insertions, 0 deletions

diff --git a/gnu/packages/patches/hdf5-mpi-deprecations.patch b/gnu/packages/patches/hdf5-mpi-deprecations.patch
new file mode 100644
index 0000000000..eb5d1cb681
--- /dev/null
+++ b/gnu/packages/patches/hdf5-mpi-deprecations.patch
@@ -0,0 +1,61 @@
+--- 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);
+             }
+         }