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.

4 files changed, 236 insertions, 2 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index 785e49a774..f1bcef2a68 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -873,6 +873,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/hdf4-reproducibility.patch 		\
   %D%/packages/patches/hdf4-shared-fortran.patch 		\
   %D%/packages/patches/hdf5-config-date.patch			\
+  %D%/packages/patches/hdf5-mpi-deprecations.patch		\
+  %D%/packages/patches/hdf5-1.8-mpi-deprecations.patch		\
   %D%/packages/patches/hdf-eos2-build-shared.patch 		\
   %D%/packages/patches/hdf-eos2-remove-gctp.patch		\
   %D%/packages/patches/hdf-eos2-fortrantests.patch		\
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 10b0978ba0..402b53ca0e 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -764,7 +764,8 @@ incompatible with HDF5.")
                                 "/src/hdf5-" version ".tar.bz2")))
       (sha256
        (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
-      (patches (list (search-patch "hdf5-config-date.patch")))))
+      (patches (search-patches "hdf5-config-date.patch"
+                               "hdf5-1.8-mpi-deprecations.patch"))))
     (build-system gnu-build-system)
     (inputs
      `(("zlib" ,zlib)))
@@ -877,7 +878,8 @@ extremely large and complex data collections.")
                                 "/src/hdf5-" version ".tar.bz2")))
       (sha256
        (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
-      (patches (list (search-patch "hdf5-config-date.patch")))))))
+      (patches (search-patches "hdf5-config-date.patch"
+                               "hdf5-mpi-deprecations.patch"))))))
 
 (define-public hdf-java
   (package
diff --git a/gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch b/gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch
new file mode 100644
index 0000000000..29242dc4e8
--- /dev/null
+++ b/gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch
@@ -0,0 +1,169 @@
+--- 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)
+--- hdf5-1.8.19/testpar/t_cache.c
++++ hdf5-1.8.19/testpar/t_cache.c
+@@ -1187,20 +1187,20 @@
+     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, fcn_name);
+         }
+ 
+@@ -1215,14 +1215,14 @@
+ 
+     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, fcn_name);
+             }
+         }
+--- hdf5-1.8.19/testpar/t_mpi.c
++++ hdf5-1.8.19/testpar/t_mpi.c
+@@ -279,7 +279,7 @@
+ 	printf("Skipped GB file range test "
+ 		"because MPI_Offset cannot support it\n");
+     }else{
+-	buf = HDmalloc(MB);
++	buf = (char *)HDmalloc(MB);
+ 	VRFY((buf!=NULL), "malloc succeed");
+ 
+ 	/* open a new file. Remove it first in case it exists. */
+@@ -624,7 +624,7 @@
+ and this platform.
+ 
+ 1. Details for the test:
+-1) Create two derived datatypes with MPI_Type_hindexed:
++1) Create two derived datatypes with MPI_Type_create_hindexed:
+         datatype1:
+ 	count = 1, blocklens = 1, offsets = 0,
+ 	base type = MPI_BYTE(essentially a char)
+@@ -633,7 +633,7 @@
+ 	base type = MPI_BYTE
+ 
+ 2) Using these two derived datatypes,
+-   Build another derived datatype with MPI_Type_struct:
++   Build another derived datatype with MPI_Type_create_struct:
+         advtype: derived from datatype1 and datatype2
+         advtype:
+ 	count = 2, blocklens[0] = 1, blocklens[1]=1,
+@@ -676,10 +676,9 @@
+     int  mpi_err_strlen;
+     int  mpi_err;
+     int  i;
+-    int  nerrors = 0;		/* number of errors */
+     MPI_Datatype  etype,filetype;
+     MPI_Datatype  adv_filetype,bas_filetype[2];
+-    MPI_Datatype  etypenew, filetypenew;
++    MPI_Datatype  filetypenew;
+     MPI_Offset    disp;
+     MPI_Status    Status;
+     MPI_Aint      adv_disp[2];
+@@ -715,7 +714,7 @@
+     blocklens[0] = 1;
+     offsets[0]   = 0;
+ 
+-    if((mpi_err= MPI_Type_hindexed(count,blocklens,offsets,MPI_BYTE,&filetype))
++    if((mpi_err= MPI_Type_create_hindexed(count,blocklens,offsets,MPI_BYTE,&filetype))
+        != MPI_SUCCESS){
+       	MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen);
+ 	printf("MPI_Type_contiguous failed (%s)\n", mpi_err_str);
+@@ -731,7 +730,7 @@
+     count = 1;
+     blocklens[0]=1;
+     offsets[0] = 1;
+-    if((mpi_err= MPI_Type_hindexed(count,blocklens,offsets,MPI_BYTE,&filetypenew))
++    if((mpi_err= MPI_Type_create_hindexed(count,blocklens,offsets,MPI_BYTE,&filetypenew))
+        != MPI_SUCCESS){
+       	MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen);
+ 	printf("MPI_Type_contiguous failed (%s)\n", mpi_err_str);
+@@ -752,10 +751,10 @@
+     bas_filetype[0]  = filetype;
+     bas_filetype[1]  = filetypenew;
+ 
+-    if((mpi_err= MPI_Type_struct(outcount,adv_blocklens,adv_disp,bas_filetype,&adv_filetype))
++    if((mpi_err= MPI_Type_create_struct(outcount,adv_blocklens,adv_disp,bas_filetype,&adv_filetype))
+        != MPI_SUCCESS){
+       	MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen);
+-	printf("MPI_Type_struct failed (%s)\n", mpi_err_str);
++	printf("MPI_Type_create_struct failed (%s)\n", mpi_err_str);
+ 	return 1;
+     }
+     if((mpi_err=MPI_Type_commit(&adv_filetype))!=MPI_SUCCESS){
+@@ -842,7 +841,7 @@
+ processes are needed.
+ 
+ 1. Details for the test:
+-1) Create one derived datatype with MPI_Type_hindexed:
++1) Create one derived datatype with MPI_Type_create_hindexed:
+ 
+ 2) Choosing at least two processes to contribute none for IO with
+    the buf size inside MPI_Write_at_all to 0.
+@@ -898,7 +897,7 @@
+     offsets[1] = (mpi_size+mpi_rank)*count;
+ 
+     if(count !=0) {
+-        if((mpi_err = MPI_Type_hindexed(2,
++        if((mpi_err = MPI_Type_create_hindexed(2,
+                                         blocklens,
+                                         offsets,
+                                         etype,
+@@ -914,7 +913,7 @@
+             return 1;
+         } /* end if */
+ 
+-        if((mpi_err = MPI_Type_hindexed(2,
++        if((mpi_err = MPI_Type_create_hindexed(2,
+                                         blocklens,
+                                         offsets,
+                                         etype,
+@@ -1098,7 +1097,7 @@
+      * calls.  By then, MPI calls may not work.
+      */
+     if (H5dont_atexit() < 0){
+-	printf("Failed to turn off atexit processing. Continue.\n", mpi_rank);
++	printf("Failed to turn off atexit processing. Continue.\n");
+     };
+     H5open();
+     if (parse_options(argc, argv) != 0){
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);
+             }
+         }