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02/04: gnu: hdf5: Remove use of deprecated MPI1 symbols.
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From: |
guix-commits |
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Subject: |
02/04: gnu: hdf5: Remove use of deprecated MPI1 symbols. |
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Date: |
Thu, 7 Feb 2019 22:21:48 -0500 (EST) |
bavier pushed a commit to branch master
in repository guix.
commit 7fedc3fdfb5fba8098c08d04a7d0cb7131c24a79
Author: Eric Bavier <address@hidden>
Date: Wed Feb 6 15:32:22 2019 -0600
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.
---
gnu/local.mk | 2 +
gnu/packages/maths.scm | 6 +-
.../patches/hdf5-1.8-mpi-deprecations.patch | 169 +++++++++++++++++++++
gnu/packages/patches/hdf5-mpi-deprecations.patch | 61 ++++++++
4 files changed, 236 insertions(+), 2 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index 785e49a..f1bcef2 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 10b0978..402b53c 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 0000000..29242dc
--- /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 0000000..eb5d1cb
--- /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);
+ }
+ }