gnu: hdf5: Update to 1.8.22.
Fixes CVE-2018-14033, CVE-2018-11206, CVE-2018-13870, CVE-2018-13869, and CVE-2018-17435 * gnu/packages/maths.scm (hdf5-1.8): Update to 1.8.22. * gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch: Delete upstreamed patch. * gnu/local/mk (dist_patch_DATA): Remove it.
This commit is contained in:
parent
a613abeb43
commit
8effdd1969
|
@ -1156,7 +1156,6 @@ dist_patch_DATA = \
|
|||
%D%/packages/patches/hdf4-shared-fortran.patch \
|
||||
%D%/packages/patches/hdf4-tirpc.patch \
|
||||
%D%/packages/patches/hdf5-config-date.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 \
|
||||
|
|
|
@ -2,7 +2,7 @@
|
|||
;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020 Andreas Enge <andreas@enge.fr>
|
||||
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
|
||||
;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
|
||||
;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Eric Bavier <bavier@posteo.net>
|
||||
;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Eric Bavier <bavier@posteo.net>
|
||||
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
|
||||
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
|
||||
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
|
||||
|
@ -1077,7 +1077,7 @@ (define-public hdf4-alt
|
|||
(define-public hdf5-1.8
|
||||
(package
|
||||
(name "hdf5")
|
||||
(version "1.8.21")
|
||||
(version "1.8.22")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
|
@ -1092,9 +1092,8 @@ (define-public hdf5-1.8
|
|||
(string-append major minor)))
|
||||
"/src/hdf5-" version ".tar.bz2")))
|
||||
(sha256
|
||||
(base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
|
||||
(patches (search-patches "hdf5-config-date.patch"
|
||||
"hdf5-1.8-mpi-deprecations.patch"))))
|
||||
(base32 "194ki2s5jrgl4czkvy5nc9nwjyapah0fj72l0gb0aysplp38i6v8"))
|
||||
(patches (search-patches "hdf5-config-date.patch"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("zlib" ,zlib)))
|
||||
|
|
|
@ -1,169 +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)
|
||||
--- hdf5-1.8.19/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){
|
Loading…
Reference in a new issue