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!76 [sync] PR-74: Update to 1.14.5 for fix cves

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From: @openeuler-sync-bot 
Reviewed-by: @starlet-dx 
Signed-off-by: @starlet-dx
This commit is contained in:
openeuler-ci-bot 2024-11-01 08:28:35 +00:00 committed by Gitee
commit 46936d851e
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14 changed files with 65 additions and 766 deletions
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96
CVE-2018-13867.patch
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@ -1,96 +0,0 @@
From: Egbert Eich <eich@suse.com>
Date: Mon Oct 10 08:43:44 2022 +0200
Subject: Validate location (offset) of the accumulated metadata when comparing
Patch-mainline: Not yet
Git-repo: ssh://eich@192.168.122.1:/home/eich/sources/HPC/hdf5
Git-commit: 2cf9918ae66f023a2b6d44eb591ee2ac479a6e53
References:
Initially, the accumulated metadata location is initialized to HADDR_UNDEF
- the highest available address. Bogus input files may provide a location
or size matching this value. Comparing this address against such bogus
values may provide false positives. This make sure, the value has been
initilized or fail the comparison early and let other parts of the
code deal with the bogus address/size.
Note: To avoid unnecessary checks, we have assumed that if the 'dirty'
member in the same structure is true the location is valid.
This fixes CVE-2018-13867.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Faccum.c | 19 +++++++++++++------
1 file changed, 13 insertions(+), 6 deletions(-)
diff --git a/src/H5Faccum.c b/src/H5Faccum.c
index aed5812e63..73bd4b811e 100644
--- a/src/H5Faccum.c
+++ b/src/H5Faccum.c
@@ -48,6 +48,7 @@
#define H5F_ACCUM_THROTTLE 8
#define H5F_ACCUM_THRESHOLD 2048
#define H5F_ACCUM_MAX_SIZE (1024 * 1024) /* Max. accum. buf size (max. I/Os will be 1/2 this size) */
+#define H5F_LOC_VALID(x) (x != HADDR_UNDEF)
/******************/
/* Local Typedefs */
@@ -126,8 +127,9 @@ H5F__accum_read(H5F_shared_t *f_sh, H5FD_mem_t map_type, haddr_t addr, size_t si
HDassert(!accum->buf || (accum->alloc_size >= accum->size));
/* Current read adjoins or overlaps with metadata accumulator */
- if (H5F_addr_overlap(addr, size, accum->loc, accum->size) || ((addr + size) == accum->loc) ||
- (accum->loc + accum->size) == addr) {
+ if (H5F_LOC_VALID(accum->loc) &&
+ (H5F_addr_overlap(addr, size, accum->loc, accum->size) || ((addr + size) == accum->loc) ||
+ (accum->loc + accum->size) == addr)) {
size_t amount_before; /* Amount to read before current accumulator */
haddr_t new_addr; /* New address of the accumulator buffer */
size_t new_size; /* New size of the accumulator buffer */
@@ -439,7 +441,8 @@ H5F__accum_write(H5F_shared_t *f_sh, H5FD_mem_t map_type, haddr_t addr, size_t s
/* Check if there is already metadata in the accumulator */
if (accum->size > 0) {
/* Check if the new metadata adjoins the beginning of the current accumulator */
- if ((addr + size) == accum->loc) {
+ if (H5F_LOC_VALID(accum->loc)
+ && (addr + size) == accum->loc) {
/* Check if we need to adjust accumulator size */
if (H5F__accum_adjust(accum, file, H5F_ACCUM_PREPEND, size) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTRESIZE, FAIL, "can't adjust metadata accumulator")
@@ -464,7 +467,8 @@ H5F__accum_write(H5F_shared_t *f_sh, H5FD_mem_t map_type, haddr_t addr, size_t s
accum->dirty_off = 0;
} /* end if */
/* Check if the new metadata adjoins the end of the current accumulator */
- else if (addr == (accum->loc + accum->size)) {
+ else if (H5F_LOC_VALID(accum->loc) &&
+ addr == (accum->loc + accum->size)) {
/* Check if we need to adjust accumulator size */
if (H5F__accum_adjust(accum, file, H5F_ACCUM_APPEND, size) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTRESIZE, FAIL, "can't adjust metadata accumulator")
@@ -485,7 +489,8 @@ H5F__accum_write(H5F_shared_t *f_sh, H5FD_mem_t map_type, haddr_t addr, size_t s
accum->size += size;
} /* end if */
/* Check if the piece of metadata being written overlaps the metadata accumulator */
- else if (H5F_addr_overlap(addr, size, accum->loc, accum->size)) {
+ else if (H5F_LOC_VALID(accum->loc) &&
+ H5F_addr_overlap(addr, size, accum->loc, accum->size)) {
size_t add_size; /* New size of the accumulator buffer */
/* Check if the new metadata is entirely within the current accumulator */
@@ -745,7 +750,8 @@ H5F__accum_write(H5F_shared_t *f_sh, H5FD_mem_t map_type, haddr_t addr, size_t s
/* (Note that this could be improved by updating the accumulator
* with [some of] the information just read in. -QAK)
*/
- if (H5F_addr_overlap(addr, size, accum->loc, accum->size)) {
+ if (H5F_LOC_VALID(accum->loc) &&
+ H5F_addr_overlap(addr, size, accum->loc, accum->size)) {
/* Check for write starting before beginning of accumulator */
if (H5F_addr_le(addr, accum->loc)) {
/* Check for write ending within accumulator */
@@ -868,6 +874,7 @@ H5F__accum_free(H5F_shared_t *f_sh, H5FD_mem_t H5_ATTR_UNUSED type, haddr_t addr
/* Adjust the metadata accumulator to remove the freed block, if it overlaps */
if ((f_sh->feature_flags & H5FD_FEAT_ACCUMULATE_METADATA) &&
+ H5F_LOC_VALID(accum->loc) &&
H5F_addr_overlap(addr, size, accum->loc, accum->size)) {
size_t overlap_size; /* Size of overlap with accumulator */

35
CVE-2018-14031.patch
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@ -1,35 +0,0 @@
From: Egbert Eich <eich@suse.com>
Date: Wed Sep 28 14:54:58 2022 +0200
Subject: H5O_dtype_decode_helper: Parent of enum needs to have same size as enum itself
Patch-mainline: Not yet
Git-repo: ssh://eich@192.168.122.1:/home/eich/sources/HPC/hdf5
Git-commit: d39a27113ef75058f236b0606a74b4af5767c4e7
References:
The size of the enumeration values is determined by the size of the parent.
Functions accessing the enumeration values use the size of the enumartion
to determine the size of each element and how much data to copy. Thus the
size of the enumeration and its parent need to match.
Check here to avoid unpleasant surprises later.
This fixes CVE-2018-14031.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Odtype.c | 3 +++
1 file changed, 3 insertions(+)
diff --git a/src/H5Odtype.c b/src/H5Odtype.c
index 9af79f4e9a..dc2b904362 100644
--- a/src/H5Odtype.c
+++ b/src/H5Odtype.c
@@ -472,6 +472,9 @@ H5O__dtype_decode_helper(unsigned *ioflags /*in,out*/, const uint8_t **pp, H5T_t
if (H5O__dtype_decode_helper(ioflags, pp, dt->shared->parent) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTDECODE, FAIL, "unable to decode parent datatype")
+ if (dt->shared->parent->shared->size != dt->shared->size)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTDECODE, FAIL, "ENUM size does not match parent")
+
/* Check if the parent of this enum has a version greater than the
* enum itself. */
H5O_DTYPE_CHECK_VERSION(dt, version, dt->shared->parent->shared->version, ioflags, "enum", FAIL)

34
CVE-2018-16438.patch
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@ -1,34 +0,0 @@
From: Egbert Eich <eich@suse.com>
Date: Sun Oct 9 08:07:23 2022 +0200
Subject: Make sure info block for external links has at least 3 bytes
Patch-mainline: Not yet
Git-repo: ssh://eich@192.168.122.1:/home/eich/sources/HPC/hdf5
Git-commit: 082bfe392b04b1137da9eabd1ecac76c212ab385
References:
According to the specification, the information block for external links
contains 1 byte of version/flag information and two 0 terminated strings
for the object linked to and the full path.
Although not very useful, the minimum string length for each would be one
byte.
This fixes CVE-2018-16438.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Olink.c | 2 ++
1 file changed, 2 insertions(+)
diff --git a/src/H5Olink.c b/src/H5Olink.c
index 51c44a36b0..074744b022 100644
--- a/src/H5Olink.c
+++ b/src/H5Olink.c
@@ -241,6 +241,8 @@ H5O__link_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UNUSE
/* A UD link. Get the user-supplied data */
UINT16DECODE(p, len)
lnk->u.ud.size = len;
+ if (lnk->type == H5L_TYPE_EXTERNAL && len < 3)
+ HGOTO_ERROR(H5E_OHDR, H5E_OVERFLOW, NULL, "external link information lenght < 3")
if (len > 0) {
/* Make sure that length doesn't exceed buffer size, which could
occur when the file is corrupted */

92
CVE-2019-8396.patch
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@ -1,92 +0,0 @@
From 8e5d36c7465699671b89023f752a378f5ee8b7cb Mon Sep 17 00:00:00 2001
From: starlet-dx <15929766099@163.com>
Date: Tue, 28 Mar 2023 17:31:29 +0800
Subject: [PATCH 1/1] H5O__pline_decode() Make more resilient to out-of-bounds read (#2210)
Malformed hdf5 files may have trunkated content which does not match the expected size. When this function attempts to decode these it may read past the end of the allocated space leading to heap overflows as bounds checking is incomplete.
Make sure each element is within bounds before reading.
This fixes CVE-2019-8396 / HDFFV-10712 / github bug #2209.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.com>
---
src/H5Opline.c | 17 +++++++++++++++--
src/H5private.h | 3 +++
2 files changed, 18 insertions(+), 2 deletions(-)
diff --git a/src/H5Opline.c b/src/H5Opline.c
index 4b76da9..eacf81a 100644
--- a/src/H5Opline.c
+++ b/src/H5Opline.c
@@ -110,6 +110,7 @@ H5FL_DEFINE(H5O_pline_t);
*
*-------------------------------------------------------------------------
*/
+
static void *
H5O__pline_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UNUSED mesg_flags,
unsigned H5_ATTR_UNUSED *ioflags, size_t p_size, const uint8_t *p)
@@ -131,6 +132,9 @@ H5O__pline_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh, unsign
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Version */
+ if (p + 4 - 1 > p_end) /* 4 byte is minimum for all versions */
+ HGOTO_ERROR(H5E_OHDR, H5E_NOSPACE, NULL, "ran off the end of the buffer: current p = %p, p_end = %p",
+ p + 4, p_end)
pline->version = *p++;
if (pline->version < H5O_PLINE_VERSION_1 || pline->version > H5O_PLINE_VERSION_LATEST)
HGOTO_ERROR(H5E_PLINE, H5E_CANTLOAD, NULL, "bad version number for filter pipeline message")
@@ -159,6 +163,9 @@ H5O__pline_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh, unsign
/* Decode filters */
for (i = 0, filter = &pline->filter[0]; i < pline->nused; i++, filter++) {
/* Filter ID */
+ if (p + 6 - 1 > p_end) /* 6 bytes minimum */
+ HGOTO_ERROR(H5E_OHDR, H5E_NOSPACE, NULL,
+ "ran off the end of the buffer: current p = %p, p_end = %p", p + 6, p_end)
UINT16DECODE(p, filter->id);
/* Length of filter name */
@@ -168,6 +175,9 @@ H5O__pline_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh, unsign
UINT16DECODE(p, name_length);
if (pline->version == H5O_PLINE_VERSION_1 && name_length % 8)
HGOTO_ERROR(H5E_PLINE, H5E_CANTLOAD, NULL, "filter name length is not a multiple of eight")
+ if (p + 4 - 1 > p_end) /* with name_length 4 bytes to go */
+ HGOTO_ERROR(H5E_OHDR, H5E_NOSPACE, NULL,
+ "ran off the end of the buffer: current p = %p, p_end = %p", p + 4, p_end)
} /* end if */
/* Filter flags */
@@ -179,9 +189,12 @@ H5O__pline_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh, unsign
/* Filter name, if there is one */
if (name_length) {
size_t actual_name_length; /* Actual length of name */
-
+ size_t len = (size_t)(p_end - p + 1);
/* Determine actual name length (without padding, but with null terminator) */
- actual_name_length = HDstrlen((const char *)p) + 1;
+ actual_name_length = HDstrnlen((const char *)p, len);
+ if (actual_name_length == len)
+ HGOTO_ERROR(H5E_OHDR, H5E_NOSPACE, NULL, "filter name not null terminated")
+ actual_name_length += 1; /* include \0 byte */
HDassert(actual_name_length <= name_length);
/* Allocate space for the filter name, or use the internal buffer */
diff --git a/src/H5private.h b/src/H5private.h
index 56ded14..58ccfef 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -1444,6 +1444,9 @@ H5_DLL void HDsrand(unsigned int seed);
#ifndef HDstrlen
#define HDstrlen(S) strlen(S)
#endif /* HDstrlen */
+#ifndef HDstrnlen
+#define HDstrnlen(S, L) strnlen(S, L)
+#endif
#ifndef HDstrncat
#define HDstrncat(X, Y, Z) strncat(X, Y, Z)
#endif /* HDstrncat */
--
2.30.0

43
CVE-2020-10812.patch
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@ -1,43 +0,0 @@
From: Egbert Eich <eich@suse.com>
Date: Wed Oct 5 09:44:02 2022 +0200
Subject: Hot fix for CVE-2020-10812
Patch-mainline: Not yet
Git-repo: ssh://eich@192.168.122.1:/home/eich/sources/HPC/hdf5
Git-commit: 2465fc41d208d57eb0d7d025286a81664148fbaf
References:
CVE-2020-10812 unveils a more fundamental design flaw in H5F__dest():
this function returns FAIL if one of multiple operations fail (in this
case H5AC_prep_for_file_close()) while it still proceeds to prepare the
close operation, free the 'shared' member in struct H5F_t and ulimately
deallocate the structure itself.
When H5F__dest() signals back FAIL to the caller, the caller itself
(H5F_try_close() in this case) will fail. This failure is signalled
up the stack, thus the file will not be considered closed and another
attempt will be made to close it - latest in the exit handler.
The next attempt to close will however need the already deallocated
H5F_t structure and the H5T_shared_t structure in its 'shared' member,
however.
This fix papers over the failure of H5AC_prep_for_file_close() by not
changing the return status of H5F__dest() to fail. There are numerous
other opportunities where this will happen.
This may call for a more fundamental solution.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Fint.c | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/H5Fint.c b/src/H5Fint.c
index 9b5613972f..01faf33495 100644
--- a/src/H5Fint.c
+++ b/src/H5Fint.c
@@ -1413,7 +1413,7 @@ H5F__dest(H5F_t *f, hbool_t flush)
*/
if (H5AC_prep_for_file_close(f) < 0)
/* Push error, but keep going */
- HDONE_ERROR(H5E_FILE, H5E_CANTFLUSH, FAIL, "metadata cache prep for close failed")
+ HDONE_ERROR(H5E_FILE, H5E_CANTFLUSH, ret_value, "metadata cache prep for close failed")
/* Flush at this point since the file will be closed (phase 2).
* Only try to flush the file if it was opened with write access, and if

66
CVE-2021-37501.patch
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@ -1,66 +0,0 @@
From: Egbert Eich <eich@suse.com>
Date: Sat Feb 11 13:54:17 2023 +0100
Subject: Check for overflow when calculating on-disk attribute data size (#2459)
Patch-mainline: Not yet
Git-repo: https://github.com/HDFGroup/hdf5
Git-commit: 0d026daa13a81be72495872f651c036fdc84ae5e
References:
A bogus hdf5 file may contain dataspace messages with sizes
which lead to the on-disk data sizes to exceed what is addressable.
When calculating the size, make sure, the multiplication does not
overflow.
The test case was crafted in a way that the overflow caused the
size to be 0.
This fixes CVE-2021-37501 / Bug #2458.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Oattr.c | 3 +++
src/H5private.h | 18 ++++++++++++++++++
2 files changed, 21 insertions(+)
diff --git a/src/H5Oattr.c b/src/H5Oattr.c
index 4dee7aa187..3ef0b99aa4 100644
--- a/src/H5Oattr.c
+++ b/src/H5Oattr.c
@@ -235,6 +235,9 @@ H5O_attr_decode(H5F_t *f, H5O_t *open_oh, unsigned H5_ATTR_UNUSED mesg_flags, un
/* Compute the size of the data */
H5_CHECKED_ASSIGN(attr->shared->data_size, size_t, ds_size * (hsize_t)dt_size, hsize_t);
+ H5_CHECK_MUL_OVERFLOW(attr->shared->data_size, ds_size, dt_size,
+ HGOTO_ERROR(H5E_RESOURCE, H5E_OVERFLOW, NULL,
+ "data size exceeds addressable range"))
/* Go get the data */
if (attr->shared->data_size) {
diff --git a/src/H5private.h b/src/H5private.h
index 931d7b9046..a115aee1a4 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -1605,6 +1605,24 @@ H5_DLL int HDvasprintf(char **bufp, const char *fmt, va_list _ap);
#define H5_CHECK_OVERFLOW(var, vartype, casttype)
#endif /* NDEBUG */
+/*
+ * A macro for checking whether a multiplication has overflown
+ * r is assumed to be the result of a prior multiplication of a and b
+ */
+#define H5_CHECK_MUL_OVERFLOW(r, a, b, err) \
+ { \
+ bool mul_overflow = false; \
+ if (r != 0) { \
+ if (r / a != b) \
+ mul_overflow = true; \
+ } else { \
+ if (a != 0 && b != 0) \
+ mul_overflow = true; \
+ } \
+ if (mul_overflow) \
+ err \
+ }
+
/*
* A macro for detecting over/under-flow when assigning between types
*/

149
add-option-to-build-HL-tools.patch
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@ -1,149 +0,0 @@
From c9c85080e9c9ba2f98cd7bf0ca69775529e280e4 Mon Sep 17 00:00:00 2001
From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Fri, 17 Sep 2021 11:01:26 -0500
Subject: [PATCH] Merge HDFFV-11266 - add option to build HL tools #1018
(#1020)
Origin: https://github.com/HDFGroup/hdf5/commit/c9c85080e9c9ba2f98cd7bf0ca69775529e280e4
---
config/cmake/hdf5-config.cmake.in | 1 +
config/cmake/libhdf5.settings.cmake.in | 1 +
configure.ac | 20 ++++++++++++++++++++
hl/CMakeLists.txt | 12 ++++++++++--
hl/Makefile.am | 4 ++++
release_docs/INSTALL_CMake.txt | 1 +
release_docs/RELEASE.txt | 8 ++++++++
7 files changed, 45 insertions(+), 2 deletions(-)
diff --git a/config/cmake/hdf5-config.cmake.in b/config/cmake/hdf5-config.cmake.in
index 4d02c9c5ff2..8faa2fe2ba2 100644
--- a/config/cmake/hdf5-config.cmake.in
+++ b/config/cmake/hdf5-config.cmake.in
@@ -38,6 +38,7 @@ set (${HDF5_PACKAGE_NAME}_BUILD_CPP_LIB @HDF5_BUILD_CPP_LIB@)
set (${HDF5_PACKAGE_NAME}_BUILD_JAVA @HDF5_BUILD_JAVA@)
set (${HDF5_PACKAGE_NAME}_BUILD_TOOLS @HDF5_BUILD_TOOLS@)
set (${HDF5_PACKAGE_NAME}_BUILD_HL_LIB @HDF5_BUILD_HL_LIB@)
+set (${HDF5_PACKAGE_NAME}_BUILD_HL_TOOLS @HDF5_BUILD_HL_TOOLS@)
set (${HDF5_PACKAGE_NAME}_ENABLE_THREADSAFE @HDF5_ENABLE_THREADSAFE@)
set (${HDF5_PACKAGE_NAME}_ENABLE_PLUGIN_SUPPORT @HDF5_ENABLE_PLUGIN_SUPPORT@)
set (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT @HDF5_ENABLE_Z_LIB_SUPPORT@)
diff --git a/config/cmake/libhdf5.settings.cmake.in b/config/cmake/libhdf5.settings.cmake.in
index dd345b4cd5c..e5b150409c5 100644
--- a/config/cmake/libhdf5.settings.cmake.in
+++ b/config/cmake/libhdf5.settings.cmake.in
@@ -70,6 +70,7 @@ Parallel Filtered Dataset Writes: @PARALLEL_FILTERED_WRITES@
High-level library: @HDF5_BUILD_HL_LIB@
Build HDF5 Tests: @BUILD_TESTING@
Build HDF5 Tools: @HDF5_BUILD_TOOLS@
+ Build High-level HDF5 Tools: @HDF5_BUILD_HL_TOOLS@
Threadsafety: @HDF5_ENABLE_THREADSAFE@ (recursive RW locks: @HDF5_USE_RECURSIVE_RW_LOCKS@)
Default API mapping: @DEFAULT_API_VERSION@
With deprecated public symbols: @HDF5_ENABLE_DEPRECATED_SYMBOLS@
diff --git a/configure.ac b/configure.ac
index df0cec59fe5..7b4c3f56647 100644
--- a/configure.ac
+++ b/configure.ac
@@ -806,6 +806,7 @@ AC_LANG_POP(C++)
## This needs to be exposed for the library info file even if the HL
## library is disabled.
AC_SUBST([HDF5_HL])
+AC_SUBST([HDF5_HL_TOOLS])
## The high-level library is enabled unless the build mode is clean.
if test "X-$BUILD_MODE" = "X-clean" ; then
@@ -822,6 +823,9 @@ HL=""
## Fortran high-level library
AC_SUBST(HL_FOR)
HL_FOR=""
+## Tools high-level library
+AC_SUBST(HL_TOOLS)
+HL_TOOLS=""
AC_MSG_CHECKING([if the high-level library is enabled])
AC_ARG_ENABLE([hl],
@@ -840,6 +844,21 @@ else
AC_MSG_RESULT([no])
fi
+AC_MSG_CHECKING([if the high-level tools are enabled])
+AC_ARG_ENABLE([hltools],
+ [AS_HELP_STRING([--enable-hltools],
+ [Enable the high-level tools.
+ [default=yes)]
+ ])],
+ [HDF5_HL_TOOLS=$enableval])
+
+if test "X${HDF5_HL}" = "Xyes" -a "X-$HDF5_HL_TOOLS" = "X-yes"; then
+ AC_MSG_RESULT([yes])
+ HL_TOOLS="tools"
+else
+ AC_MSG_RESULT([no])
+fi
+
## ----------------------------------------------------------------------
## Check which archiving tool to use. This needs to be done before
@@ -3992,6 +4011,7 @@ AM_CONDITIONAL([BUILD_HDF5_HL_CONDITIONAL], [test "X$HDF5_HL" = "Xyes"])
AM_CONDITIONAL([BUILD_TESTS_CONDITIONAL], [test "X$HDF5_TESTS" = "Xyes"])
AM_CONDITIONAL([BUILD_TESTS_PARALLEL_CONDITIONAL], [test -n "$TESTPARALLEL"])
AM_CONDITIONAL([BUILD_TOOLS_CONDITIONAL], [test "X$HDF5_TOOLS" = "Xyes"])
+AM_CONDITIONAL([BUILD_TOOLS_HL_CONDITIONAL], [test "X$HDF5_HL_TOOLS" = "Xyes"])
AM_CONDITIONAL([BUILD_DOXYGEN_CONDITIONAL], [test "X$HDF5_DOXYGEN" = "Xyes"])
## ----------------------------------------------------------------------
diff --git a/hl/CMakeLists.txt b/hl/CMakeLists.txt
index 083c60eb39e..5061c6c5a47 100644
--- a/hl/CMakeLists.txt
+++ b/hl/CMakeLists.txt
@@ -7,9 +7,17 @@ project (HDF5_HL C)
add_subdirectory (src)
-#-- Build the High level Tools
+# Build HDF5 Tools
if (HDF5_BUILD_TOOLS)
- add_subdirectory (tools)
+ #-----------------------------------------------------------------------------
+ #-- Option to build the High level Tools
+ #-----------------------------------------------------------------------------
+ if (EXISTS "${HDF5_HL_SOURCE_DIR}/tools" AND IS_DIRECTORY "${HDF5_HL_SOURCE_DIR}/tools")
+ option (HDF5_BUILD_HL_TOOLS "Build HDF5 HL Tools" ON)
+ if (HDF5_BUILD_HL_TOOLS)
+ add_subdirectory (tools)
+ endif ()
+ endif ()
endif ()
#-- Add High Level Examples
diff --git a/hl/Makefile.am b/hl/Makefile.am
index 80ef66a2a2c..ad035fe5073 100644
--- a/hl/Makefile.am
+++ b/hl/Makefile.am
@@ -37,10 +37,14 @@ else
TEST_DIR =
endif
if BUILD_TOOLS_CONDITIONAL
+if BUILD_TOOLS_HL_CONDITIONAL
TOOLS_DIR = tools
else
TOOLS_DIR =
endif
+else
+ TOOLS_DIR =
+endif
## Don't recurse into any subdirectories if HDF5 is not configured to
## use the HL library
diff --git a/release_docs/INSTALL_CMake.txt b/release_docs/INSTALL_CMake.txt
index 84044c7ee7e..adceb702aea 100644
--- a/release_docs/INSTALL_CMake.txt
+++ b/release_docs/INSTALL_CMake.txt
@@ -740,6 +740,7 @@ HDF5_BUILD_FORTRAN "Build FORTRAN support" OFF
HDF5_BUILD_JAVA "Build JAVA support" OFF
HDF5_BUILD_HL_LIB "Build HIGH Level HDF5 Library" ON
HDF5_BUILD_TOOLS "Build HDF5 Tools" ON
+HDF5_BUILD_HL_TOOLS "Build HIGH Level HDF5 Tools" ON
---------------- HDF5 Advanced Options ---------------------
ONLY_SHARED_LIBS "Only Build Shared Libraries" OFF

BIN
hdf5-1.12.1.tar.bz2
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BIN
hdf5-1.14.5.tar.gz Normal file
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20
hdf5-LD_LIBRARY_PATH.patch
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@ -1,20 +0,0 @@
--- hdf5-1.12.0/src/Makefile.am~ 2020-02-29 00:29:58.000000000 +0100
+++ hdf5-1.12.0/src/Makefile.am 2021-02-26 16:10:03.612252484 +0100
@@ -156,8 +156,6 @@
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error.
H5Tinit.c: H5detect$(EXEEXT)
- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \
- sed -e 's/-L/:/g' -e 's/ //g'`" \
$(RUNSERIAL) ./H5detect$(EXEEXT) $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1)
@@ -168,8 +166,6 @@
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error.
H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings
- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \
- sed -e 's/-L/:/g' -e 's/ //g'`" \
$(RUNSERIAL) ./H5make_libsettings$(EXEEXT) $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1)

145
hdf5-build.patch
View File

@ -1,145 +0,0 @@
diff --git a/java/examples/datasets/JavaDatasetExample.sh.in b/java/examples/datasets/JavaDatasetExample.sh.in
index f29739a..fc9cddb 100644
--- a/java/examples/datasets/JavaDatasetExample.sh.in
+++ b/java/examples/datasets/JavaDatasetExample.sh.in
@@ -39,7 +39,7 @@ HDFLIB_HOME="$top_srcdir/java/lib"
BLDDIR="."
BLDLIBDIR="$BLDDIR/testlibs"
HDFTEST_HOME="$top_srcdir/java/examples/datasets"
-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
+JARFILE=@PACKAGE_TARNAME@.jar
TESTJARFILE=jar@PACKAGE_TARNAME@datasets.jar
test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
diff --git a/java/examples/datasets/Makefile.am b/java/examples/datasets/Makefile.am
index 41a914b..195201a 100644
--- a/java/examples/datasets/Makefile.am
+++ b/java/examples/datasets/Makefile.am
@@ -26,7 +26,7 @@ classes:
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
pkgpath = examples/datasets
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)datasets.jar
diff --git a/java/examples/datatypes/JavaDatatypeExample.sh.in b/java/examples/datatypes/JavaDatatypeExample.sh.in
index e26d8c0..f6a9d87 100644
--- a/java/examples/datatypes/JavaDatatypeExample.sh.in
+++ b/java/examples/datatypes/JavaDatatypeExample.sh.in
@@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib"
BLDDIR="."
BLDLIBDIR="$BLDDIR/testlibs"
HDFTEST_HOME="$top_srcdir/java/examples/datatypes"
-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
+JARFILE=@PACKAGE_TARNAME@.jar
TESTJARFILE=jar@PACKAGE_TARNAME@datatypes.jar
test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
diff --git a/java/examples/datatypes/Makefile.am b/java/examples/datatypes/Makefile.am
index 90790f7..450edef 100644
--- a/java/examples/datatypes/Makefile.am
+++ b/java/examples/datatypes/Makefile.am
@@ -26,7 +26,7 @@ classes:
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
pkgpath = examples/datatypes
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)datatypes.jar
diff --git a/java/examples/groups/JavaGroupExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in
index 3b0e9d1..416c69f 100644
--- a/java/examples/groups/JavaGroupExample.sh.in
+++ b/java/examples/groups/JavaGroupExample.sh.in
@@ -37,7 +37,7 @@ BLDDIR="."
BLDLIBDIR="$BLDDIR/testlibs"
BLDITERDIR="./groups"
HDFTEST_HOME="$top_srcdir/java/examples/groups"
-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
+JARFILE=@PACKAGE_TARNAME@.jar
TESTJARFILE=jar@PACKAGE_TARNAME@groups.jar
test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
test -d $BLDITERDIR || mkdir -p $BLDITERDIR
diff --git a/java/examples/groups/Makefile.am b/java/examples/groups/Makefile.am
index bfde9ae..f48a5b9 100644
--- a/java/examples/groups/Makefile.am
+++ b/java/examples/groups/Makefile.am
@@ -26,7 +26,7 @@ classes:
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
pkgpath = examples/groups
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)groups.jar
diff --git a/java/examples/intro/JavaIntroExample.sh.in b/java/examples/intro/JavaIntroExample.sh.in
index db741e5..d0ba65d 100644
--- a/java/examples/intro/JavaIntroExample.sh.in
+++ b/java/examples/intro/JavaIntroExample.sh.in
@@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib"
BLDDIR="."
BLDLIBDIR="$BLDDIR/testlibs"
HDFTEST_HOME="$top_srcdir/java/examples/intro"
-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
+JARFILE=@PACKAGE_TARNAME@.jar
TESTJARFILE=jar@PACKAGE_TARNAME@intro.jar
test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
diff --git a/java/examples/intro/Makefile.am b/java/examples/intro/Makefile.am
index 7d1aeab..01a10c9 100644
--- a/java/examples/intro/Makefile.am
+++ b/java/examples/intro/Makefile.am
@@ -26,7 +26,7 @@ classes:
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
pkgpath = examples/intro
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)intro.jar
diff --git a/java/src/Makefile.am b/java/src/Makefile.am
index 98630e6..fd8d057 100644
--- a/java/src/Makefile.am
+++ b/java/src/Makefile.am
@@ -32,8 +32,8 @@ JAVAROOT = .classes
classes:
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
-jarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
-hdf5_javadir = $(libdir)
+jarfile = $(PACKAGE_TARNAME).jar
+hdf5_javadir = $(prefix)/lib/java
pkgpath = hdf/hdf5lib
CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$$CLASSPATH
diff --git a/java/test/Makefile.am b/java/test/Makefile.am
index 08e79e3..b336c2f 100644
--- a/java/test/Makefile.am
+++ b/java/test/Makefile.am
@@ -26,7 +26,7 @@ classes:
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
pkgpath = test
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/junit.jar:$(top_srcdir)/java/lib/hamcrest-core.jar:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)test.jar
diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in
index 39db296..83d6c7c 100644
--- a/java/test/junit.sh.in
+++ b/java/test/junit.sh.in
@@ -47,7 +47,7 @@ BLDLIBDIR="$BLDDIR/testlibs"
HDFTEST_HOME="$top_srcdir/java/test"
TOOLS_TESTFILES="$top_srcdir/tools/testfiles"
-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
+JARFILE=@PACKAGE_TARNAME@.jar
TESTJARFILE=jar@PACKAGE_TARNAME@test.jar
test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR

37
hdf5-gfortran12.patch
View File

@ -1,37 +0,0 @@
commit 3ea6f8c17228d2629e419563138a6180bc4a5a6a
Author: Orion Poplawski <orion@nwra.com>
Date: Sun Jan 30 15:21:08 2022 -0700
Mark minusone as a PARAMETER in tH5A_1_8.F90.
diff --git a/fortran/test/tH5A_1_8.F90 b/fortran/test/tH5A_1_8.F90
index 4e02c58a39..c2f8e9984a 100644
--- a/fortran/test/tH5A_1_8.F90
+++ b/fortran/test/tH5A_1_8.F90
@@ -776,7 +776,7 @@ SUBROUTINE test_attr_info_by_idx(new_format, fcpl, fapl, total_error)
INTEGER :: Input1
INTEGER(HSIZE_T) :: hzero = 0_HSIZE_T
- INTEGER :: minusone = -1
+ INTEGER, PARAMETER :: minusone = -1
INTEGER(HSIZE_T) :: htmp
data_dims = 0
@@ -1427,7 +1427,7 @@ SUBROUTINE test_attr_delete_by_idx(new_format, fcpl, fapl, total_error)
INTEGER :: u ! Local index variable
INTEGER :: Input1
INTEGER(HSIZE_T) :: hzero = 0_HSIZE_T
- INTEGER :: minusone = -1
+ INTEGER, PARAMETER :: minusone = -1
data_dims = 0
@@ -2268,7 +2268,7 @@ SUBROUTINE test_attr_corder_create_basic( fcpl, fapl, total_error )
INTEGER :: error
INTEGER :: crt_order_flags
- INTEGER :: minusone = -1
+ INTEGER, PARAMETER :: minusone = -1
! Output message about test being performed
! WRITE(*,*) " - Testing Basic Code for Attributes with Creation Order Info"

45
hdf5-wrappers.patch
View File

@ -1,7 +1,8 @@
diff -up hdf5-1.10.7/bin/h5cc.in.wrappers hdf5-1.10.7/bin/h5cc.in diff --git a/bin/h5cc.in b/bin/h5cc.in
--- hdf5-1.10.7/bin/h5cc.in.wrappers 2020-10-07 20:24:29.127283333 -0600 index 9938c31..194818a 100644
+++ hdf5-1.10.7/bin/h5cc.in 2020-10-07 20:27:05.289536904 -0600 --- a/bin/h5cc.in
@@ -89,10 +89,10 @@ CLINKERBASE="@CC@" +++ b/bin/h5cc.in
@@ -87,10 +87,10 @@ CLINKERBASE="@CC@"
# paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
# from the hdf5 build. The order of the flags is intended to give precedence # from the hdf5 build. The order of the flags is intended to give precedence
# to the user's flags. # to the user's flags.
@ -15,17 +16,16 @@ diff -up hdf5-1.10.7/bin/h5cc.in.wrappers hdf5-1.10.7/bin/h5cc.in
CC="${HDF5_CC:-$CCBASE}" CC="${HDF5_CC:-$CCBASE}"
CLINKER="${HDF5_CLINKER:-$CLINKERBASE}" CLINKER="${HDF5_CLINKER:-$CLINKERBASE}"
@@ -105,7 +105,8 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}" @@ -103,7 +103,7 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}"
# available library is shared, it will be used by default. The user can # available library is shared, it will be used by default. The user can
# override either default, although choosing an unavailable library will result # override either default, although choosing an unavailable library will result
# in link errors. # in link errors.
-STATIC_AVAILABLE="@enable_static@" -STATIC_AVAILABLE="@enable_static@"
+# Fedora prefers shared libraries
+STATIC_AVAILABLE=no +STATIC_AVAILABLE=no
if test "${STATIC_AVAILABLE}" = "yes"; then if test "${STATIC_AVAILABLE}" = "yes"; then
USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}" USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
else else
@@ -385,7 +386,7 @@ if test "x$do_link" = "xyes"; then @@ -380,7 +380,7 @@ if test "x$do_link" = "xyes"; then
# paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
# from the hdf5 build. The order of the flags is intended to give precedence # from the hdf5 build. The order of the flags is intended to give precedence
# to the user's flags. # to the user's flags.
@ -34,10 +34,11 @@ diff -up hdf5-1.10.7/bin/h5cc.in.wrappers hdf5-1.10.7/bin/h5cc.in
status=$? status=$?
fi fi
diff -up hdf5-1.10.7/c++/src/h5c++.in.wrappers hdf5-1.10.7/c++/src/h5c++.in diff --git a/c++/src/h5c++.in b/c++/src/h5c++.in
--- hdf5-1.10.7/c++/src/h5c++.in.wrappers 2020-08-27 21:38:23.000000000 -0600 index 8830f3c..994a77f 100644
+++ hdf5-1.10.7/c++/src/h5c++.in 2020-10-07 20:24:29.126283325 -0600 --- a/c++/src/h5c++.in
@@ -87,10 +87,10 @@ CXXLINKERBASE="@CXX@" +++ b/c++/src/h5c++.in
@@ -85,10 +85,10 @@ CXXLINKERBASE="@CXX@"
# paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
# from the hdf5 build. The order of the flags is intended to give precedence # from the hdf5 build. The order of the flags is intended to give precedence
# to the user's flags. # to the user's flags.
@ -50,18 +51,17 @@ diff -up hdf5-1.10.7/c++/src/h5c++.in.wrappers hdf5-1.10.7/c++/src/h5c++.in
+H5BLD_LIBS= +H5BLD_LIBS=
CXX="${HDF5_CXX:-$CXXBASE}" CXX="${HDF5_CXX:-$CXXBASE}"
CXXLINKER="${HDF5_CLINKER:-$CXXLINKERBASE}" CXXLINKER="${HDF5_CXXLINKER:-$CXXLINKERBASE}"
@@ -103,7 +103,8 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}" @@ -101,7 +101,7 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}"
# available library is shared, it will be used by default. The user can # available library is shared, it will be used by default. The user can
# override either default, although choosing an unavailable library will result # override either default, although choosing an unavailable library will result
# in link errors. # in link errors.
-STATIC_AVAILABLE="@enable_static@" -STATIC_AVAILABLE="@enable_static@"
+# Fedora prefers shared libraries
+STATIC_AVAILABLE=no +STATIC_AVAILABLE=no
if test "${STATIC_AVAILABLE}" = "yes"; then if test "${STATIC_AVAILABLE}" = "yes"; then
USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}" USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
else else
@@ -385,7 +386,7 @@ if test "x$do_link" = "xyes"; then @@ -372,7 +372,7 @@ if test "x$do_link" = "xyes"; then
# from the hdf5 build. The order of the flags is intended to give precedence # from the hdf5 build. The order of the flags is intended to give precedence
# to the user's flags. # to the user's flags.
@ -70,10 +70,11 @@ diff -up hdf5-1.10.7/c++/src/h5c++.in.wrappers hdf5-1.10.7/c++/src/h5c++.in
status=$? status=$?
fi fi
diff -up hdf5-1.10.7/fortran/src/h5fc.in.wrappers hdf5-1.10.7/fortran/src/h5fc.in diff --git a/fortran/src/h5fc.in b/fortran/src/h5fc.in
--- hdf5-1.10.7/fortran/src/h5fc.in.wrappers 2020-08-27 21:38:23.000000000 -0600 index 3c04425..450b71d 100644
+++ hdf5-1.10.7/fortran/src/h5fc.in 2020-10-07 20:25:53.793962985 -0600 --- a/fortran/src/h5fc.in
@@ -83,11 +83,11 @@ FLINKERBASE="@FC@" +++ b/fortran/src/h5fc.in
@@ -82,11 +82,11 @@ FLINKERBASE="@FC@"
# libraries in $link_args, followed by any external library paths and libraries # libraries in $link_args, followed by any external library paths and libraries
# from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in from the hdf5 build. # from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in from the hdf5 build.
# The order of the flags is intended to give precedence to the user's flags. # The order of the flags is intended to give precedence to the user's flags.
@ -88,17 +89,16 @@ diff -up hdf5-1.10.7/fortran/src/h5fc.in.wrappers hdf5-1.10.7/fortran/src/h5fc.i
FC="${HDF5_FC:-$FCBASE}" FC="${HDF5_FC:-$FCBASE}"
FLINKER="${HDF5_FLINKER:-$FLINKERBASE}" FLINKER="${HDF5_FLINKER:-$FLINKERBASE}"
@@ -99,7 +99,8 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}" @@ -98,7 +98,7 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}"
# available library is shared, it will be used by default. The user can # available library is shared, it will be used by default. The user can
# override either default, although choosing an unavailable library will result # override either default, although choosing an unavailable library will result
# in link errors. # in link errors.
-STATIC_AVAILABLE="@enable_static@" -STATIC_AVAILABLE="@enable_static@"
+# Fedora prefers shared libraries
+STATIC_AVAILABLE=no +STATIC_AVAILABLE=no
if test "${STATIC_AVAILABLE}" = "yes"; then if test "${STATIC_AVAILABLE}" = "yes"; then
USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}" USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
else else
@@ -363,7 +364,7 @@ if test "x$do_link" = "xyes"; then @@ -359,7 +359,7 @@ if test "x$do_link" = "xyes"; then
# libraries in $link_args, followed by any external library paths and libraries # libraries in $link_args, followed by any external library paths and libraries
# from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in from the hdf5 build. # from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in from the hdf5 build.
# The order of the flags is intended to give precedence to the user's flags. # The order of the flags is intended to give precedence to the user's flags.
@ -107,3 +107,4 @@ diff -up hdf5-1.10.7/fortran/src/h5fc.in.wrappers hdf5-1.10.7/fortran/src/h5fc.i
status=$? status=$?
fi fi

69
hdf5.spec
View File

@ -7,29 +7,19 @@
%global mpi_list %{?mpi_list} openmpi %global mpi_list %{?mpi_list} openmpi
%endif %endif
%global so_version 200 %global so_version 310
Name: hdf5 Name: hdf5
Version: 1.12.1 Version: 1.14.5
Release: 6 Release: 1
Summary: A data model, library, and file format for storing and managing data Summary: A data model, library, and file format for storing and managing data
License: GPL-2.0-or-later License: BSD-3-Clause
URL: https://portal.hdfgroup.org/display/HDF5/HDF5 URL: https://www.hdfgroup.org/solutions/hdf5/
Source0: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/src/hdf5-1.12.1.tar.bz2 Source0: https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_5/downloads/hdf5-1.14.5.tar.gz
Source1: h5comp Source1: h5comp
Patch0: hdf5-LD_LIBRARY_PATH.patch Patch0: hdf5-wrappers.patch
Patch1: hdf5-gfortran12.patch
Patch2: hdf5-build.patch
Patch3: hdf5-wrappers.patch
Patch4: CVE-2018-13867.patch
Patch5: CVE-2018-14031.patch
Patch6: CVE-2018-16438.patch
Patch7: CVE-2019-8396.patch
Patch8: CVE-2020-10812.patch
Patch9: CVE-2021-37501.patch
Patch10: add-option-to-build-HL-tools.patch
BuildRequires: gcc, gcc-c++ BuildRequires: gcc, gcc-c++
BuildRequires: krb5-devel, openssl-devel, zlib-devel, gcc-gfortran, time BuildRequires: krb5-devel, openssl-devel, zlib-devel, gcc-gfortran, time
@ -125,13 +115,13 @@ sed -e 's|-O -finline-functions|-O3 -finline-functions|g' -i config/gnu-flags
%build %build
%global _configure ../configure %global _configure ../configure
%global configure_opts \\\ %global configure_opts \\\
--disable-hltools \\\
--disable-silent-rules \\\ --disable-silent-rules \\\
--enable-fortran \\\ --enable-fortran \\\
--enable-fortran2003 \\\
--enable-hl \\\ --enable-hl \\\
--enable-shared \\\ --enable-shared \\\
--with-szlib \\\ --with-szlib \\\
--enable-mirror-vfd \\\
--disable-nonstandard-feature-float16 \\\
%{nil} %{nil}
export CC=gcc export CC=gcc
@ -192,8 +182,6 @@ do
module purge module purge
done done
find ${RPM_BUILD_ROOT}%{_datadir} \( -name '*.[ch]*' -o -name '*.f90' \) -exec chmod -x {} +
%ifarch x86_64 %ifarch x86_64
sed -i -e s/H5pubconf.h/H5pubconf-64.h/ ${RPM_BUILD_ROOT}%{_includedir}/H5public.h sed -i -e s/H5pubconf.h/H5pubconf-64.h/ ${RPM_BUILD_ROOT}%{_includedir}/H5public.h
mv ${RPM_BUILD_ROOT}%{_includedir}/H5pubconf.h \ mv ${RPM_BUILD_ROOT}%{_includedir}/H5pubconf.h \
@ -228,14 +216,16 @@ make %{?_smp_mflags} -C build check
%files %files
%license COPYING %license COPYING
%doc MANIFEST README.txt release_docs/RELEASE.txt %doc release_docs/RELEASE.txt
%doc release_docs/HISTORY*.txt %doc release_docs/HISTORY*.txt
%{_bindir}/h5clear %{_bindir}/h5clear
%{_bindir}/h5copy %{_bindir}/h5copy
%{_bindir}/h5debug %{_bindir}/h5debug
%{_bindir}/h5delete
%{_bindir}/h5diff %{_bindir}/h5diff
%{_bindir}/h5dump %{_bindir}/h5dump
%{_bindir}/h5format_convert %{_bindir}/h5format_convert
%{_bindir}/h5fuse
%{_bindir}/h5import %{_bindir}/h5import
%{_bindir}/h5jam %{_bindir}/h5jam
%{_bindir}/h5ls %{_bindir}/h5ls
@ -245,6 +235,7 @@ make %{?_smp_mflags} -C build check
%{_bindir}/h5repart %{_bindir}/h5repart
%{_bindir}/h5stat %{_bindir}/h5stat
%{_bindir}/h5unjam %{_bindir}/h5unjam
%{_bindir}/h5watch
%{_bindir}/mirror_server %{_bindir}/mirror_server
%{_bindir}/mirror_server_stop %{_bindir}/mirror_server_stop
%{_libdir}/libhdf5.so.%{so_version}* %{_libdir}/libhdf5.so.%{so_version}*
@ -260,24 +251,26 @@ make %{?_smp_mflags} -C build check
%{_bindir}/h5fc* %{_bindir}/h5fc*
%{_bindir}/h5redeploy %{_bindir}/h5redeploy
%{_includedir}/*.h %{_includedir}/*.h
%{_includedir}/H5config_f.inc
%{_libdir}/*.so %{_libdir}/*.so
%{_libdir}/*.settings %{_libdir}/*.settings
%{_fmoddir}/*.mod %{_fmoddir}/*.mod
%{_datadir}/hdf5_examples/
%{_libdir}/*.a %{_libdir}/*.a
%{_rpmmacrodir}/macros.hdf5 %{_rpmmacrodir}/macros.hdf5
%if %{with_mpich} %if %{with_mpich}
%files mpich %files mpich
%license COPYING %license COPYING
%doc MANIFEST README.txt release_docs/RELEASE.txt %doc release_docs/RELEASE.txt
%doc release_docs/HISTORY*.txt %doc release_docs/HISTORY*.txt
%{_libdir}/mpich/bin/h5clear %{_libdir}/mpich/bin/h5clear
%{_libdir}/mpich/bin/h5copy %{_libdir}/mpich/bin/h5copy
%{_libdir}/mpich/bin/h5debug %{_libdir}/mpich/bin/h5debug
%{_libdir}/mpich/bin/h5delete
%{_libdir}/mpich/bin/h5diff %{_libdir}/mpich/bin/h5diff
%{_libdir}/mpich/bin/h5dump %{_libdir}/mpich/bin/h5dump
%{_libdir}/mpich/bin/h5format_convert %{_libdir}/mpich/bin/h5format_convert
%{_libdir}/mpich/bin/h5fuse
%{_libdir}/mpich/bin/h5import %{_libdir}/mpich/bin/h5import
%{_libdir}/mpich/bin/h5jam %{_libdir}/mpich/bin/h5jam
%{_libdir}/mpich/bin/h5ls %{_libdir}/mpich/bin/h5ls
@ -289,6 +282,7 @@ make %{?_smp_mflags} -C build check
%{_libdir}/mpich/bin/h5repart %{_libdir}/mpich/bin/h5repart
%{_libdir}/mpich/bin/h5stat %{_libdir}/mpich/bin/h5stat
%{_libdir}/mpich/bin/h5unjam %{_libdir}/mpich/bin/h5unjam
%{_libdir}/mpich/bin/h5watch
%{_libdir}/mpich/bin/mirror_server %{_libdir}/mpich/bin/mirror_server
%{_libdir}/mpich/bin/mirror_server_stop %{_libdir}/mpich/bin/mirror_server_stop
%{_libdir}/mpich/bin/ph5diff %{_libdir}/mpich/bin/ph5diff
@ -301,7 +295,6 @@ make %{?_smp_mflags} -C build check
%{_libdir}/mpich/bin/h5pfc %{_libdir}/mpich/bin/h5pfc
%{_libdir}/mpich/lib/lib*.so %{_libdir}/mpich/lib/lib*.so
%{_libdir}/mpich/lib/lib*.settings %{_libdir}/mpich/lib/lib*.settings
%{_libdir}/mpich/share/hdf5_examples/
%files mpich-static %files mpich-static
%{_libdir}/mpich/lib/*.a %{_libdir}/mpich/lib/*.a
@ -310,14 +303,16 @@ make %{?_smp_mflags} -C build check
%if %{with_openmpi} %if %{with_openmpi}
%files openmpi %files openmpi
%license COPYING %license COPYING
%doc MANIFEST README.txt release_docs/RELEASE.txt %doc release_docs/RELEASE.txt
%doc release_docs/HISTORY*.txt %doc release_docs/HISTORY*.txt
%{_libdir}/openmpi/bin/h5clear %{_libdir}/openmpi/bin/h5clear
%{_libdir}/openmpi/bin/h5copy %{_libdir}/openmpi/bin/h5copy
%{_libdir}/openmpi/bin/h5debug %{_libdir}/openmpi/bin/h5debug
%{_libdir}/openmpi/bin/h5delete
%{_libdir}/openmpi/bin/h5diff %{_libdir}/openmpi/bin/h5diff
%{_libdir}/openmpi/bin/h5dump %{_libdir}/openmpi/bin/h5dump
%{_libdir}/openmpi/bin/h5format_convert %{_libdir}/openmpi/bin/h5format_convert
%{_libdir}/openmpi/bin/h5fuse
%{_libdir}/openmpi/bin/h5import %{_libdir}/openmpi/bin/h5import
%{_libdir}/openmpi/bin/h5jam %{_libdir}/openmpi/bin/h5jam
%{_libdir}/openmpi/bin/h5ls %{_libdir}/openmpi/bin/h5ls
@ -329,6 +324,7 @@ make %{?_smp_mflags} -C build check
%{_libdir}/openmpi/bin/h5repart %{_libdir}/openmpi/bin/h5repart
%{_libdir}/openmpi/bin/h5stat %{_libdir}/openmpi/bin/h5stat
%{_libdir}/openmpi/bin/h5unjam %{_libdir}/openmpi/bin/h5unjam
%{_libdir}/openmpi/bin/h5watch
%{_libdir}/openmpi/bin/mirror_server %{_libdir}/openmpi/bin/mirror_server
%{_libdir}/openmpi/bin/mirror_server_stop %{_libdir}/openmpi/bin/mirror_server_stop
%{_libdir}/openmpi/bin/ph5diff %{_libdir}/openmpi/bin/ph5diff
@ -341,13 +337,32 @@ make %{?_smp_mflags} -C build check
%{_libdir}/openmpi/bin/h5pfc %{_libdir}/openmpi/bin/h5pfc
%{_libdir}/openmpi/lib/lib*.so %{_libdir}/openmpi/lib/lib*.so
%{_libdir}/openmpi/lib/lib*.settings %{_libdir}/openmpi/lib/lib*.settings
%{_libdir}/openmpi/share/hdf5_examples/
%files openmpi-static %files openmpi-static
%{_libdir}/openmpi/lib/*.a %{_libdir}/openmpi/lib/*.a
%endif %endif
%changelog %changelog
* Wed Oct 30 2024 yaoxin <yao_xin001@hoperun.com> - 1.14.5-1
- Update to 1.14.5:
* Added signed Windows msi binary and signed Apple dmg binary files.
* Moved examples to the HDF5Examples folder in the source tree.
* Added support for using zlib-ng package as the zlib library
* Disable CMake UNITY_BUILD for hdf5
* Removed "function/code stack" debugging configuration option
* Added configure options for enabling/disabling non-standard programming language features
* Added the CMake variable HDF5_ENABLE_ROS3_VFD to the HDF5 CMake config
file hdf5-config.cmake. This allows it to easily detect if the library
has been built with or without read-only S3 functionality.
* Fixed many CVE:
CVE-2024-29157,CVE-2024-29158,CVE-2024-29159,CVE-2024-29160,CVE-2024-29161,CVE-2024-29162
CVE-2024-29163,CVE-2024-29164,CVE-2024-29165,CVE-2024-29166,CVE-2024-32605,CVE-2024-32606
CVE-2024-32607,CVE-2024-32608,CVE-2024-32609,CVE-2024-32610,CVE-2024-32611,CVE-2024-32612
CVE-2024-32613,CVE-2024-32614,CVE-2024-32615,CVE-2024-32616,CVE-2024-32617,CVE-2024-32618
CVE-2024-32619,CVE-2024-32620,CVE-2024-32621,CVE-2024-32622,CVE-2024-32623,CVE-2024-32624
CVE-2024-33873,CVE-2024-33874,CVE-2024-33875,CVE-2024-33876,CVE-2024-33877,CVE-2018-13871
CVE-2018-13875,CVE-2018-14034
* Wed Dec 20 2023 wangkai <13474090681@163.com> - 1.12.1-6 * Wed Dec 20 2023 wangkai <13474090681@163.com> - 1.12.1-6
- Add disable-hltools flag to fix CVE-2018-17433, CVE-2018-17436, CVE-2020-10809 - Add disable-hltools flag to fix CVE-2018-17433, CVE-2018-17436, CVE-2020-10809