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Sync from SUSE:SLFO:Main hdf5 revision 2b2c4d975fc4e3ab2e2093b936dc59fd

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Adrian Schröter 2024-05-03 13:31:58 +02:00
commit d2abe55ac0
30 changed files with 3638 additions and 0 deletions
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23
.gitattributes vendored Normal file
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## Default LFS
*.7z filter=lfs diff=lfs merge=lfs -text
*.bsp filter=lfs diff=lfs merge=lfs -text
*.bz2 filter=lfs diff=lfs merge=lfs -text
*.gem filter=lfs diff=lfs merge=lfs -text
*.gz filter=lfs diff=lfs merge=lfs -text
*.jar filter=lfs diff=lfs merge=lfs -text
*.lz filter=lfs diff=lfs merge=lfs -text
*.lzma filter=lfs diff=lfs merge=lfs -text
*.obscpio filter=lfs diff=lfs merge=lfs -text
*.oxt filter=lfs diff=lfs merge=lfs -text
*.pdf filter=lfs diff=lfs merge=lfs -text
*.png filter=lfs diff=lfs merge=lfs -text
*.rpm filter=lfs diff=lfs merge=lfs -text
*.tbz filter=lfs diff=lfs merge=lfs -text
*.tbz2 filter=lfs diff=lfs merge=lfs -text
*.tgz filter=lfs diff=lfs merge=lfs -text
*.ttf filter=lfs diff=lfs merge=lfs -text
*.txz filter=lfs diff=lfs merge=lfs -text
*.whl filter=lfs diff=lfs merge=lfs -text
*.xz filter=lfs diff=lfs merge=lfs -text
*.zip filter=lfs diff=lfs merge=lfs -text
*.zst filter=lfs diff=lfs merge=lfs -text

66
Check-for-overflow-when-calculating-on-disk-attribute-data-size-2459.patch Normal file
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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
*/

51
Compound-datatypes-may-not-have-members-of-size-0.patch Normal file
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From: Egbert Eich <eich@suse.com>
Date: Wed Oct 5 15:47:54 2022 +0200
Subject: Compound datatypes may not have members of size 0
Patch-mainline: Not yet
Git-repo: ssh://eich@192.168.122.1:/home/eich/sources/HPC/hdf5
Git-commit: 88ea94d38fdfecba173dbea18502a5f82a46601b
References:
A member size of 0 may lead to an FPE later on as reported in
CVE-2021-46244. To avoid this, check for this as soon as the
member is decoded.
This should probably be done in H5O_dtype_decode_helper() already,
however it is not clear whether all sizes are expected to be != 0.
This fixes CVE-2021-46244.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Odtype.c | 6 ++++++
src/H5T.c | 2 ++
2 files changed, 8 insertions(+)
diff --git a/src/H5Odtype.c b/src/H5Odtype.c
index 9af79f4e9a..d35fc65322 100644
--- a/src/H5Odtype.c
+++ b/src/H5Odtype.c
@@ -333,6 +333,12 @@ H5O__dtype_decode_helper(unsigned *ioflags /*in,out*/, const uint8_t **pp, H5T_t
H5MM_xfree(dt->shared->u.compnd.memb);
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTDECODE, FAIL, "unable to decode member type")
} /* end if */
+ if (temp_type->shared->size == 0) {
+ for (j = 0; j <= i; j++)
+ H5MM_xfree(dt->shared->u.compnd.memb[j].name);
+ H5MM_xfree(dt->shared->u.compnd.memb);
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTDECODE, FAIL, "invalid field size in member type")
+ }
/* Upgrade the version if we can and it is necessary */
if (can_upgrade && temp_type->shared->version > version) {
diff --git a/src/H5T.c b/src/H5T.c
index 3bb220ac26..04b96c5676 100644
--- a/src/H5T.c
+++ b/src/H5T.c
@@ -3591,6 +3591,8 @@ H5T__complete_copy(H5T_t *new_dt, const H5T_t *old_dt, H5T_shared_t *reopened_fo
if (new_dt->shared->u.compnd.memb[i].type->shared->size !=
old_dt->shared->u.compnd.memb[old_match].type->shared->size) {
/* Adjust the size of the member */
+ if (old_dt->shared->u.compnd.memb[old_match].size == 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_BADVALUE, FAIL, "invalid field size in datatype")
new_dt->shared->u.compnd.memb[i].size =
(old_dt->shared->u.compnd.memb[old_match].size * tmp->shared->size) /
old_dt->shared->u.compnd.memb[old_match].type->shared->size;

36
Disable-phdf5-tests.patch Normal file
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From: Egbert Eich <eich@suse.com>
Date: Sat Nov 17 20:11:13 2018 +0100
Subject: Disable phdf5 tests
Patch-mainline: never
Git-commit: 16d758d17d9c49ab9e34d510675929b9ccc8be5a
References:
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
Index: hdf5-1.12.2/testpar/CMakeTests.cmake
===================================================================
--- hdf5-1.12.2.orig/testpar/CMakeTests.cmake
+++ hdf5-1.12.2/testpar/CMakeTests.cmake
@@ -43,7 +43,7 @@ foreach (skiptest ${SKIP_tests})
set (SKIP_testphdf5 "${SKIP_testphdf5};-x;${skiptest}")
endforeach ()
-add_test (NAME MPI_TEST_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS} ${SKIP_testphdf5})
+##add_test (NAME MPI_TEST_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS} ${SKIP_testphdf5})
set_tests_properties (MPI_TEST_testphdf5 PROPERTIES
FIXTURES_REQUIRED par_clear_testphdf5
ENVIRONMENT "HDF5_ALARM_SECONDS=3600;srcdir=${HDF5_TEST_PAR_BINARY_DIR}"
Index: hdf5-1.12.2/testpar/Makefile.am
===================================================================
--- hdf5-1.12.2.orig/testpar/Makefile.am
+++ hdf5-1.12.2/testpar/Makefile.am
@@ -30,7 +30,7 @@ check_SCRIPTS = $(TEST_SCRIPT_PARA)
# Test programs. These are our main targets.
#
-TEST_PROG_PARA=t_mpi t_bigio testphdf5 t_cache t_cache_image t_pread t_pshutdown t_prestart t_init_term t_shapesame t_filters_parallel t_2Gio
+TEST_PROG_PARA=t_mpi t_bigio t_cache t_cache_image t_pread t_pshutdown t_prestart t_init_term t_shapesame t_filters_parallel t_2Gio
# t_pflush1 and t_pflush2 are used by testpflush.sh
check_PROGRAMS = $(TEST_PROG_PARA) t_pflush1 t_pflush2

26
Fix-error-message-not-the-name-but-the-link-information-is-parsed.patch Normal file
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From: Egbert Eich <eich@suse.com>
Date: Sun Oct 9 08:08:24 2022 +0200
Subject: Fix error message: not the name but the link information is parsed
Patch-mainline: Not yet
Git-repo: ssh://eich@192.168.122.1:/home/eich/sources/HPC/hdf5
Git-commit: 7b0b8bc5703ace47aec51d7f60c1149cd3e383b1
References:
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Olink.c | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/H5Olink.c b/src/H5Olink.c
index 51c44a36b0..ee2a413dc1 100644
--- a/src/H5Olink.c
+++ b/src/H5Olink.c
@@ -245,7 +245,7 @@ H5O__link_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UNUSE
/* Make sure that length doesn't exceed buffer size, which could
occur when the file is corrupted */
if (p + len > p_end)
- HGOTO_ERROR(H5E_OHDR, H5E_OVERFLOW, NULL, "name length causes read past end of buffer")
+ HGOTO_ERROR(H5E_OHDR, H5E_OVERFLOW, NULL, "link information length causes read past end of buffer")
if (NULL == (lnk->u.ud.udata = H5MM_malloc((size_t)len)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")

33
H5IMget_image_info-H5Sget_simple_extent_dims-does-not-exceed-array-size.patch Normal file
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From: Egbert Eich <eich@suse.com>
Date: Tue Sep 27 10:29:56 2022 +0200
Subject: H5IMget_image_info: H5Sget_simple_extent_dims() does not exceed array size
Patch-mainline: Not yet
Git-repo: ssh://eich@192.168.122.1:/home/eich/sources/HPC/hdf5
Git-commit: c1baab0937c8956a15efc41240f68d573c7b7324
References:
Malformed hdf5 files may provide more dimensions than the array dim[] is
able to hold. Check number of elements first by calling
H5Sget_simple_extent_dims() with NULL for both 'dims' and 'maxdims' arguments.
This will cause the function to return only the number of dimensions.
This fixes CVE-2018-17439
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
hl/src/H5IM.c | 2 ++
1 file changed, 2 insertions(+)
diff --git a/hl/src/H5IM.c b/hl/src/H5IM.c
index ff10d573c7..e37c696e25 100644
--- a/hl/src/H5IM.c
+++ b/hl/src/H5IM.c
@@ -283,6 +283,8 @@ H5IMget_image_info(hid_t loc_id, const char *dset_name, hsize_t *width, hsize_t
if ((sid = H5Dget_space(did)) < 0)
goto out;
+ if (H5Sget_simple_extent_dims(sid, NULL, NULL) > IMAGE24_RANK)
+ goto out;
/* Get dimensions */
if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
goto out;

85
H5O__pline_decode-Make-more-resilient-to-out-of-bounds-read.patch Normal file
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From: Egbert Eich <eich@suse.com>
Date: Tue Oct 4 23:09:01 2022 +0200
Subject: H5O__pline_decode() Make more resilient to out-of-bounds read
Patch-mainline: Not yet
Git-repo: ssh://eich@192.168.122.1:/home/eich/sources/HPC/hdf5
Git-commit: 35b798ca7542ce45ef016859b8e70d57b7f89cfe
References:
Malformed hdf5 files may have trunkated content which does not match
the expected size. This function attempts to decode these it will read
past the end of the allocated space which may lead to a crash. Make sure
each element is within bounds before reading.
This fixes CVE-2019-8396.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
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 ffc4557ffc..a532aa4512 100644
--- a/src/H5Opline.c
+++ b/src/H5Opline.c
@@ -110,6 +110,14 @@ H5FL_DEFINE(H5O_pline_t);
*
*-------------------------------------------------------------------------
*/
+static char err[] = "ran off the end of the buffer: current p = %p, p_end = %p";
+
+#define VERIFY_LIMIT(p,s,l) \
+ if (p + s - 1 > l) { \
+ HCOMMON_ERROR(H5E_RESOURCE, H5E_NOSPACE, err, p + s, l); \
+ HGOTO_DONE(NULL) \
+ };
+
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)
@@ -159,6 +167,7 @@ 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 */
+ VERIFY_LIMIT(p, 6, p_end) /* 6 bytes minimum */
UINT16DECODE(p, filter->id);
/* Length of filter name */
@@ -168,6 +177,7 @@ 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")
+ VERIFY_LIMIT(p, 4, p_end) /* with name_length 4 bytes to go */
} /* 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_RESOURCE, 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 bc00f120d2..3285c36441 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -1485,6 +1485,9 @@ H5_DLL H5_ATTR_CONST int Nflock(int fd, int operation);
#ifndef HDstrlen
#define HDstrlen(S) strlen(S)
#endif
+#ifndef HDstrnlen
+#define HDstrnlen(S,L) strnlen(S,L)
+#endif
#ifndef HDstrncat
#define HDstrncat(X, Y, Z) strncat(X, Y, Z)
#endif

35
H5O_dtype_decode_helper-Parent-of-enum-needs-to-have-same-size-as-enum-itself.patch Normal file
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@ -0,0 +1,35 @@
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)

76
H5O_fsinfo_decode-Make-more-resilient-to-out-of-bounds-read.patch Normal file
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From: Egbert Eich <eich@suse.com>
Date: Wed Oct 5 07:17:24 2022 +0200
Subject: H5O_fsinfo_decode() Make more resilient to out-of-bounds read
Patch-mainline: Not yet
Git-repo: ssh://eich@192.168.122.1:/home/eich/sources/HPC/hdf5
Git-commit: 8aee14b3a19858a08e3fabdef6ff925b47d4ce2c
References:
Malformed hdf5 files may have trunkated content which does not match
the expected size. This function attempts to decode these it will read
past the end of the allocated space which may lead to a crash. Make sure
each element is within bounds before reading.
This fixes CVE-2021-45830.
Signed-off-by: Egbert Eich <eich@suse.com>
Additions
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Ofsinfo.c | 14 +++++++++++++-
1 file changed, 13 insertions(+), 1 deletion(-)
diff --git a/src/H5Ofsinfo.c b/src/H5Ofsinfo.c
index 9f6514a291..15cbb5ae7b 100644
--- a/src/H5Ofsinfo.c
+++ b/src/H5Ofsinfo.c
@@ -88,6 +88,13 @@ H5FL_DEFINE_STATIC(H5O_fsinfo_t);
*
*-------------------------------------------------------------------------
*/
+static char err[] = "ran off end of input buffer while decoding";
+#define VERIFY_LIMIT(p,s,l) \
+ if (p + s - 1 > l) { \
+ HCOMMON_ERROR(H5E_RESOURCE, H5E_NOSPACE, err); \
+ HGOTO_DONE(NULL) \
+ }
+
static void *
H5O__fsinfo_decode(H5F_t *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)
@@ -112,6 +119,7 @@ H5O__fsinfo_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UNU
fsinfo->fs_addr[ptype - 1] = HADDR_UNDEF;
/* Version of message */
+ VERIFY_LIMIT(p,1,p_end)
vers = *p++;
if (vers == H5O_FSINFO_VERSION_0) {
@@ -125,6 +133,7 @@ H5O__fsinfo_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UNU
fsinfo->pgend_meta_thres = H5F_FILE_SPACE_PGEND_META_THRES;
fsinfo->eoa_pre_fsm_fsalloc = HADDR_UNDEF;
+ VERIFY_LIMIT(p, 1 + H5F_SIZEOF_SIZE(f), p_end);
strategy = (H5F_file_space_type_t)*p++; /* File space strategy */
H5F_DECODE_LENGTH(f, p, threshold); /* Free-space section threshold */
@@ -170,6 +179,7 @@ H5O__fsinfo_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UNU
HDassert(vers >= H5O_FSINFO_VERSION_1);
fsinfo->version = vers;
+ VERIFY_LIMIT(p, 1 + 1 + 2 * H5F_SIZEOF_SIZE(f) + 2 + H5F_SIZEOF_ADDR(f), p_end);
fsinfo->strategy = (H5F_fspace_strategy_t)*p++; /* File space strategy */
fsinfo->persist = *p++; /* Free-space persist or not */
H5F_DECODE_LENGTH(f, p, fsinfo->threshold); /* Free-space section threshold */
@@ -181,9 +191,11 @@ H5O__fsinfo_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UNU
/* Decode addresses of free space managers, if persisting */
if (fsinfo->persist)
- for (ptype = H5F_MEM_PAGE_SUPER; ptype < H5F_MEM_PAGE_NTYPES; ptype++)
+ for (ptype = H5F_MEM_PAGE_SUPER; ptype < H5F_MEM_PAGE_NTYPES; ptype++) {
+ VERIFY_LIMIT(p, H5F_SIZEOF_SIZE(f), p_end);
H5F_addr_decode(f, &p, &(fsinfo->fs_addr[ptype - 1]));
+ }
fsinfo->mapped = FALSE;
}

43
Hot-fix-for-CVE-2020-10812.patch Normal file
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@ -0,0 +1,43 @@
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

34
Make-sure-info-block-for-external-links-has-at-least-3-bytes.patch Normal file
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@ -0,0 +1,34 @@
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
PPC64LE-Fix-long-double-handling.patch Normal file
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@ -0,0 +1,92 @@
From: Egbert Eich <eich@suse.com>
Date: Tue Nov 7 14:16:53 2017 +0100
Subject: [PATCH]PPC64LE: Fix long double handling
Git-commit: ad6559a71b7ba3cacb4b56d4747db63f28a12f55
References:
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.com>
---
hdf5-1.10.1/config/cmake/ConversionTests.c | 16 ++++++++++++++++
hdf5-1.10.1/test/dt_arith.c | 26 ++++++++++++++++++++++++--
2 files changed, 40 insertions(+), 2 deletions(-)
Index: hdf5-1.12.2/config/cmake/ConversionTests.c
===================================================================
--- hdf5-1.12.2.orig/config/cmake/ConversionTests.c
+++ hdf5-1.12.2/config/cmake/ConversionTests.c
@@ -34,6 +34,14 @@ int HDF_NO_UBSAN main(void)
unsigned char s2[8];
int ret = 1;
+#if defined __powerpc64__ && defined _LITTLE_ENDIAN
+ /* Don't bother checking on ppc64le, we know it'll work, and
+ that what hdf5 calls 'special algorithm' simply is
+ IBM ldouble 128 (i.e. two seperately scaled doubles).
+ The check below assumes big endian. */
+ ret = 0;
+#endif
+
if(sizeof(long double) == 16 && sizeof(long) == 8) {
/*make sure the long double type has 16 bytes in size and
* 11 bits of exponent. If it is,
@@ -157,6 +165,14 @@ int HDF_NO_UBSAN main(void)
unsigned char s[16];
int ret = 0;
+#if defined __powerpc64__ && defined _LITTLE_ENDIAN
+ /* Don't bother checking on ppc64le, we know it'll work, and
+ that what hdf5 calls 'special algorithm' simply is
+ IBM ldouble 128 (i.e. two seperately scaled doubles).
+ The check below assumes big endian. */
+ ret = 0;
+#endif
+
if(sizeof(long double) == 16) {
/*make sure the long double type is the same as the failing type
*which has 16 bytes in size and 11 bits of exponent. If it is,
Index: hdf5-1.12.2/test/dt_arith.c
===================================================================
--- hdf5-1.12.2.orig/test/dt_arith.c
+++ hdf5-1.12.2/test/dt_arith.c
@@ -3036,7 +3036,19 @@ test_conv_flt_1(const char *name, int ru
#if H5_SIZEOF_LONG_DOUBLE != H5_SIZEOF_DOUBLE
}
else if (src_type == FLT_LDOUBLE) {
- INIT_FP_SPECIAL(src_size, src_nbits, sendian, LDBL_MANT_DIG, dst_size, buf, saved, nelmts);
+ size_t mant_dig = LDBL_MANT_DIG;
+ if (mant_dig >= src_nbits) {
+ /* This happens for IBM long double in little endian.
+ The macro LDBL_MANT_DIG says 106 mantissa bits, but the
+ HDF5 detection code actually represents it as a normal 64bit
+ double (52 bit mantissa) with the upper double being
+ unspec bits (which is sort of okay as the testsuite
+ wouldn't deal with that format correctly anyway). So
+ override the mantissa size. */
+ mant_dig = 52;
+ }
+ INIT_FP_SPECIAL(src_size, src_nbits, sendian, mant_dig, dst_size,
+ buf, saved, nelmts);
#endif
}
else
@@ -3736,7 +3748,18 @@ test_conv_int_fp(const char *name, int r
nelmts);
}
else {
- INIT_FP_SPECIAL(src_size, src_nbits, sendian, LDBL_MANT_DIG, dst_size, buf, saved, nelmts);
+ size_t mant_dig = LDBL_MANT_DIG;
+ if (mant_dig >= src_nbits) {
+ /* This happens for IBM long double in little endian.
+ The macro LDBL_MANT_DIG says 106 mantissa bits, but the
+ HDF5 detection code actually represents it as a normal 64bit
+ double (52 bit mantissa) with the upper double being
+ unspec bits (which is sort of okay as the testsuite
+ wouldn't deal with that format correctly anyway). So
+ override the mantissa size. */
+ mant_dig = 52;
+ }
+ INIT_FP_SPECIAL(src_size, src_nbits, sendian, mant_dig, dst_size, buf, saved, nelmts);
}
#endif
}

258
Pass-compact-chunk-size-info-to-ensure-requested-elements-are-within-bounds.patch Normal file
View File

@ -0,0 +1,258 @@
From: Egbert Eich <eich@suse.com>
Date: Sat Oct 1 15:13:52 2022 +0200
Subject: Pass compact chunk size info to ensure requested elements are within bounds
Patch-mainline: Not yet
Git-repo: ssh://eich@192.168.122.1:/home/eich/sources/HPC/hdf5
Git-commit: 18300944261a9fa8f0087f99d9176f3757b1ec38
References:
To avoid reading/writing elements out of bounds of a compact chunk, pass
size info and check whether all elements are within the size before attempting
to read/write these elements. Such accesses can occur when accessing malformed
hdf5 files.
This fixes CVE-2018-11205
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Dchunk.c | 34 +++++++++++++++++++++++++++-------
src/H5Dcompact.c | 5 +++++
src/H5Dpkg.h | 1 +
3 files changed, 33 insertions(+), 7 deletions(-)
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index e6bf26ce89..94ad392cb7 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -128,6 +128,7 @@ typedef struct H5D_rdcc_ent_t {
H5F_block_t chunk_block; /*offset/length of chunk in file */
hsize_t chunk_idx; /*index of chunk in dataset */
uint8_t * chunk; /*the unfiltered chunk data */
+ size_t size; /*size of chunk */
unsigned idx; /*index in hash table */
struct H5D_rdcc_ent_t *next; /*next item in doubly-linked list */
struct H5D_rdcc_ent_t *prev; /*previous item in doubly-linked list */
@@ -303,7 +304,7 @@ static unsigned H5D__chunk_hash_val(const H5D_shared_t *shared, const hsize_t *s
static herr_t H5D__chunk_flush_entry(const H5D_t *dset, H5D_rdcc_ent_t *ent, hbool_t reset);
static herr_t H5D__chunk_cache_evict(const H5D_t *dset, H5D_rdcc_ent_t *ent, hbool_t flush);
static void * H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t relax,
- hbool_t prev_unfilt_chunk);
+ hbool_t prev_unfilt_chunk, size_t *ret_size);
static herr_t H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, hbool_t dirty,
void *chunk, uint32_t naccessed);
static herr_t H5D__chunk_cache_prune(const H5D_t *dset, size_t size);
@@ -2480,6 +2481,7 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_
uint32_t src_accessed_bytes = 0; /* Total accessed size in a chunk */
hbool_t skip_missing_chunks = FALSE; /* Whether to skip missing chunks */
herr_t ret_value = SUCCEED; /*return value */
+ size_t chunk_size = 0;
FUNC_ENTER_STATIC
@@ -2565,11 +2567,12 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_
src_accessed_bytes = chunk_info->chunk_points * (uint32_t)type_info->src_type_size;
/* Lock the chunk into the cache */
- if (NULL == (chunk = H5D__chunk_lock(io_info, &udata, FALSE, FALSE)))
+ if (NULL == (chunk = H5D__chunk_lock(io_info, &udata, FALSE, FALSE, &chunk_size)))
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
/* Set up the storage buffer information for this chunk */
cpt_store.compact.buf = chunk;
+ cpt_store.compact.size = chunk_size;
/* Point I/O info at contiguous I/O info for this chunk */
chk_io_info = &cpt_io_info;
@@ -2629,6 +2632,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize
hbool_t cpt_dirty; /* Temporary placeholder for compact storage "dirty" flag */
uint32_t dst_accessed_bytes = 0; /* Total accessed size in a chunk */
herr_t ret_value = SUCCEED; /* Return value */
+ size_t chunk_size;
FUNC_ENTER_STATIC
@@ -2699,11 +2703,12 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize
entire_chunk = FALSE;
/* Lock the chunk into the cache */
- if (NULL == (chunk = H5D__chunk_lock(io_info, &udata, entire_chunk, FALSE)))
+ if (NULL == (chunk = H5D__chunk_lock(io_info, &udata, entire_chunk, FALSE, &chunk_size)))
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
/* Set up the storage buffer information for this chunk */
cpt_store.compact.buf = chunk;
+ cpt_store.compact.size = chunk_size;
/* Point I/O info at main I/O info for this chunk */
chk_io_info = &cpt_io_info;
@@ -3714,7 +3719,7 @@ done:
*-------------------------------------------------------------------------
*/
static void *
-H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t relax, hbool_t prev_unfilt_chunk)
+H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t relax, hbool_t prev_unfilt_chunk, size_t *ret_size)
{
const H5D_t * dset = io_info->dset; /* Local pointer to the dataset info */
const H5O_pline_t *pline =
@@ -3731,6 +3736,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t rel
hbool_t disable_filters = FALSE; /* Whether to disable filters (when adding to cache) */
void * chunk = NULL; /*the file chunk */
void * ret_value = NULL; /* Return value */
+ size_t chunk_size_ret = 0;
FUNC_ENTER_STATIC
@@ -3796,6 +3802,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t rel
ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk, old_pline);
ent->chunk = (uint8_t *)chunk;
chunk = NULL;
+ ent->size = chunk_size;
/* Mark the chunk as having filters disabled as well as "newly
* disabled" so it is inserted on flush */
@@ -3823,6 +3830,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t rel
ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk, old_pline);
ent->chunk = (uint8_t *)chunk;
chunk = NULL;
+ ent->size = chunk_size;
/* Mark the chunk as having filters enabled */
ent->edge_chunk_state &= ~(H5D_RDCC_DISABLE_FILTERS | H5D_RDCC_NEWLY_DISABLED_FILTERS);
@@ -3902,6 +3910,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t rel
/* In the case that some dataset functions look through this data,
* clear it to all 0s. */
HDmemset(chunk, 0, chunk_size);
+ chunk_size_ret = chunk_size;
} /* end if */
else {
/*
@@ -3924,6 +3933,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t rel
my_chunk_alloc, chunk) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk")
+ chunk_size_ret = my_chunk_alloc;
if (old_pline && old_pline->nused) {
H5Z_EDC_t err_detect; /* Error detection info */
H5Z_cb_t filter_cb; /* I/O filter callback function */
@@ -3937,6 +3947,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t rel
if (H5Z_pipeline(old_pline, H5Z_FLAG_REVERSE, &(udata->filter_mask), err_detect,
filter_cb, &my_chunk_alloc, &buf_alloc, &chunk) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFILTER, NULL, "data pipeline read failed")
+ chunk_size_ret = buf_alloc;
/* Reallocate chunk if necessary */
if (udata->new_unfilt_chunk) {
@@ -3947,6 +3958,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t rel
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL,
"memory allocation failed for raw data chunk")
} /* end if */
+ chunk_size_ret = my_chunk_alloc;
H5MM_memcpy(chunk, tmp_chunk, chunk_size);
(void)H5D__chunk_mem_xfree(tmp_chunk, old_pline);
} /* end if */
@@ -3967,6 +3979,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t rel
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL,
"memory allocation failed for raw data chunk")
+ chunk_size_ret = chunk_size;
if (H5P_is_fill_value_defined(fill, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't tell if fill value defined")
@@ -4032,6 +4045,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t rel
H5_CHECKED_ASSIGN(ent->rd_count, uint32_t, chunk_size, size_t);
H5_CHECKED_ASSIGN(ent->wr_count, uint32_t, chunk_size, size_t);
ent->chunk = (uint8_t *)chunk;
+ ent->size = chunk_size_ret;
/* Add it to the cache */
HDassert(NULL == rdcc->slot[udata->idx_hint]);
@@ -4065,6 +4079,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t rel
HDassert(!ent->locked);
ent->locked = TRUE;
chunk = ent->chunk;
+ chunk_size_ret = ent->size;
} /* end if */
else
/*
@@ -4076,6 +4091,8 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t rel
/* Set return value */
ret_value = chunk;
+ if (ret_size != NULL)
+ *ret_size = chunk_size_ret;
done:
/* Release the fill buffer info, if it's been initialized */
@@ -4084,8 +4101,11 @@ done:
/* Release the chunk allocated, on error */
if (!ret_value)
- if (chunk)
+ if (chunk) {
chunk = H5D__chunk_mem_xfree(chunk, pline);
+ if (ret_size != NULL)
+ *ret_size = 0;
+ }
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__chunk_lock() */
@@ -4884,7 +4904,7 @@ H5D__chunk_update_old_edge_chunks(H5D_t *dset, hsize_t old_dim[])
if (H5F_addr_defined(chk_udata.chunk_block.offset) || (UINT_MAX != chk_udata.idx_hint)) {
/* Lock the chunk into cache. H5D__chunk_lock will take care of
* updating the chunk to no longer be an edge chunk. */
- if (NULL == (chunk = (void *)H5D__chunk_lock(&chk_io_info, &chk_udata, FALSE, TRUE)))
+ if (NULL == (chunk = (void *)H5D__chunk_lock(&chk_io_info, &chk_udata, FALSE, TRUE, NULL)))
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to lock raw data chunk")
/* Unlock the chunk */
@@ -5274,7 +5294,7 @@ H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata, hbool_t new_unfilt_chunk)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "unable to select hyperslab")
/* Lock the chunk into the cache, to get a pointer to the chunk buffer */
- if (NULL == (chunk = (void *)H5D__chunk_lock(io_info, &chk_udata, FALSE, FALSE)))
+ if (NULL == (chunk = (void *)H5D__chunk_lock(io_info, &chk_udata, FALSE, FALSE, NULL)))
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to lock raw data chunk")
/* Fill the selection in the memory buffer */
diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c
index b78693660d..21c37e8a08 100644
--- a/src/H5Dcompact.c
+++ b/src/H5Dcompact.c
@@ -245,6 +245,7 @@ H5D__compact_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t H5_ATTR
FUNC_ENTER_STATIC_NOERR
io_info->store->compact.buf = io_info->dset->shared->layout.storage.u.compact.buf;
+ io_info->store->compact.size = io_info->dset->shared->layout.storage.u.compact.size;
io_info->store->compact.dirty = &io_info->dset->shared->layout.storage.u.compact.dirty;
FUNC_LEAVE_NOAPI(SUCCEED)
@@ -278,6 +279,8 @@ H5D__compact_readvv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *
FUNC_ENTER_STATIC
HDassert(io_info);
+ if (io_info->store->compact.size < *(dset_offset_arr + dset_max_nseq - 1) + *(dset_size_arr + dset_max_nseq - 1))
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "source size less than requested data")
/* Use the vectorized memory copy routine to do actual work */
if ((ret_value = H5VM_memcpyvv(io_info->u.rbuf, mem_max_nseq, mem_curr_seq, mem_size_arr, mem_offset_arr,
@@ -320,6 +323,8 @@ H5D__compact_writevv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t
FUNC_ENTER_STATIC
HDassert(io_info);
+ if (io_info->store->compact.size < *(dset_offset_arr + dset_max_nseq - 1) + *(dset_size_arr + dset_max_nseq - 1))
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "source size less than requested data")
/* Use the vectorized memory copy routine to do actual work */
if ((ret_value = H5VM_memcpyvv(io_info->store->compact.buf, dset_max_nseq, dset_curr_seq, dset_size_arr,
diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h
index 64692c5d1d..8a4acd62e3 100644
--- a/src/H5Dpkg.h
+++ b/src/H5Dpkg.h
@@ -196,6 +196,7 @@ typedef struct {
typedef struct {
void * buf; /* Buffer for compact dataset */
hbool_t *dirty; /* Pointer to dirty flag to mark */
+ size_t size; /* Buffer size for compact dataset */
} H5D_compact_storage_t;
typedef union H5D_storage_t {

28
Remove-duplicate-code.patch Normal file
View File

@ -0,0 +1,28 @@
From: Egbert Eich <eich@suse.com>
Date: Sat Feb 11 18:08:15 2023 +0100
Subject: Remove duplicate code
Patch-mainline: Not yet
Git-repo: https://github.com/HDFGroup/hdf5
Git-commit: 539bca81e2b5713b1c6c5723d742377fb92c1ac1
References:
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Oattr.c | 4 ----
1 file changed, 4 deletions(-)
diff --git a/src/H5Oattr.c b/src/H5Oattr.c
index 3ef0b99aa4..19d3abfb4c 100644
--- a/src/H5Oattr.c
+++ b/src/H5Oattr.c
@@ -222,10 +222,6 @@ H5O_attr_decode(H5F_t *f, H5O_t *open_oh, unsigned H5_ATTR_UNUSED mesg_flags, un
else
p += attr->shared->ds_size;
- /* Get the datatype's size */
- if (0 == (dt_size = H5T_get_size(attr->shared->dt)))
- HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, NULL, "unable to get datatype size")
-
/* Get the datatype & dataspace sizes */
if (0 == (dt_size = H5T_get_size(attr->shared->dt)))
HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, NULL, "unable to get datatype size")

48
Report-error-if-dimensions-of-chunked-storage-in-data-layout-2.patch Normal file
View File

@ -0,0 +1,48 @@
From: Egbert Eich <eich@suse.com>
Date: Wed Sep 28 19:11:16 2022 +0200
Subject: Report error if dimensions of chunked storage in data layout < 2
Patch-mainline: Not yet
Git-repo: ssh://eich@192.168.122.1:/home/eich/sources/HPC/hdf5
Git-commit: 34b621424504265cff3c33cf634a70efb52db180
References:
For Data Layout Messages version 1 & 2 the specification state
that the value stored in the data field is 1 greater than the
number of dimensions in the dataspace. For version 3 this is
not explicitly stated but the implementation suggests it to be
the case.
Thus the set value needs to be at least 2. For dimensionality
< 2 an out-of-bounds access occurs as in CVE-2021-45833.
This fixes CVE-2021-45833.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Olayout.c | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/src/H5Olayout.c b/src/H5Olayout.c
index c939e72744..9fa9e36e8c 100644
--- a/src/H5Olayout.c
+++ b/src/H5Olayout.c
@@ -168,6 +168,10 @@ H5O__layout_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UNU
p += ndims * 4; /* Skip over dimension sizes (32-bit quantities) */
} /* end if */
else {
+ if (ndims < 2)
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL,
+ "bad dimensions for chunked storage")
+
mesg->u.chunk.ndims = ndims;
for (u = 0; u < ndims; u++)
UINT32DECODE(p, mesg->u.chunk.dim[u]);
@@ -241,6 +245,9 @@ H5O__layout_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UNU
mesg->u.chunk.ndims = *p++;
if (mesg->u.chunk.ndims > H5O_LAYOUT_NDIMS)
HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "dimensionality is too large")
+ if (mesg->u.chunk.ndims < 2)
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL,
+ "bad dimensions for chunked storage")
/* B-tree address */
H5F_addr_decode(f, &p, &(mesg->storage.u.chunk.idx_addr));

96
Validate-location-offset-of-the-accumulated-metadata-when-comparing.patch Normal file
View File

@ -0,0 +1,96 @@
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 */

31
When-evicting-driver-info-block-NULL-the-corresponding-entry.patch Normal file
View File

@ -0,0 +1,31 @@
From: Egbert Eich <eich@suse.com>
Date: Thu Sep 29 13:47:30 2022 +0200
Subject: When evicting driver info block, NULL the corresponding entry
Patch-mainline: Not yet
Git-repo: ssh://eich@192.168.122.1:/home/eich/sources/HPC/hdf5
Git-commit: 6d5496f17ed5aa65cbb0498e0bf70b0d599dc336
References:
This prevents it from another attempt to unpin it in H5F__dest() which may
happen due to malformed hdf5 files which leads to a segfault.
This fixes CVE-2021-46242
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Fsuper.c | 2 ++
1 file changed, 2 insertions(+)
diff --git a/src/H5Fsuper.c b/src/H5Fsuper.c
index 60b045ae29..1283790c57 100644
--- a/src/H5Fsuper.c
+++ b/src/H5Fsuper.c
@@ -1044,6 +1044,8 @@ done:
/* Evict the driver info block from the cache */
if (sblock && H5AC_expunge_entry(f, H5AC_DRVRINFO, sblock->driver_addr, H5AC__NO_FLAGS_SET) < 0)
HDONE_ERROR(H5E_FILE, H5E_CANTEXPUNGE, FAIL, "unable to expunge driver info block")
+
+ f->shared->drvinfo = NULL;
} /* end if */
/* Unpin & discard superblock */

10
_constraints Normal file
View File

@ -0,0 +1,10 @@
<constraints>
<hardware>
<physicalmemory>
<size unit="M">4000</size>
</physicalmemory>
<disk>
<size unit="G">6</size>
</disk>
</hardware>
</constraints>

9
_multibuild Normal file
View File

@ -0,0 +1,9 @@
<multibuild>
<package>serial</package>
<package>openmpi4</package>
<package>mvapich2</package>
<package>gnu-openmpi4-hpc</package>
<package>gnu-mvapich2-hpc</package>
<package>gnu-mpich-hpc</package>
<package>gnu-hpc</package>
</multibuild>

BIN
hdf5-1.12.2.tar.bz2 (Stored with Git LFS) Normal file
View File

Binary file not shown.

12
hdf5-1.8.10-tests-arm.patch Normal file
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@ -0,0 +1,12 @@
Index: hdf5-1.12.2/test/testhdf5.c
===================================================================
--- hdf5-1.12.2.orig/test/testhdf5.c
+++ hdf5-1.12.2/test/testhdf5.c
@@ -53,7 +53,6 @@ main(int argc, char *argv[])
AddTest("coords", test_coords, cleanup_coords, "Dataspace coordinates", NULL);
AddTest("sohm", test_sohm, cleanup_sohm, "Shared Object Header Messages", NULL);
AddTest("attr", test_attr, cleanup_attr, "Attributes", NULL);
- AddTest("select", test_select, cleanup_select, "Selections", NULL);
AddTest("time", test_time, cleanup_time, "Time Datatypes", NULL);
AddTest("ref_deprec", test_reference_deprec, cleanup_reference_deprec, "Deprecated References", NULL);
AddTest("ref", test_reference, cleanup_reference, "References", NULL);

26
hdf5-1.8.11-abort_unknown_host_config.patch Normal file
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@ -0,0 +1,26 @@
Index: configure
===================================================================
--- configure.orig
+++ configure
@@ -4343,6 +4343,8 @@ done
if test "X$host_config" != "Xnone"; then
CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`"
. $host_config
+else
+ as_fn_error $? "no usable host config found" "$LINENO" 5
fi
## Source any special site-specific file
Index: configure.ac
===================================================================
--- configure.ac.orig
+++ configure.ac
@@ -330,6 +330,8 @@ done
if test "X$host_config" != "Xnone"; then
CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`"
. $host_config
+else
+ AC_MSG_ERROR([no usable host config found])
fi
## Source any special site-specific file

22
hdf5-LD_LIBRARY_PATH.patch Normal file
View File

@ -0,0 +1,22 @@
Index: hdf5-1.12.2/src/Makefile.in
===================================================================
--- hdf5-1.12.2.orig/src/Makefile.in
+++ hdf5-1.12.2/src/Makefile.in
@@ -1998,8 +1998,6 @@ help:
# 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) $@ ; exit 1)
@@ -2010,8 +2008,6 @@ H5Tinit.c: H5detect$(EXEEXT)
# 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)

39
hdf5-Remove-timestamps-from-binaries.patch Normal file
View File

@ -0,0 +1,39 @@
From: Egbert Eich <eich@suse.com>
Date: Sat Nov 17 18:15:13 2018 +0100
Subject: hdf5: Remove timestamps from binaries
Patch-mainline: never
Git-commit: 3b88045491c0b43f385edce47e3aae07660cd9f3
References:
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5detect.c | 15 ---------------
1 file changed, 15 deletions(-)
Index: hdf5-1.12.2/src/H5detect.c
===================================================================
--- hdf5-1.12.2.orig/src/H5detect.c
+++ hdf5-1.12.2/src/H5detect.c
@@ -1224,22 +1224,6 @@ bit.\n";
fprintf(rawoutstream, "/* Generated automatically by H5detect -- do not edit */\n\n\n");
HDfputs(FileHeader, rawoutstream); /*the copyright notice--see top of this file */
- fprintf(rawoutstream, " *\n * Created:\t\t%s %2d, %4d\n", month_name[tm->tm_mon], tm->tm_mday,
- 1900 + tm->tm_year);
- if (pwd || real_name[0] || host_name[0]) {
- fprintf(rawoutstream, " *\t\t\t");
- if (real_name[0])
- fprintf(rawoutstream, "%s <", real_name);
-#ifdef H5_HAVE_GETPWUID
- if (pwd)
- HDfputs(pwd->pw_name, rawoutstream);
-#endif
- if (host_name[0])
- fprintf(rawoutstream, "@%s", host_name);
- if (real_name[0])
- fprintf(rawoutstream, ">");
- HDfputc('\n', rawoutstream);
- }
fprintf(rawoutstream, " *\n * Purpose:\t\t");
for (s = purpose; *s; s++) {
HDfputc(*s, rawoutstream);

30
hdf5-mpi.patch Normal file
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@ -0,0 +1,30 @@
diff -up hdf5-1.8.16/testpar/t_pflush1.c.mpi hdf5-1.8.16/testpar/t_pflush1.c
--- hdf5-1.8.16/testpar/t_pflush1.c.mpi 2015-10-23 23:13:44.000000000 -0600
+++ hdf5-1.8.16/testpar/t_pflush1.c 2016-03-20 21:46:42.089409776 -0600
@@ -171,6 +171,7 @@ main(int argc, char* argv[])
* because MPI_File_close wants to modify the file-handle variable.
*/
+#if 0
/* close file1 */
if(H5Fget_vfd_handle(file1, fapl, (void **)&mpifh_p) < 0) {
printf("H5Fget_vfd_handle for file1 failed\n");
@@ -189,14 +190,17 @@ main(int argc, char* argv[])
printf("MPI_File_close for file2 failed\n");
goto error;
} /* end if */
+#endif
fflush(stdout);
fflush(stderr);
+ MPI_Finalize();
HD_exit(0);
error:
fflush(stdout);
fflush(stderr);
+ MPI_Finalize();
HD_exit(1);
}

109
hdf5-wrappers.patch Normal file
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@ -0,0 +1,109 @@
diff -Naur hdf5-1.10.8.orig/bin/h5cc.in hdf5-1.10.8/bin/h5cc.in
--- hdf5-1.10.8.orig/bin/h5cc.in 2022-04-07 18:23:46.000000000 -0600
+++ hdf5-1.10.8/bin/h5cc.in 2022-04-07 18:24:04.000000000 -0600
@@ -89,10 +89,10 @@
# 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
# to the user's flags.
-H5BLD_CFLAGS="@AM_CFLAGS@ @CFLAGS@"
+H5BLD_CFLAGS=
H5BLD_CPPFLAGS="@AM_CPPFLAGS@ @CPPFLAGS@"
-H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
-H5BLD_LIBS="@LIBS@"
+H5BLD_LDFLAGS=
+H5BLD_LIBS=
CC="${HDF5_CC:-$CCBASE}"
CLINKER="${HDF5_CLINKER:-$CLINKERBASE}"
@@ -105,7 +105,8 @@
# available library is shared, it will be used by default. The user can
# override either default, although choosing an unavailable library will result
# in link errors.
-STATIC_AVAILABLE="@enable_static@"
+# openSUSE prefers shared libraries
+STATIC_AVAILABLE=no
if test "${STATIC_AVAILABLE}" = "yes"; then
USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
else
@@ -385,7 +386,7 @@
# 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
# to the user's flags.
- $SHOW $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args $shared_link
+ $SHOW $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args
status=$?
fi
diff -Naur hdf5-1.10.8.orig/c++/src/h5c++.in hdf5-1.10.8/c++/src/h5c++.in
--- hdf5-1.10.8.orig/c++/src/h5c++.in 2022-04-07 18:23:45.000000000 -0600
+++ hdf5-1.10.8/c++/src/h5c++.in 2022-04-07 18:24:04.000000000 -0600
@@ -87,10 +87,10 @@
# 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
# to the user's flags.
-H5BLD_CXXFLAGS="@AM_CXXFLAGS@ @CXXFLAGS@"
+H5BLD_CXXFLAGS=
H5BLD_CPPFLAGS="@AM_CPPFLAGS@ @CPPFLAGS@"
-H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
-H5BLD_LIBS="@LIBS@"
+H5BLD_LDFLAGS=
+H5BLD_LIBS=
CXX="${HDF5_CXX:-$CXXBASE}"
CXXLINKER="${HDF5_CXXLINKER:-$CXXLINKERBASE}"
@@ -103,7 +103,8 @@
# available library is shared, it will be used by default. The user can
# override either default, although choosing an unavailable library will result
# in link errors.
-STATIC_AVAILABLE="@enable_static@"
+# openSUSE prefers shared libraries
+STATIC_AVAILABLE=no
if test "${STATIC_AVAILABLE}" = "yes"; then
USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
else
@@ -385,7 +386,7 @@
# from the hdf5 build. The order of the flags is intended to give precedence
# to the user's flags.
- $SHOW $CXXLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CXXFLAGS $CXXFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args $shared_link
+ $SHOW $CXXLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CXXFLAGS $CXXFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args
status=$?
fi
diff -Naur hdf5-1.10.8.orig/fortran/src/h5fc.in hdf5-1.10.8/fortran/src/h5fc.in
--- hdf5-1.10.8.orig/fortran/src/h5fc.in 2022-04-07 18:23:46.000000000 -0600
+++ hdf5-1.10.8/fortran/src/h5fc.in 2022-04-07 18:24:04.000000000 -0600
@@ -83,11 +83,11 @@
# libraries in $link_args, followed by any external library paths and libraries
# from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in from the hdf5 build.
# The order of the flags is intended to give precedence to the user's flags.
-H5BLD_FCFLAGS="@AM_FCFLAGS@ @FCFLAGS@"
+H5BLD_FCFLAGS=
F9XMODFLAG="@F9XMODFLAG@"
F9XSUFFIXFLAG="@F9XSUFFIXFLAG@"
-H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
-H5BLD_LIBS="@LIBS@"
+H5BLD_LDFLAGS=
+H5BLD_LIBS=
FC="${HDF5_FC:-$FCBASE}"
FLINKER="${HDF5_FLINKER:-$FLINKERBASE}"
@@ -99,7 +99,8 @@
# available library is shared, it will be used by default. The user can
# override either default, although choosing an unavailable library will result
# in link errors.
-STATIC_AVAILABLE="@enable_static@"
+# openSUSE prefers shared libraries
+STATIC_AVAILABLE=no
if test "${STATIC_AVAILABLE}" = "yes"; then
USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
else
@@ -363,7 +364,7 @@
# 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.
# The order of the flags is intended to give precedence to the user's flags.
- $SHOW $FLINKER $FCFLAGS $H5BLD_FCFLAGS $F9XSUFFIXFLAG $LDFLAGS $fmodules $link_objs $LIBS $link_args $shared_link
+ $SHOW $FLINKER $FCFLAGS $H5BLD_FCFLAGS $F9XSUFFIXFLAG $LDFLAGS $fmodules $link_objs $LIBS $link_args
status=$?
fi

1302
hdf5.changes Normal file
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File diff suppressed because it is too large Load Diff

945
hdf5.spec Normal file
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@ -0,0 +1,945 @@
#
# spec file
#
# Copyright (c) 2023 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.
# Please submit bugfixes or comments via https://bugs.opensuse.org/
#
%global flavor @BUILD_FLAVOR@%{nil}
%if 0%{?sle_version} >= 150200
%define DisOMPI1 ExclusiveArch: do_not_build
%endif
%if !0%{?is_opensuse} && 0%{?sle_version:1} && 0%{?sle_version} < 150200
%define DisOMPI3 ExclusiveArch: do_not_build
%endif
%if 0%{?sle_version:1} && 0%{?sle_version} < 150300
%define DisOMPI4 ExclusiveArch: do_not_build
%endif
# Disable until resource issue is resolved.
%bcond_with check
%define use_sz2 0
%define short_ver 1.12
%define vers %{short_ver}.2
%define _vers %( echo %{vers} | tr '.' '_' )
%define src_ver %{version}
%define pname hdf5
%global _lto_cflags %{_lto_cflags} -ffat-lto-objects
%if "%{flavor}" == ""
ExclusiveArch: do_not_build
%define package_name %pname
%endif
%if "%{flavor}" == "serial"
%bcond_with hpc
%endif
%if "%{flavor}" == "openmpi4"
%{?DisOMPI4}
%global mpi_flavor openmpi
%define mpi_vers 4
%bcond_with hpc
%endif
%if "%{flavor}" == "openmpi5"
%{?DisOMPI5}
%global mpi_flavor openmpi
%define mpi_vers 5
%bcond_with hpc
%endif
%if "%{flavor}" == "mvapich2"
%global mpi_flavor %{flavor}
%bcond_with hpc
%endif
%if "%{flavor}" == "gnu-hpc"
%bcond_without hpc
%global compiler_family gnu
%undefine c_f_ver
%endif
%if "%{flavor}" == "gnu-openmpi4-hpc"
%{?DisOMPI4}
%bcond_without hpc
%define compiler_family gnu
%undefine c_f_ver
%global mpi_flavor openmpi
%define mpi_vers 4
%endif
%if "%{flavor}" == "gnu-openmpi5-hpc"
%{?DisOMPI5}
%bcond_without hpc
%define compiler_family gnu
%undefine c_f_ver
%global mpi_flavor openmpi
%define mpi_vers 5
%endif
%if "%{flavor}" == "gnu-mvapich2-hpc"
%bcond_without hpc
%define compiler_family gnu
%undefine c_f_ver
%global mpi_flavor mvapich2
%endif
%if "%{flavor}" == "gnu-mpich-hpc"
%bcond_without hpc
%define compiler_family gnu
%undefine c_f_ver
%global mpi_flavor mpich
%endif
%if "%{flavor}" == "gnu7-hpc"
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 7
%undefine mpi_flavor
%endif
%if "%{flavor}" == "gnu7-openmpi4-hpc"
%{?DisOMPI4}
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 7
%global mpi_flavor openmpi
%define mpi_vers 4
%endif
%if "%{flavor}" == "gnu7-openmpi5-hpc"
%{?DisOMPI5}
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 7
%global mpi_flavor openmpi
%define mpi_vers 5
%endif
%if "%{flavor}" == "gnu7-mvapich2-hpc"
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 7
%global mpi_flavor mvapich2
%endif
%if "%{flavor}" == "gnu7-mpich-hpc"
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 7
%global mpi_flavor mpich
%endif
%if "%{flavor}" == "gnu8-hpc"
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 8
%undefine mpi_flavor
%endif
%if "%{flavor}" == "gnu8-openmpi4-hpc"
%{?DisOMPI4}
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 8
%global mpi_flavor openmpi
%define mpi_vers 4
%endif
%if "%{flavor}" == "gnu8-openmpi5-hpc"
%{?DisOMPI5}
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 8
%global mpi_flavor openmpi
%define mpi_vers 5
%endif
%if "%{flavor}" == "gnu8-mvapich2-hpc"
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 8
%global mpi_flavor mvapich2
%endif
%if "%{flavor}" == "gnu8-mpich-hpc"
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 8
%global mpi_flavor mpich
%endif
%if "%{flavor}" == "gnu9-hpc"
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 9
%undefine mpi_flavor
%endif
%if "%{flavor}" == "gnu9-openmpi4-hpc"
%{?DisOMPI4}
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 9
%global mpi_flavor openmpi
%define mpi_vers 4
%endif
%if "%{flavor}" == "gnu9-openmpi5-hpc"
%{?DisOMPI5}
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 9
%global mpi_flavor openmpi
%define mpi_vers 5
%endif
%if "%{flavor}" == "gnu9-mvapich2-hpc"
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 9
%global mpi_flavor mvapich2
%endif
%if "%{flavor}" == "gnu9-mpich-hpc"
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 9
%global mpi_flavor mpich
%endif
%if "%{flavor}" == "gnu10-hpc"
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 10
%undefine mpi_flavor
%endif
%if "%{flavor}" == "gnu10-openmpi4-hpc"
%{?DisOMPI4}
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 10
%global mpi_flavor openmpi
%define mpi_vers 4
%endif
%if "%{flavor}" == "gnu10-openmpi5-hpc"
%{?DisOMPI5}
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 10
%global mpi_flavor openmpi
%define mpi_vers 5
%endif
%if "%{flavor}" == "gnu10-mvapich2-hpc"
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 10
%global mpi_flavor mvapich2
%endif
%if "%{flavor}" == "gnu10-mpich-hpc"
%bcond_without hpc
%define compiler_family gnu
%define c_f_ver 10
%global mpi_flavor mpich
%endif
%{?mpi_flavor:%{bcond_without mpi}}%{!?mpi_flavor:%{bcond_with mpi}}
%{?with_hpc:%{!?compiler_family:%global compiler_family gnu}}
%{?with_mpi:%{!?mpi_flavor:error "No MPI family specified!"}}
# For compatibility package names
%define mpi_ext %{?mpi_vers}
%if %{with hpc}
%{hpc_init -c %compiler_family %{?with_mpi:-m %mpi_flavor} %{?c_f_ver:-v %{c_f_ver}} %{?mpi_vers:-V %{mpi_vers}} %{?ext:-e %{ext}}}
%{?with_mpi:%global hpc_module_pname p%{pname}}
%define my_prefix %hpc_prefix
%define my_bindir %hpc_bindir
%ifarch x86_64
%define my_libdir %hpc_prefix/lib64
%else
%define my_libdir %hpc_libdir
%endif
%define my_incdir %hpc_includedir
%define package_name %{hpc_package_name %_vers}
%define libname(l:s:) lib%{pname}%{-l*}%{hpc_package_name_tail %{?_vers}}
%define vname %{pname}_%{_vers}-hpc
%else
%if %{without mpi}
%define my_prefix %_prefix
%define my_bindir %_bindir
%define my_libdir %_libdir
%define my_incdir %_includedir
%else
%define my_prefix %{_libdir}/mpi/gcc/%{mpi_flavor}%{?mpi_ext}
%define my_suffix -%{mpi_flavor}%{?mpi_ext}
%define my_bindir %{my_prefix}/bin
%define my_libdir %{my_prefix}/%{_lib}/
%define my_incdir %{my_prefix}/include/
%endif
%if 0%{!?package_name:1}
%define package_name %pname%{?my_suffix}
%endif
%define libname(l:s:) lib%{pname}%{!-l:%{-s:-}}%{-l*}%{-s*}%{?my_suffix}
%define vname %{pname}
%endif
# Run 'sh ./update_so_version.sh' when updating hdf5!
%include %{_sourcedir}/so_versions
Name: %{package_name}
Version: %vers
Release: 0
Summary: Command-line programs for the HDF5 scientific data format
License: BSD-3-Clause
Group: Productivity/Scientific/Other
URL: https://www.hdfgroup.org/HDF5/
Source0: https://www.hdfgroup.org/ftp/HDF5/releases/%{pname}-%{short_ver}/%{pname}-%{src_ver}/src/%{pname}-%{src_ver}.tar.bz2
Source100: so_versions
Source1000: update_so_version.sh
Patch0: hdf5-LD_LIBRARY_PATH.patch
# not really needed but we want to get noticed if hdf5 doesn' t know our host
Patch2: hdf5-1.8.11-abort_unknown_host_config.patch
%ifarch %arm
Patch4: hdf5-1.8.10-tests-arm.patch
%endif
Patch5: PPC64LE-Fix-long-double-handling.patch
Patch6: hdf5-Remove-timestamps-from-binaries.patch
# Could be ported but it's unknown if it's still needed
Patch7: hdf5-mpi.patch
Patch8: Disable-phdf5-tests.patch
Patch9: Fix-error-message-not-the-name-but-the-link-information-is-parsed.patch
# Imported from Fedora, strip flags from h5cc wrapper
Patch10: hdf5-wrappers.patch
Patch101: H5O_fsinfo_decode-Make-more-resilient-to-out-of-bounds-read.patch
Patch102: H5O__pline_decode-Make-more-resilient-to-out-of-bounds-read.patch
Patch103: H5O_dtype_decode_helper-Parent-of-enum-needs-to-have-same-size-as-enum-itself.patch
Patch104: Report-error-if-dimensions-of-chunked-storage-in-data-layout-2.patch
Patch105: When-evicting-driver-info-block-NULL-the-corresponding-entry.patch
Patch106: Pass-compact-chunk-size-info-to-ensure-requested-elements-are-within-bounds.patch
Patch107: Validate-location-offset-of-the-accumulated-metadata-when-comparing.patch
Patch108: Make-sure-info-block-for-external-links-has-at-least-3-bytes.patch
Patch109: Hot-fix-for-CVE-2020-10812.patch
Patch110: Compound-datatypes-may-not-have-members-of-size-0.patch
Patch111: H5IMget_image_info-H5Sget_simple_extent_dims-does-not-exceed-array-size.patch
Patch112: Check-for-overflow-when-calculating-on-disk-attribute-data-size-2459.patch
Patch113: Remove-duplicate-code.patch
BuildRequires: fdupes
%if 0%{?use_sz2}
BuildRequires: libsz2-devel
%endif
BuildRequires: zlib-devel
%if %{without hpc}
BuildRequires: gcc-c++
BuildRequires: gcc-fortran
%if %{with mpi}
BuildRequires: %{mpi_flavor}%{?mpi_ext}-devel
%else
Requires: lib%{pname}_cpp%{sonum_CXX} = %{version}
Requires: lib%{pname}_hl_cpp%{sonum_HL_CXX} = %{version}
%endif
Requires: lib%{pname}-%{sonum} = %{version}
Requires: lib%{pname}_fortran%{sonum_F} = %{version}
Requires: lib%{pname}_hl%{sonum_HL} = %{version}
Requires: lib%{pname}hl_fortran%{sonum_HL_F} = %{version}
%else # hpc
%hpc_requires
Requires: %{libname -l _fortran}
%if %{without mpi}
Requires: %{libname -l _cpp}
Requires: %{libname -l _hl_cpp}
%endif
Requires: %{libname -l _hl}
Requires: %{libname -l hl_fortran}
Requires: %{libname}
BuildRequires: %{compiler_family}%{?c_f_ver}-compilers-hpc-macros-devel
BuildRequires: lua-lmod
BuildRequires: suse-hpc >= 0.2
%if %{with mpi}
BuildRequires: %{mpi_flavor}%{?mpi_vers}-%{compiler_family}%{?c_f_ver}-hpc-macros-devel
%endif
%endif # ?hpc
BuildRoot: %{_tmppath}/%{name}-%{version}-build
%description
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes.
This package contains the %{flavor} version utility functions for working
with HDF5 files.
%{?with_hpc:%{hpc_master_package}}
%package -n %{libname -s %{sonum}}
Summary: Shared libraries for the HDF5 scientific data format
# To avoid unresolvable errors due to multiple providers of the library
Group: System/Libraries
Provides: %{libname} = %{version}
Obsoletes: %{libname} < %{version}
%{?with_hpc:Requires: %{name}-module = %version}
%description -n %{libname -s %{sonum}}
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes.
This package contains the %{flavor} version of the HDF5 runtime libraries.
%{?with_hpc:%{hpc_master_package -l -n lib%{pname}%{hpc_package_name_tail}}}
%package -n %{libname -l _hl -s %{sonum_HL}}
Summary: High-level shared libraries for the HDF5 scientific data format
# To avoid unresolvable errors due to multiple providers of the library
Group: System/Libraries
Provides: %{libname -l _hl} = %{version}
Obsoletes: %{libname -l _hl} < %{version}
%{?with_hpc:Requires: %{name}-module = %version}
%description -n %{libname -l _hl -s %{sonum_HL}}
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes.
This package contains the %{flavor} version of the high-level HDF5
runtime libraries.
%{?with_hpc:%{hpc_master_package -l -n lib%{pname}_hl%{hpc_package_name_tail} -N %{pname}_hl}}
%package -n %{libname -l _cpp -s %{sonum_CXX}}
Summary: Shared libraries for the HDF5 scientific data format
# To avoid unresolvable errors due to multiple providers of the library
Group: System/Libraries
Provides: %{libname -l _cpp} = %{version}
Obsoletes: %{libname -l _cpp} < %{version}
%{?with_hpc:Requires: %{name}-module = %version}
%description -n %{libname -l _cpp -s %{sonum_CXX}}
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes.
This package contains the HDF5 runtime libraries.
%{?with_hpc:%{hpc_master_package -l -n lib%{pname}_cpp%{hpc_package_name_tail} -N %{pname}_cpp}}
%package -n %{libname -l _hl_cpp -s %{sonum_HL_CXX}}
Summary: High-level shared libraries for the HDF5 scientific data format
# To avoid unresolvable errors due to multiple providers of the library
Group: System/Libraries
Provides: %{libname -l _hl_cpp} = %{version}
Obsoletes: %{libname -l _hl_cpp} < %{version}
%{?with_hpc:Requires: %{name}-module = %version}
%description -n %{libname -l _hl_cpp -s %{sonum_HL_CXX}}
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes.
This package contains the the high-level HDF5 runtime libraries.
%{?with_hpc:%{hpc_master_package -l -n lib%{pname}_hl_cpp%{hpc_package_name_tail} -N %{pname}_hl_cpp}}
%package -n %{libname -l _fortran -s %{sonum_F}}
Summary: Shared libraries for the HDF5 scientific data format
# To avoid unresolvable errors due to multiple providers of the library
Group: System/Libraries
Provides: %{libname -l _fortran} = %{version}
Obsoletes: %{libname -l _fortran} < %{version}
%{?with_hpc:Requires: %{name}-module = %version}
%description -n %{libname -l _fortran -s %{sonum_F}}
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes.
This package contains the %{flavor} version of the HDF5 runtime libraries.
%{?with_hpc:%{hpc_master_package -l -n lib%{pname}_fortran%{hpc_package_name_tail} -N %{pname}_fortran}}
%package -n %{libname -l hl_fortran -s %{sonum_HL_F}}
Summary: High-level shared libraries for the HDF5 scientific data format
# To avoid unresolvable errors due to multiple providers of the library
Group: System/Libraries
Provides: %{libname -l hl_fortran} = %{version}
Obsoletes: %{libname -l hl_fortran} < %{version}
%{?with_hpc:Requires: %{name}-module = %version}
%description -n %{libname -l hl_fortran -s %{sonum_HL_F}}
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes.
This package contains the %{flavor} version of the high-level HDF5
runtime libraries.
%{?with_hpc:%{hpc_master_package -l -n lib%{pname}_hl_fortran%{hpc_package_name_tail} -N %{pname}hl_fortran}}
%package -n %{pname}-devel-data
Summary: Development data files for %{name}
Group: Development/Libraries/Other
%description -n %{pname}-devel-data
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes.
This package contains generic files needed to create projects that use
any version of HDF5.
%package devel
Summary: Development files for %{name}
Group: Development/Libraries/Parallel
Requires: %{libname -l _cpp -s %{sonum_CXX}} = %{version}
Requires: %{libname -l _hl_cpp -s %{sonum_HL_CXX}} = %{version}
Requires: %{name} = %{version}
%{!?with_hpc:Requires: %{pname}-devel-data = %{version}}
Requires: zlib-devel
%if 0%{?use_sz2}
Requires: libsz2-devel
%endif
Requires: %{libname -s %{sonum}} = %{version}
# Required by Fortran programs?
Requires: %{libname -l _fortran -s %{sonum_F}} = %{version}
Requires: %{libname -l _hl -s %{sonum_HL}} = %{version}
Requires: %{libname -l hl_fortran -s %{sonum_HL_F}} = %{version}
%{?with_hpc:%hpc_requires_devel}
%description devel
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes.
This package contains all files needed to create projects that use
the %{flavor} version of HDF5.
%{?with_hpc:%{hpc_master_package devel}}
%package devel-static
Summary: Static development files for %{name}
Group: Development/Libraries/Parallel
Requires: %{name}-devel = %{version}
%description devel-static
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes.
This package provides the static libraries for the %{flavor} version of HDF5.
%package -n %{vname}-examples
Summary: Examples for %{name}
Group: Documentation/Other
%description -n %{vname}-examples
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes.
This package provides examples of HDF5 library use.
%{?!with_mpi:%{?with_hpc:%{hpc_master_package -n %{pname}-hpc-examples -M %{vname}-examples}}}
%if %{with hpc}
%package module
Summary: Module files for %{name}
Group: Development/Libraries/Parallel
Provides: %{name}-module = %version
Requires: lua-lmod
%description module
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes.
This package contains the environment module needed for the HDF5
library packages.
%endif
%prep
%{?with_hpc: %hpc_debug}
%setup -q -n %{pname}-%{version}
%patch0 -p1 -b .LD_LIBRARY_PATH
%patch2 -p0 -b .abort_unknown_host_config
%ifarch %arm
%patch4 -p0 -b .tests-arm
%endif
%patch5 -p1
%patch6 -p1
# %%patch7 -p1
%patch8 -p1
%patch9 -p1
%patch10 -p1
%patch101 -p1
%patch102 -p1
%patch103 -p1
%patch104 -p1
%patch105 -p1
%patch106 -p1
%patch107 -p1
%patch108 -p1
%patch109 -p1
%patch110 -p1
%patch111 -p1
%patch112 -p1
%patch113 -p1
%if %{without hpc}
# baselibs looks different for different flavors - generate it on the fly
cat > %{_sourcedir}/baselibs.conf <<EOF
libhdf5-%{sonum}%{?my_suffix}
libhdf5_hl%{sonum_HL}%{?my_suffix}
libhdf5_fortran%{sonum_F}%{?my_suffix}
libhdf5hl_fortran%{sonum_HL_F}%{?my_suffix}
libhdf5_cpp%{sonum_CXX}%{?my_suffix}
libhdf5_hl_cpp%{sonum_HL_CXX}%{?my_suffix}
hdf5%{?my_suffix}-devel
requires %{?my_suffix}-<targettype>
requires "libhdf5-%{sonum}%{?my_suffix}-<targettype> = <version>"
requires "libhdf5_hl%{sonum_HL}%{?my_suffix}-<targettype> = <version>"
requires "libhdf5_fortran%{sonum_F}%{?my_suffix}-<targettype> = <version>"
requires "libhdf5hl_fortran%{sonum_HL_F}%{?my_suffix}-<targettype> = <version>"
requires "libhdf5_cpp%{sonum_CXX}%{?my_suffix}-<targettype> = <version>"
requires "libhdf5_hl_cpp%{sonum_HL_CXX}%{?my_suffix}-<targettype> = <version>"
EOF
%endif
%build
%{?with_hpc:%hpc_setup}
%{?with_hpc:%hpc_debug}
export CC=gcc
export CXX=g++
export F9X=gfortran
export CFLAGS="%{optflags}"
%ifarch %arm
# we want to have useful H5_CFLAGS on arm too
test -e config/linux-gnueabi || cp config/linux-gnu config/linux-gnueabi
%endif
# NOTE: --enable-unsupported is required when --enable-fortran
# and/or --enable-cxx is enabled along with --enable-threadsafe.
# Building with thise combination results in thread-safe C
# libraries and non-thread-safe fotran and/or C++ libraries. So
# you have to explicitly allow building the thread-safe C
# library and the non-thread-safe C++ and fortran libraries in
# order to make sure people don't assume that their fotran or
# C++ code is thread-safe. Since our users are going to be
# accessing this through other programs, this doesn't matter.
%if %{without hpc}
%if %{with mpi}
export CC="%{my_bindir}/mpicc"
export CXX="%{my_bindir}/mpicxx"
export FC="%{my_bindir}/mpif90"
export F77="%{my_bindir}/mpif77"
export LD_LIBRARY_PATH="%{my_libdir}"
%endif
%configure \
%if %{with mpi}
--prefix=%{my_prefix} \
--exec-prefix=%{_prefix} \
--bindir=%{my_bindir} \
--libdir=%{my_libdir} \
--includedir=%{my_incdir} \
--datadir=%{_datadir} \
%endif
--docdir=%{_docdir}/%{name} \
%else # hpc
%global _hpc_exec_prefix %hpc_exec_prefix
%global hpc_exec_prefix %_prefix
%if %{with mpi}
export CC=mpicc
export CXX=mpicxx
export F77=mpif77
export FC=mpif90
export MPICC=mpicc
export MPIFC=mpifc
export MPICXX=mpicxx
%endif
%hpc_configure \
%define hpc_exec_prefix %{expand:%_hpc_exec_prefix}
%endif # ?hpc
--disable-hltools \
--disable-dependency-tracking \
--enable-fortran \
--enable-unsupported \
--enable-hl \
--enable-shared \
--enable-threadsafe \
--enable-build-mode=production \
%if %{with mpi}
--enable-parallel \
%endif
--enable-cxx \
%if 0%{?use_sz2}
--with-szlib \
%endif
--with-pthread \
%{nil}
# Remove timestamp/buildhost/kernel version
export SDE_DATE=$(date -d @${SOURCE_DATE_EPOCH} -u)
export UNAME_M_O=$(uname -m -o)
sed -i -e "s/\(Configured on: \).*/\1 $SDE_DATE/" \
-e "s#\(Uname information: \).*#\1 $UNAME_M_O#" \
-e "s/\(Configured by: \).*/\1 abuild@OBS/" \
src/libhdf5.settings
make V=1 %{?_smp_mflags}
%install
%{?with_hpc:%hpc_setup}
%{?with_hpc:%hpc_debug}
make install DESTDIR=%{buildroot}
find %{buildroot} -type f -name "*.la" -delete -print
%if %{without mpi}
%if %{with hpc}
# copy to versioned subdir
install -m 755 -d %{buildroot}%{_prefix}/share/%{version}
install -m 755 -d %{buildroot}%{_prefix}/share/hdf5_examples
mv %{buildroot}%{_prefix}/lib/hpc/*/hdf5/*/share/hdf5_examples/* \
%{buildroot}%{_prefix}/share/%{version}/
mv %{buildroot}%{_prefix}/share/%{version} \
%{buildroot}%{_prefix}/share/hdf5_examples
%else
# rpm macro for version checking
mkdir -p %{buildroot}%{_rpmconfigdir}/macros.d/
cat > %{buildroot}%{_rpmconfigdir}/macros.d/macros.hdf5 <<EOF
#
# RPM macros for hdf5 packaging
#
%_hdf5_sonum %{sonum}
%_hdf5_version %{version}
EOF
%endif
%else
# delete examples from parallel builds
find %{buildroot} -type d -name "hdf5_examples" -exec rm -rf {} +;
%endif
%fdupes -s %{buildroot}/%{_datadir}
%if %{with hpc}
%{hpc_write_pkgconfig -n hdf5 -l hdf5}
%{hpc_write_pkgconfig -n hdf5_hl -l hdf5_hl}
%{hpc_write_pkgconfig -n hdf5_fortran -l hdf5_fortran}
%{hpc_write_pkgconfig -n hdf5_hl_fortran -l hdf5hl_fortran}
%{hpc_write_pkgconfig -n hdf5_cpp -l hdf5_cpp}
%{hpc_write_pkgconfig -n hdf5_hl_cpp -l hdf5_hl_cpp}
%hpc_write_modules_files
#%%Module1.0#####################################################################
proc ModulesHelp { } {
puts stderr " "
puts stderr "This module loads the %{pname} library built with the %{compiler_family} compiler toolchain."
puts stderr "\nVersion %{version}\n"
}
module-whatis "Name: %{pname} built with %{compiler_family} toolchain"
module-whatis "Version: %{version}"
module-whatis "Category: runtime library"
module-whatis "Description: %{SUMMARY:0}"
module-whatis "%{url}"
set version %{version}
prepend-path PATH %{hpc_bindir}
prepend-path LD_LIBRARY_PATH %{hpc_libdir}
setenv %{hpc_upcase %pname}_DIR %{hpc_prefix}
setenv %{hpc_upcase %pname}_BIN %{hpc_bindir}
setenv %{hpc_upcase %pname}_LIB %{hpc_libdir}
if {[file isdirectory %{hpc_includedir}]} {
prepend-path LIBRARY_PATH %{hpc_libdir}
prepend-path CPATH %{hpc_includedir}
prepend-path C_INCLUDE_PATH %{hpc_includedir}
prepend-path CPLUS_INCLUDE_PATH %{hpc_includedir}
prepend-path INCLUDE %{hpc_includedir}
%hpc_modulefile_add_pkgconfig_path
setenv %{hpc_upcase %pname}_INC %{hpc_includedir}
}
family "%pname"
EOF
%endif
%if %{with check}
%check
%if 0%{?qemu_user_space_build}
# default timeout is 1200 seconds
export HDF5_ALARM_SECONDS=3600
%endif
%if %{with mpi}
export HDF5_Make_Ignore=yes
%endif
%{?with_hpc:%hpc_setup}
%ifarch ppc ppc64 ppc64le aarch64
make %{?_smp_mflags} check || { echo "Ignore transient make check failures for PowerPC or aarch64. boo#1058563"; }
%else
%if "%{?mpi_flavor}" != "mpich" || ("%_arch" != "s390" && "%_arch" != "s390x")
make %{?_smp_mflags} check
%endif
%endif
%endif
%post -n %{libname -l _cpp -s %{sonum_CXX}} -p /sbin/ldconfig
%postun -n %{libname -l _cpp -s %{sonum_CXX}} -p /sbin/ldconfig
%post -n %{libname -l _hl_cpp -s %{sonum_HL_CXX}} -p /sbin/ldconfig
%postun -n %{libname -l _hl_cpp -s %{sonum_HL_CXX}} -p /sbin/ldconfig
%post -n %{libname -s %{sonum}} -p /sbin/ldconfig
%postun -n %{libname -s %{sonum}} -p /sbin/ldconfig
%post -n %{libname -l _hl -s %{sonum_HL}} -p /sbin/ldconfig
%postun -n %{libname -l _hl -s %{sonum_HL}} -p /sbin/ldconfig
%post -n %{libname -l _fortran -s %{sonum_F}} -p /sbin/ldconfig
%postun -n %{libname -l _fortran -s %{sonum_F}} -p /sbin/ldconfig
%post -n %{libname -l hl_fortran -s %{sonum_HL_F}} -p /sbin/ldconfig
%postun -n %{libname -l hl_fortran -s %{sonum_HL_F}} -p /sbin/ldconfig
%if %{with hpc}
%postun module
%hpc_module_delete_if_default
%endif
%if 0%{?sle_version} > 120200 || 0%{?suse_version} > 1320
%define mylicense %license
%else
%define mylicense %doc
%endif
%if %{without mpi}
%files -n %{vname}-examples
%{?with_hpc:%dir %{_prefix}/share/hdf5_examples}
%{_prefix}/share/hdf5_examples%{?with_hpc:/%{version}}
%if %{without hpc}
%files -n %{pname}-devel-data
%{_rpmconfigdir}/macros.d/macros.hdf5
%endif
%endif # ?mpi
%files -n %{name}
%{?with_hpc:%dir %my_bindir}
%{my_bindir}/h5clear
%{my_bindir}/h5copy
%{my_bindir}/h5debug
%{my_bindir}/h5diff
%{my_bindir}/h5dump
%{my_bindir}/h5format_convert
%{my_bindir}/h5import
%{my_bindir}/h5jam
%{my_bindir}/h5ls
%{my_bindir}/h5mkgrp
%if %{with mpi}
%{my_bindir}/ph5diff
%{my_bindir}/h5perf
%{my_bindir}/perf
%endif
%{my_bindir}/h5perf_serial
%{my_bindir}/h5redeploy
%{my_bindir}/h5repack
%{my_bindir}/h5repart
%{my_bindir}/h5stat
%{my_bindir}/h5unjam
%files -n %{libname -s %{sonum}}
%doc ACKNOWLEDGMENTS README.md
%mylicense COPYING
##
%if %{without mpi}
%doc release_docs/HISTORY-1_10_0-1_12_0.txt
%doc release_docs/RELEASE.txt
%endif
%defattr(0755,root,root)
%{?with_hpc:%hpc_dirs}
%{my_libdir}/libhdf5.so.%{sonum}
%{my_libdir}/libhdf5.so.%{sonum}.*
%files -n %{libname -l _hl -s %{sonum_HL}}
%mylicense COPYING
%defattr(0755,root,root)
%{?with_hpc:%hpc_dirs}
%{my_libdir}/libhdf5_hl.so.%{sonum_HL}
%{my_libdir}/libhdf5_hl.so.%{sonum_HL}.*
%files -n %{libname -l _cpp -s %{sonum_CXX}}
%mylicense COPYING
%defattr(0755,root,root)
%{?with_hpc:%hpc_dirs}
%{my_libdir}/libhdf5_cpp.so.%{sonum_CXX}
%{my_libdir}/libhdf5_cpp.so.%{sonum_CXX}.*
%files -n %{libname -l _hl_cpp -s %{sonum_HL_CXX}}
%mylicense COPYING
%defattr(0755,root,root)
%{?with_hpc:%hpc_dirs}
%{my_libdir}/libhdf5_hl_cpp.so.%{sonum_HL_CXX}
%{my_libdir}/libhdf5_hl_cpp.so.%{sonum_HL_CXX}.*
%files -n %{libname -l _fortran -s %{sonum_F}}
%mylicense COPYING
%defattr(0755,root,root)
%{?with_hpc:%hpc_dirs}
%{my_libdir}/libhdf5_fortran.so.%{sonum_F}
%{my_libdir}/libhdf5_fortran.so.%{sonum_F}.*
%files -n %{libname -l hl_fortran -s %{sonum_HL_F}}
%mylicense COPYING
%defattr(0755,root,root)
%{?with_hpc:%hpc_dirs}
%{my_libdir}/libhdf5hl_fortran.so.%{sonum_HL_F}
%{my_libdir}/libhdf5hl_fortran.so.%{sonum_HL_F}.*
%if %{with hpc}
%files module
%hpc_modules_files
%endif
%files devel
##
%{?with_hpc:%dir %{my_incdir}}
%doc release_docs/HISTORY-1_10_0-1_12_0.txt
%doc release_docs/RELEASE.txt
%doc ACKNOWLEDGMENTS README.md
%{?with_hpc:%{hpc_pkgconfig_file -n hdf5}}
%{?with_hpc:%{hpc_pkgconfig_file -N -n hdf5_hl}}
%{?with_hpc:%{hpc_pkgconfig_file -N -n hdf5_fortran}}
%{?with_hpc:%{hpc_pkgconfig_file -N -n hdf5_hl_fortran}}
%{?with_hpc:%{hpc_pkgconfig_file -N -n hdf5_cpp}}
%{?with_hpc:%{hpc_pkgconfig_file -N -n hdf5_hl_cpp}}
%{my_bindir}/h5c++
%if %{without mpi}
%{my_bindir}/h5cc
%{my_bindir}/h5fc
%else
%{my_bindir}/h5pcc
%{my_bindir}/h5pfc
%endif
%{my_incdir}/*.h
%{my_libdir}/*.so
%{my_libdir}/*.settings
%{my_incdir}/*.mod
%files devel-static
%{my_libdir}/*.a
%changelog

6
so_versions Normal file
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@ -0,0 +1,6 @@
%define sonum 200
%define sonum_CXX 200
%define sonum_F 200
%define sonum_HL 200
%define sonum_HL_CXX 200
%define sonum_HL_F 200

64
update_so_version.sh Normal file
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@ -0,0 +1,64 @@
#!/bin/bash
exit_error()
{
echo "$0: $@" >&2
exit 1
}
cleanup()
{
rm -f ${spectmp}
rm -f ${shtmp}
}
## We are going to parse these variables from tarball:
# LT_VERS_INTERFACE
# LT_CXX_VERS_INTERFACE
# LT_F_VERS_INTERFACE
# LT_HL_VERS_INTERFACE
# LT_HL_CXX_VERS_INTERFACE
# LT_HL_F_VERS_INTERFACE
cleanup
spectmp=$(mktemp hdf-XXXX.spec)
shtmp=$(mktemp lt-XXXX.sh)
outtmp=$(mktemp so-XXXX)
sed -e "s/@BUILD_FLAVOR@/standard/" hdf5.spec > ${spectmp}
VER="$(rpmspec --define "_sourcedir $(pwd)" -P ${spectmp} | grep -m1 "^Version:")" || \
exit_error "can't grep version"
read x VER <<<$VER
SRC="$(rpmspec --define "_sourcedir $(pwd)" -P ${spectmp} | grep -m1 "^Source0:")" || \
exit_error "can't grep source"
read x SRC <<<$SRC
SRC=$(basename "$SRC" | sed "s/%{version}/$VER/")
test -f "$SRC" || exit_error "tarball '$SRC' does not exist"
tar --wildcards -x -O -f "$SRC" "*/config/lt_vers.am" \
| tr -d ' \t' \
| grep -E "^LT_.*INTERFACE=|^LT_.*AGE=" \
> ${shtmp} \
|| exit_error "can't grep interface versions"
source ./${shtmp} || exit_error "can't source ${shtmp}"
for infix in "" _CXX _F _HL _HL_CXX _HL_F; do
current="LT${infix}_VERS_INTERFACE"
age="LT${infix}_VERS_AGE"
currv=$(eval "echo \$$current")
agev=$(eval "echo \$$age")
if [ -n "$currv" -a -n "$agev" ]; then
echo %define sonum${infix} $((currv - agev)) >> ${outtmp}
else
rm -f ${outtmp}
cleanup
exit 1
fi
done
[ -e ${outtmp} ] && mv ${outtmp} so_versions
cleanup