File Add-unused-bits-checks-and-tools-patches.patch of Package hdf5.34857
From: Egbert Eich <eich@suse.com>
Date: Wed May 22 10:01:50 2024 +0200
Subject: Add unused bits checks and tools patches
Patch-mainline: Upstream
Git-repo: https://github.com/HDFGroup/hdf5
Git-commit: 7d9d4988e9edd7b692eb8513eb3c3a7f8609e2b7
References: bsc#1224158
NOTE: Requires fixup!
* Sizes are tweaked by one byte for unknown reasons
Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5Dint.c | 6 ++++
src/H5Odtype.c | 9 +++++
tools/test/h5dump/h5dumpgentest.c | 2 +-
tools/test/h5stat/testfiles/h5stat_filters-F.ddl | 6 ++--
tools/test/h5stat/testfiles/h5stat_filters-UD.ddl | 2 +-
tools/test/h5stat/testfiles/h5stat_filters-d.ddl | 2 +-
tools/test/h5stat/testfiles/h5stat_filters-dT.ddl | 2 +-
tools/test/h5stat/testfiles/h5stat_filters.ddl | 16 ++++-----
tools/test/h5stat/testfiles/h5stat_filters.h5 | Bin 46272 -> 46696 bytes
tools/testfiles/tallfilters.ddl | 2 +-
tools/testfiles/tfilters.h5 | Bin 46496 -> 46696 bytes
tools/testfiles/tnbit.ddl | 4 +--
tools/testfiles/treadintfilter.ddl | 42 +++++++++++-----------
13 files changed, 54 insertions(+), 39 deletions(-)
diff --git a/src/H5Dint.c b/src/H5Dint.c
index 02154d4f4c..ae62ce5416 100644
--- a/src/H5Dint.c
+++ b/src/H5Dint.c
@@ -932,6 +932,12 @@ H5D__update_oh_info(H5F_t *file, H5D_t *dset, hid_t dapl_id)
if (NULL == (oh = H5O_pin(oloc)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header")
+ /* Check for creating dataset with unusual datatype */
+ if (H5T_is_numeric_with_unusual_unused_bits(type) &&
+ !(H5O_has_chksum(oh) ||
+ (H5F_RFIC_FLAGS(file) & H5F_RFIC_UNUSUAL_NUM_UNUSED_NUMERIC_BITS)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "creating dataset with unusual datatype, see documentation for H5Pset_relax_file_integrity_checks for details.");
+
/* Write the dataspace header message */
if (H5S_append(file, oh, dset->shared->space) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update dataspace header message")
diff --git a/src/H5Odtype.c b/src/H5Odtype.c
index 101f9520fb..16a12eb95c 100644
--- a/src/H5Odtype.c
+++ b/src/H5Odtype.c
@@ -782,6 +782,15 @@ H5O_dtype_decode_helper(H5F_t *f, unsigned *ioflags /*in,out*/, const uint8_t **
HGOTO_ERROR(H5E_DATATYPE, H5E_UNSUPPORTED, FAIL, "unknown datatype class found")
} /* end switch */
+ /* Check for numeric type w/unusual # of unused bits */
+ if (H5T_is_numeric_with_unusual_unused_bits(dt))
+ /* Throw an error if the object header is not checksummed, unless the
+ * H5F_RFIC_UNUSUAL_NUM_UNUSED_NUMERIC_BITS flag is set with
+ * H5Pset_relax_file_integrity_checks() to suppress it.
+ */
+ if (!(*ioflags & H5O_DECODEIO_RFIC_UNUBNT))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_BADVALUE, FAIL, "datatype has unusually large # of unused bits (prec = %zu bits, size = %zu bytes), possibly corrupted file. See documentation for H5Pset_relax_file_integrity_checks for details.", dt->shared->u.atomic.prec, dt->shared->size);
+
done:
/* Cleanup on error */
if (ret_value < 0)
diff --git a/tools/test/h5dump/h5dumpgentest.c b/tools/test/h5dump/h5dumpgentest.c
index 28caedb92f..18b6af5131 100644
--- a/tools/test/h5dump/h5dumpgentest.c
+++ b/tools/test/h5dump/h5dumpgentest.c
@@ -5578,7 +5578,7 @@ gent_filters(void)
HDassert(ret >= 0);
tid = H5Tcopy(H5T_NATIVE_INT);
- H5Tset_precision(tid, H5Tget_size(tid) - 1);
+ H5Tset_precision(tid, (H5Tget_size(tid) * 4) + 1);
ret = make_dset(fid, "nbit", sid, tid, dcpl, buf1);
HDassert(ret >= 0);
diff --git a/tools/test/h5stat/testfiles/h5stat_filters-F.ddl b/tools/test/h5stat/testfiles/h5stat_filters-F.ddl
index d44445bb2e..065d0c9747 100644
--- a/tools/test/h5stat/testfiles/h5stat_filters-F.ddl
+++ b/tools/test/h5stat/testfiles/h5stat_filters-F.ddl
@@ -4,12 +4,12 @@ File space information for file metadata (in bytes):
Superblock extension: 0
User block: 0
Object headers: (total/unused)
- Groups: 48/8
- Datasets(exclude compact data): 4136/1344
+ Groups: 40/0
+ Datasets(exclude compact data): 4128/1088
Datatypes: 80/0
Groups:
B-tree/List: 1200
- Heap: 288
+ Heap: 384
Attributes:
B-tree/List: 0
Heap: 0
diff --git a/tools/test/h5stat/testfiles/h5stat_filters-UD.ddl b/tools/test/h5stat/testfiles/h5stat_filters-UD.ddl
index 4efafd13c4..9f6335aaed 100644
--- a/tools/test/h5stat/testfiles/h5stat_filters-UD.ddl
+++ b/tools/test/h5stat/testfiles/h5stat_filters-UD.ddl
@@ -1,5 +1,5 @@
Filename: h5stat_filters.h5
File space information for datasets' metadata (in bytes):
- Object headers (total/unused): 4136/1344
+ Object headers (total/unused): 4128/1088
Index for Chunked datasets: 31392
Heap: 72
diff --git a/tools/test/h5stat/testfiles/h5stat_filters-d.ddl b/tools/test/h5stat/testfiles/h5stat_filters-d.ddl
index 6e6dd6140d..eee7e1845d 100644
--- a/tools/test/h5stat/testfiles/h5stat_filters-d.ddl
+++ b/tools/test/h5stat/testfiles/h5stat_filters-d.ddl
@@ -12,7 +12,7 @@ Dataset dimension information:
# of datasets with dimension size 100 - 999: 1
Total # of datasets: 1
Dataset storage information:
- Total raw data size: 8659
+ Total raw data size: 9046
Total external raw data size: 400
Dataset layout information:
Dataset layout counts[COMPACT]: 1
diff --git a/tools/test/h5stat/testfiles/h5stat_filters-dT.ddl b/tools/test/h5stat/testfiles/h5stat_filters-dT.ddl
index b14ca9f974..e513b3a5f2 100644
--- a/tools/test/h5stat/testfiles/h5stat_filters-dT.ddl
+++ b/tools/test/h5stat/testfiles/h5stat_filters-dT.ddl
@@ -12,7 +12,7 @@ Dataset dimension information:
# of datasets with dimension size 100 - 999: 1
Total # of datasets: 1
Dataset storage information:
- Total raw data size: 8659
+ Total raw data size: 9046
Total external raw data size: 400
Dataset layout information:
Dataset layout counts[COMPACT]: 1
diff --git a/tools/test/h5stat/testfiles/h5stat_filters.ddl b/tools/test/h5stat/testfiles/h5stat_filters.ddl
index 9f9e146f08..7383f0b31f 100644
--- a/tools/test/h5stat/testfiles/h5stat_filters.ddl
+++ b/tools/test/h5stat/testfiles/h5stat_filters.ddl
@@ -12,12 +12,12 @@ File space information for file metadata (in bytes):
Superblock extension: 0
User block: 0
Object headers: (total/unused)
- Groups: 48/8
- Datasets(exclude compact data): 4136/1344
+ Groups: 40/0
+ Datasets(exclude compact data): 4128/1088
Datatypes: 80/0
Groups:
B-tree/List: 1200
- Heap: 288
+ Heap: 384
Attributes:
B-tree/List: 0
Heap: 0
@@ -50,7 +50,7 @@ Dataset dimension information:
# of datasets with dimension size 100 - 999: 1
Total # of datasets: 1
Dataset storage information:
- Total raw data size: 8659
+ Total raw data size: 9046
Total external raw data size: 400
Dataset layout information:
Dataset layout counts[COMPACT]: 1
@@ -91,9 +91,9 @@ Free-space section bins:
File space management strategy: H5F_FSPACE_STRATEGY_FSM_AGGR
File space page size: 4096 bytes
Summary of file space information:
- File metadata: 37312 bytes
- Raw data: 8659 bytes
+ File metadata: 37392 bytes
+ Raw data: 9046 bytes
Amount/Percent of tracked free space: 0 bytes/0.0%
- Unaccounted space: 301 bytes
-Total space: 46272 bytes
+ Unaccounted space: 258 bytes
+Total space: 46696 bytes
External raw data: 400 bytes
diff --git a/tools/test/h5stat/testfiles/h5stat_filters.h5 b/tools/test/h5stat/testfiles/h5stat_filters.h5
index 5b5f4bb7a6..23d68a9b72 100644
Binary files a/tools/test/h5stat/testfiles/h5stat_filters.h5 and b/tools/test/h5stat/testfiles/h5stat_filters.h5 differ
diff --git a/tools/testfiles/tallfilters.ddl b/tools/testfiles/tallfilters.ddl
index ff2454cef7..4fa1742158 100644
--- a/tools/testfiles/tallfilters.ddl
+++ b/tools/testfiles/tallfilters.ddl
@@ -4,7 +4,7 @@ DATASET "all" {
DATASPACE SIMPLE { ( 20, 10 ) / ( 20, 10 ) }
STORAGE_LAYOUT {
CHUNKED ( 10, 5 )
- SIZE 458 (1.747:1 COMPRESSION)
+ SIZE 457 (1.751:1 COMPRESSION)
}
FILTERS {
PREPROCESSING SHUFFLE
diff --git a/tools/testfiles/tfilters.h5 b/tools/testfiles/tfilters.h5
index 7c33e55aae..23d68a9b72 100644
Binary files a/tools/testfiles/tfilters.h5 and b/tools/testfiles/tfilters.h5 differ
diff --git a/tools/testfiles/tnbit.ddl b/tools/testfiles/tnbit.ddl
index cf2ac1fdb9..4fa21c3c8f 100644
--- a/tools/testfiles/tnbit.ddl
+++ b/tools/testfiles/tnbit.ddl
@@ -1,10 +1,10 @@
HDF5 "tfilters.h5" {
DATASET "nbit" {
- DATATYPE 32-bit little-endian integer 3-bit precision
+ DATATYPE 32-bit little-endian integer 17-bit precision
DATASPACE SIMPLE { ( 20, 10 ) / ( 20, 10 ) }
STORAGE_LAYOUT {
CHUNKED ( 10, 5 )
- SIZE 76 (10.526:1 COMPRESSION)
+ SIZE 428 (1.869:1 COMPRESSION)
}
FILTERS {
COMPRESSION NBIT
diff --git a/tools/testfiles/treadintfilter.ddl b/tools/testfiles/treadintfilter.ddl
index fbad3f6736..7a670a2a25 100644
--- a/tools/testfiles/treadintfilter.ddl
+++ b/tools/testfiles/treadintfilter.ddl
@@ -78,29 +78,29 @@ DATASET "fletcher32" {
}
}
DATASET "nbit" {
- DATATYPE 32-bit little-endian integer 3-bit precision
+ DATATYPE 32-bit little-endian integer 17-bit precision
DATASPACE SIMPLE { ( 20, 10 ) / ( 20, 10 ) }
DATA {
- (0,0): 0, 1, 2, 3, -4, -3, -2, -1, 0, 1,
- (1,0): 2, 3, -4, -3, -2, -1, 0, 1, 2, 3,
- (2,0): -4, -3, -2, -1, 0, 1, 2, 3, -4, -3,
- (3,0): -2, -1, 0, 1, 2, 3, -4, -3, -2, -1,
- (4,0): 0, 1, 2, 3, -4, -3, -2, -1, 0, 1,
- (5,0): 2, 3, -4, -3, -2, -1, 0, 1, 2, 3,
- (6,0): -4, -3, -2, -1, 0, 1, 2, 3, -4, -3,
- (7,0): -2, -1, 0, 1, 2, 3, -4, -3, -2, -1,
- (8,0): 0, 1, 2, 3, -4, -3, -2, -1, 0, 1,
- (9,0): 2, 3, -4, -3, -2, -1, 0, 1, 2, 3,
- (10,0): -4, -3, -2, -1, 0, 1, 2, 3, -4, -3,
- (11,0): -2, -1, 0, 1, 2, 3, -4, -3, -2, -1,
- (12,0): 0, 1, 2, 3, -4, -3, -2, -1, 0, 1,
- (13,0): 2, 3, -4, -3, -2, -1, 0, 1, 2, 3,
- (14,0): -4, -3, -2, -1, 0, 1, 2, 3, -4, -3,
- (15,0): -2, -1, 0, 1, 2, 3, -4, -3, -2, -1,
- (16,0): 0, 1, 2, 3, -4, -3, -2, -1, 0, 1,
- (17,0): 2, 3, -4, -3, -2, -1, 0, 1, 2, 3,
- (18,0): -4, -3, -2, -1, 0, 1, 2, 3, -4, -3,
- (19,0): -2, -1, 0, 1, 2, 3, -4, -3, -2, -1
+ (0,0): 0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
+ (1,0): 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
+ (2,0): 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,
+ (3,0): 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,
+ (4,0): 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
+ (5,0): 50, 51, 52, 53, 54, 55, 56, 57, 58, 59,
+ (6,0): 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
+ (7,0): 70, 71, 72, 73, 74, 75, 76, 77, 78, 79,
+ (8,0): 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,
+ (9,0): 90, 91, 92, 93, 94, 95, 96, 97, 98, 99,
+ (10,0): 100, 101, 102, 103, 104, 105, 106, 107, 108, 109,
+ (11,0): 110, 111, 112, 113, 114, 115, 116, 117, 118, 119,
+ (12,0): 120, 121, 122, 123, 124, 125, 126, 127, 128, 129,
+ (13,0): 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,
+ (14,0): 140, 141, 142, 143, 144, 145, 146, 147, 148, 149,
+ (15,0): 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
+ (16,0): 160, 161, 162, 163, 164, 165, 166, 167, 168, 169,
+ (17,0): 170, 171, 172, 173, 174, 175, 176, 177, 178, 179,
+ (18,0): 180, 181, 182, 183, 184, 185, 186, 187, 188, 189,
+ (19,0): 190, 191, 192, 193, 194, 195, 196, 197, 198, 199
}
}
DATASET "scaleoffset" {
