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-rw-r--r--MANIFEST2
-rwxr-xr-xconfigure2
-rw-r--r--release_docs/RELEASE.txt5
-rw-r--r--src/H5HLcache.c10
-rw-r--r--test/Makefile.am2
-rw-r--r--test/Makefile.in36
-rw-r--r--test/gen_sizes_lheap.c82
-rw-r--r--test/lheap.c26
-rw-r--r--test/tsizeslheap.h5bin0 -> 1028 bytes
9 files changed, 148 insertions, 17 deletions
diff --git a/MANIFEST b/MANIFEST
index 1462196..65e3353 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -827,6 +827,7 @@
./test/gen_old_group.c _DO_NOT_DISTRIBUTE_
./test/gen_old_layout.c _DO_NOT_DISTRIBUTE_
./test/gen_old_mtime.c _DO_NOT_DISTRIBUTE_
+./test/gen_sizes_lheap.c _DO_NOT_DISTRIBUTE_
./test/gen_udlinks.c _DO_NOT_DISTRIBUTE_
./test/getname.c
./test/gheap.c
@@ -887,6 +888,7 @@
./test/trefer.c
./test/trefstr.c
./test/tselect.c
+./test/tsizeslheap.h5
./test/tskiplist.c
./test/tsohm.c
./test/ttst.c
diff --git a/configure b/configure
index ff65e6e..031b42a 100755
--- a/configure
+++ b/configure
@@ -1,5 +1,5 @@
#! /bin/sh
-# From configure.in Id: configure.in 19065 2010-07-12 04:45:53Z hdftest .
+# From configure.in Id: configure.in 19067 2010-07-14 15:55:53Z acheng .
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.65 for HDF5 1.8.5-snap4.
#
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 5614cf7..78d69a0 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -109,7 +109,10 @@ Bug Fixes since HDF5-1.8.5
Library
-------
- - None
+ - Fixed a bug that could cause file corruption when using non-default sizes
+ of addresses and/or lengths. This bug could also cause uncorrupted files
+ with this property to be unreadable. This bug was introduced in 1.8.5.
+ (NAF - 2010/07/16 - 1951)
Parallel Library
----------------
diff --git a/src/H5HLcache.c b/src/H5HLcache.c
index 83e2fd3..6c5c5d2 100644
--- a/src/H5HLcache.c
+++ b/src/H5HLcache.c
@@ -328,6 +328,11 @@ H5HL_prefix_load(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_udata)
/* Check if the current buffer from the speculative read already has the heap data */
if(spec_read_size >= (heap->prfx_size + heap->dblk_size)) {
+ /* Set p to the start of the data block. This is necessary
+ * because there may be a gap between the used portion of the
+ * prefix and the data block due to alignment constraints. */
+ p = buf + heap->prfx_size;
+
/* Copy the heap data from the speculative read buffer */
HDmemcpy(heap->dblk_image, p, heap->dblk_size);
} /* end if */
@@ -433,6 +438,11 @@ H5HL_prefix_flush(H5F_t *f, hid_t dxpl_id, hbool_t destroy, haddr_t addr,
/* Check if the local heap is a single object in cache */
if(heap->single_cache_obj) {
+ /* Set p to the start of the data block. This is necessary because
+ * there may be a gap between the used portion of the prefix and the
+ * data block due to alignment constraints. */
+ p = buf + heap->prfx_size;
+
/* Serialize the free list into the heap data's image */
H5HL_fl_serialize(heap);
diff --git a/test/Makefile.am b/test/Makefile.am
index 307d207..cb5cd90 100644
--- a/test/Makefile.am
+++ b/test/Makefile.am
@@ -62,7 +62,7 @@ check_PROGRAMS=$(TEST_PROG) error_test err_compat tcheck_version testmeta
# so do not appear in this list.
BUILD_ALL_PROGS=gen_bad_ohdr gen_bogus gen_cross gen_deflate gen_filters gen_idx \
gen_new_array gen_new_fill gen_new_group gen_new_mtime gen_new_super \
- gen_noencoder gen_nullspace gen_udlinks space_overflow
+ gen_noencoder gen_nullspace gen_udlinks space_overflow gen_sizes_lheap
if BUILD_ALL_CONDITIONAL
noinst_PROGRAMS=$(BUILD_ALL_PROGS)
diff --git a/test/Makefile.in b/test/Makefile.in
index dfdd5ab..48f3d39 100644
--- a/test/Makefile.in
+++ b/test/Makefile.in
@@ -94,7 +94,7 @@ am__EXEEXT_2 = gen_bad_ohdr$(EXEEXT) gen_bogus$(EXEEXT) \
gen_new_group$(EXEEXT) gen_new_mtime$(EXEEXT) \
gen_new_super$(EXEEXT) gen_noencoder$(EXEEXT) \
gen_nullspace$(EXEEXT) gen_udlinks$(EXEEXT) \
- space_overflow$(EXEEXT)
+ space_overflow$(EXEEXT) gen_sizes_lheap$(EXEEXT)
PROGRAMS = $(noinst_PROGRAMS)
app_ref_SOURCES = app_ref.c
app_ref_OBJECTS = app_ref.$(OBJEXT)
@@ -240,6 +240,10 @@ gen_nullspace_SOURCES = gen_nullspace.c
gen_nullspace_OBJECTS = gen_nullspace.$(OBJEXT)
gen_nullspace_LDADD = $(LDADD)
gen_nullspace_DEPENDENCIES = libh5test.la $(LIBHDF5)
+gen_sizes_lheap_SOURCES = gen_sizes_lheap.c
+gen_sizes_lheap_OBJECTS = gen_sizes_lheap.$(OBJEXT)
+gen_sizes_lheap_LDADD = $(LDADD)
+gen_sizes_lheap_DEPENDENCIES = libh5test.la $(LIBHDF5)
gen_udlinks_SOURCES = gen_udlinks.c
gen_udlinks_OBJECTS = gen_udlinks.$(OBJEXT)
gen_udlinks_LDADD = $(LDADD)
@@ -366,12 +370,12 @@ SOURCES = $(libh5test_la_SOURCES) app_ref.c big.c bittests.c btree2.c \
flush2.c freespace.c gen_bad_ohdr.c gen_bogus.c gen_cross.c \
gen_deflate.c gen_filters.c gen_idx.c gen_new_array.c \
gen_new_fill.c gen_new_group.c gen_new_mtime.c gen_new_super.c \
- gen_noencoder.c gen_nullspace.c gen_udlinks.c getname.c \
- gheap.c hyperslab.c istore.c lheap.c links.c mf.c mount.c \
- mtime.c ntypes.c objcopy.c ohdr.c pool.c reserved.c \
- set_extent.c space_overflow.c stab.c tcheck_version.c \
- $(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c \
- vfd.c
+ gen_noencoder.c gen_nullspace.c gen_sizes_lheap.c \
+ gen_udlinks.c getname.c gheap.c hyperslab.c istore.c lheap.c \
+ links.c mf.c mount.c mtime.c ntypes.c objcopy.c ohdr.c pool.c \
+ reserved.c set_extent.c space_overflow.c stab.c \
+ tcheck_version.c $(testhdf5_SOURCES) testmeta.c \
+ $(ttsafe_SOURCES) unlink.c vfd.c
DIST_SOURCES = $(libh5test_la_SOURCES) app_ref.c big.c bittests.c \
btree2.c cache.c cache_api.c cmpd_dset.c cross_read.c dangle.c \
dsets.c dt_arith.c dtransform.c dtypes.c enum.c err_compat.c \
@@ -379,12 +383,12 @@ DIST_SOURCES = $(libh5test_la_SOURCES) app_ref.c big.c bittests.c \
flush2.c freespace.c gen_bad_ohdr.c gen_bogus.c gen_cross.c \
gen_deflate.c gen_filters.c gen_idx.c gen_new_array.c \
gen_new_fill.c gen_new_group.c gen_new_mtime.c gen_new_super.c \
- gen_noencoder.c gen_nullspace.c gen_udlinks.c getname.c \
- gheap.c hyperslab.c istore.c lheap.c links.c mf.c mount.c \
- mtime.c ntypes.c objcopy.c ohdr.c pool.c reserved.c \
- set_extent.c space_overflow.c stab.c tcheck_version.c \
- $(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c \
- vfd.c
+ gen_noencoder.c gen_nullspace.c gen_sizes_lheap.c \
+ gen_udlinks.c getname.c gheap.c hyperslab.c istore.c lheap.c \
+ links.c mf.c mount.c mtime.c ntypes.c objcopy.c ohdr.c pool.c \
+ reserved.c set_extent.c space_overflow.c stab.c \
+ tcheck_version.c $(testhdf5_SOURCES) testmeta.c \
+ $(ttsafe_SOURCES) unlink.c vfd.c
ETAGS = etags
CTAGS = ctags
am__tty_colors = \
@@ -710,7 +714,7 @@ TEST_PROG = testhdf5 lheap ohdr stab gheap cache cache_api \
# so do not appear in this list.
BUILD_ALL_PROGS = gen_bad_ohdr gen_bogus gen_cross gen_deflate gen_filters gen_idx \
gen_new_array gen_new_fill gen_new_group gen_new_mtime gen_new_super \
- gen_noencoder gen_nullspace gen_udlinks space_overflow
+ gen_noencoder gen_nullspace gen_udlinks space_overflow gen_sizes_lheap
# The libh5test library provides common support code for the tests.
@@ -931,6 +935,9 @@ gen_noencoder$(EXEEXT): $(gen_noencoder_OBJECTS) $(gen_noencoder_DEPENDENCIES)
gen_nullspace$(EXEEXT): $(gen_nullspace_OBJECTS) $(gen_nullspace_DEPENDENCIES)
@rm -f gen_nullspace$(EXEEXT)
$(LINK) $(gen_nullspace_OBJECTS) $(gen_nullspace_LDADD) $(LIBS)
+gen_sizes_lheap$(EXEEXT): $(gen_sizes_lheap_OBJECTS) $(gen_sizes_lheap_DEPENDENCIES)
+ @rm -f gen_sizes_lheap$(EXEEXT)
+ $(LINK) $(gen_sizes_lheap_OBJECTS) $(gen_sizes_lheap_LDADD) $(LIBS)
gen_udlinks$(EXEEXT): $(gen_udlinks_OBJECTS) $(gen_udlinks_DEPENDENCIES)
@rm -f gen_udlinks$(EXEEXT)
$(LINK) $(gen_udlinks_OBJECTS) $(gen_udlinks_LDADD) $(LIBS)
@@ -1047,6 +1054,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gen_new_super.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gen_noencoder.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gen_nullspace.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gen_sizes_lheap.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gen_udlinks.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/getname.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gheap.Po@am__quote@
diff --git a/test/gen_sizes_lheap.c b/test/gen_sizes_lheap.c
new file mode 100644
index 0000000..de7e261
--- /dev/null
+++ b/test/gen_sizes_lheap.c
@@ -0,0 +1,82 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * Copyright by the Board of Trustees of the University of Illinois. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the files COPYING and Copyright.html. COPYING can be found at the root *
+ * of the source code distribution tree; Copyright.html can be found at the *
+ * root level of an installed copy of the electronic HDF5 document set and *
+ * is linked from the top-level documents page. It can also be found at *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
+ * access to either file, you may request a copy from help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Programmer: Neil Fortner <nfortne2@hdfgroup.org>
+ * Thursday, July 15, 2010
+ *
+ * Purpose: Creates a file with non-default sizes of lengths and addresses.
+ * This is used to make sure that the local heap code is able to
+ * handle this case correctly, even when the heap prefix and data
+ * are contiguous.
+ */
+
+#include "hdf5.h"
+
+#define TESTFILE "tsizeslheap.h5"
+
+
+/*-------------------------------------------------------------------------
+ * Function: main
+ *
+ * Purpose:
+ *
+ * Return: Success:
+ *
+ * Failure:
+ *
+ * Programmer: Neil Fortner
+ * Thursday, July 15, 2010
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(void)
+{
+ hid_t file, space, dset, fcpl;
+
+ /* Create the FCPL */
+ fcpl = H5Pcreate(H5P_FILE_CREATE);
+ if(fcpl < 0)
+ printf("fcpl < 0!\n");
+
+ /* Set sizeof_addr and sizeof_size to be 4 */
+ if(H5Pset_sizes(fcpl, 4, 4) < 0)
+ printf("H5Pset_sizes < 0!\n");
+
+ /* Create the file */
+ file = H5Fcreate(TESTFILE, H5F_ACC_TRUNC, fcpl, H5P_DEFAULT);
+ if(file < 0)
+ printf("file < 0!\n");
+
+ /* Create the dataspace (for dataset) */
+ space = H5Screate(H5S_SCALAR);
+ if(space < 0)
+ printf("space < 0!\n");
+
+ /* Create the dataset with compound array fields */
+ dset = H5Dcreate2(file, "Dataset1", H5T_NATIVE_INT, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ if(dset < 0)
+ printf("dset < 0!\n");
+
+ H5Dclose(dset);
+ H5Sclose(space);
+ H5Fclose(file);
+ H5Pclose(fcpl);
+
+ return 0;
+}
diff --git a/test/lheap.c b/test/lheap.c
index 52af202..dd7ff48 100644
--- a/test/lheap.c
+++ b/test/lheap.c
@@ -20,6 +20,7 @@
* Purpose: Test local heaps used by symbol tables (groups).
*/
#include "h5test.h"
+#include "H5srcdir.h"
#include "H5ACprivate.h"
#include "H5HLprivate.h"
#include "H5Iprivate.h"
@@ -29,6 +30,8 @@ const char *FILENAME[] = {
NULL
};
+#define TESTFILE "tsizeslheap.h5"
+
#define NOBJS 40
@@ -160,6 +163,29 @@ main(void)
if (H5Fclose(file)<0) goto error;
PASSED();
+
+ /* Check opening existing file non-default sizes of lengths and addresses */
+ TESTING("opening pre-created file with non-default sizes");
+ {
+ const char *testfile = H5_get_srcdir_filename(TESTFILE); /* Corrected test file name */
+ hid_t dset = -1;
+
+ file = H5Fopen(testfile, H5F_ACC_RDONLY, H5P_DEFAULT);
+ if(file >= 0){
+ if((dset = H5Dopen2(file, "/Dataset1", H5P_DEFAULT)) < 0)
+ TEST_ERROR
+ if(H5Dclose(dset) < 0) TEST_ERROR
+ if(H5Fclose(file) < 0) TEST_ERROR
+ }
+ else {
+ H5_FAILED();
+ printf("***cannot open the pre-created non-default sizes test file (%s)\n",
+ testfile);
+ goto error;
+ } /* end else */
+ }
+ PASSED();
+
puts("All local heap tests passed.");
h5_cleanup(FILENAME, fapl);
diff --git a/test/tsizeslheap.h5 b/test/tsizeslheap.h5
new file mode 100644
index 0000000..c7f2adb
--- /dev/null
+++ b/test/tsizeslheap.h5
Binary files differ