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[svn-r19076] Purpose: Fix bug 1951
Description: A bug introduced in 1.8.5 causes local heap data blocks to be mis-aligned when sizeof_offsets + 2*sizeof_lengths is not a multiple of 8. In this case, the address of the data block as stored in the heap prefix is aligned but the actual data block is not. This causes files created with these sizes to be corrupted, and prevents uncorrupted files with these sizes to be unreadable. Modified local heap code to account for alignment. Tested: jam, amani, linew (h5committest)
This commit is contained in:
Neil Fortner
parent
0dce71a0a3
commit
c22b8a94f2
2
MANIFEST
2
MANIFEST
@ -856,6 +856,7 @@
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./test/gen_old_group.c _DO_NOT_DISTRIBUTE_
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./test/gen_old_layout.c _DO_NOT_DISTRIBUTE_
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./test/gen_old_mtime.c _DO_NOT_DISTRIBUTE_
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./test/gen_sizes_lheap.c _DO_NOT_DISTRIBUTE_
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./test/gen_specmetaread.c _DO_NOT_DISTRIBUTE_
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./test/gen_udlinks.c _DO_NOT_DISTRIBUTE_
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./test/getname.c
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@ -917,6 +918,7 @@
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./test/trefer.c
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./test/trefstr.c
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./test/tselect.c
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./test/tsizeslheap.h5
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./test/tskiplist.c
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./test/tsohm.c
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./test/ttst.c
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2
configure
vendored
2
configure
vendored
@ -1,5 +1,5 @@
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#! /bin/sh
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# From configure.in Id: configure.in 19064 2010-07-11 17:06:05Z hdftest .
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# From configure.in Id: configure.in 19068 2010-07-14 15:56:42Z acheng .
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# Guess values for system-dependent variables and create Makefiles.
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# Generated by GNU Autoconf 2.65 for HDF5 1.9.74.
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#
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@ -234,6 +234,10 @@ Bug Fixes since HDF5-1.8.0 release
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Library
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-------
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- Fixed a bug that could cause file corruption when using non-default
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sizes of addresses and/or lengths. This bug could also cause
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uncorrupted files with this property to be unreadable. This bug
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was introduced in 1.8.5. (NAF - 2010/07/16 - 1951)
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- Fixed a file corruption bug that could happen when shrinking a
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compressed dataset. (NAF - 2010/05/20)
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- Fixed some memory leaks in VL datatype conversion when strings are
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@ -330,6 +330,11 @@ H5HL_prefix_load(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_udata)
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/* Check if the current buffer from the speculative read already has the heap data */
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if(spec_read_size >= (heap->prfx_size + heap->dblk_size)) {
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/* Set p to the start of the data block. This is necessary
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* because there may be a gap between the used portion of the
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* prefix and the data block due to alignment constraints. */
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p = buf + heap->prfx_size;
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/* Copy the heap data from the speculative read buffer */
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HDmemcpy(heap->dblk_image, p, heap->dblk_size);
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} /* end if */
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@ -435,6 +440,11 @@ H5HL_prefix_flush(H5F_t *f, hid_t dxpl_id, hbool_t destroy, haddr_t addr,
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/* Check if the local heap is a single object in cache */
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if(heap->single_cache_obj) {
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/* Set p to the start of the data block. This is necessary because
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* there may be a gap between the used portion of the prefix and the
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* data block due to alignment constraints. */
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p = buf + heap->prfx_size;
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/* Serialize the free list into the heap data's image */
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H5HL_fl_serialize(heap);
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@ -62,7 +62,8 @@ check_PROGRAMS=$(TEST_PROG) error_test err_compat tcheck_version testmeta
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# so do not appear in this list.
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BUILD_ALL_PROGS=gen_bad_ohdr gen_bogus gen_cross gen_deflate gen_filters gen_new_array \
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gen_new_fill gen_new_group gen_new_mtime gen_new_super gen_noencoder \
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gen_nullspace gen_udlinks space_overflow gen_filespace gen_specmetaread
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gen_nullspace gen_udlinks space_overflow gen_filespace gen_specmetaread \
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gen_sizes_lheap
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if BUILD_ALL_CONDITIONAL
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noinst_PROGRAMS=$(BUILD_ALL_PROGS)
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@ -96,7 +96,7 @@ am__EXEEXT_2 = gen_bad_ohdr$(EXEEXT) gen_bogus$(EXEEXT) \
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gen_new_super$(EXEEXT) gen_noencoder$(EXEEXT) \
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gen_nullspace$(EXEEXT) gen_udlinks$(EXEEXT) \
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space_overflow$(EXEEXT) gen_filespace$(EXEEXT) \
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gen_specmetaread$(EXEEXT)
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gen_specmetaread$(EXEEXT) gen_sizes_lheap$(EXEEXT)
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PROGRAMS = $(noinst_PROGRAMS)
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app_ref_SOURCES = app_ref.c
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app_ref_OBJECTS = app_ref.$(OBJEXT)
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@ -254,6 +254,10 @@ gen_nullspace_SOURCES = gen_nullspace.c
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gen_nullspace_OBJECTS = gen_nullspace.$(OBJEXT)
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gen_nullspace_LDADD = $(LDADD)
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gen_nullspace_DEPENDENCIES = libh5test.la $(LIBHDF5)
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gen_sizes_lheap_SOURCES = gen_sizes_lheap.c
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gen_sizes_lheap_OBJECTS = gen_sizes_lheap.$(OBJEXT)
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gen_sizes_lheap_LDADD = $(LDADD)
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gen_sizes_lheap_DEPENDENCIES = libh5test.la $(LIBHDF5)
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gen_specmetaread_SOURCES = gen_specmetaread.c
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gen_specmetaread_OBJECTS = gen_specmetaread.$(OBJEXT)
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gen_specmetaread_LDADD = $(LDADD)
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@ -385,12 +389,12 @@ SOURCES = $(libh5test_la_SOURCES) app_ref.c big.c bittests.c btree2.c \
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gen_bogus.c gen_cross.c gen_deflate.c gen_filespace.c \
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gen_filters.c gen_new_array.c gen_new_fill.c gen_new_group.c \
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gen_new_mtime.c gen_new_super.c gen_noencoder.c \
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gen_nullspace.c gen_specmetaread.c gen_udlinks.c getname.c \
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gheap.c hyperslab.c istore.c lheap.c links.c mf.c mount.c \
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mtime.c ntypes.c objcopy.c ohdr.c pool.c reserved.c \
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set_extent.c space_overflow.c stab.c tcheck_version.c \
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$(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c \
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vfd.c
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gen_nullspace.c gen_sizes_lheap.c gen_specmetaread.c \
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gen_udlinks.c getname.c gheap.c hyperslab.c istore.c lheap.c \
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links.c mf.c mount.c mtime.c ntypes.c objcopy.c ohdr.c pool.c \
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reserved.c set_extent.c space_overflow.c stab.c \
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tcheck_version.c $(testhdf5_SOURCES) testmeta.c \
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$(ttsafe_SOURCES) unlink.c vfd.c
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DIST_SOURCES = $(libh5test_la_SOURCES) app_ref.c big.c bittests.c \
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btree2.c cache.c cache_api.c cache_tagging.c cmpd_dset.c \
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cross_read.c dangle.c dsets.c dt_arith.c dtransform.c dtypes.c \
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@ -399,12 +403,12 @@ DIST_SOURCES = $(libh5test_la_SOURCES) app_ref.c big.c bittests.c \
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gen_bad_ohdr.c gen_bogus.c gen_cross.c gen_deflate.c \
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gen_filespace.c gen_filters.c gen_new_array.c gen_new_fill.c \
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gen_new_group.c gen_new_mtime.c gen_new_super.c \
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gen_noencoder.c gen_nullspace.c gen_specmetaread.c \
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gen_udlinks.c getname.c gheap.c hyperslab.c istore.c lheap.c \
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links.c mf.c mount.c mtime.c ntypes.c objcopy.c ohdr.c pool.c \
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reserved.c set_extent.c space_overflow.c stab.c \
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tcheck_version.c $(testhdf5_SOURCES) testmeta.c \
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$(ttsafe_SOURCES) unlink.c vfd.c
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gen_noencoder.c gen_nullspace.c gen_sizes_lheap.c \
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gen_specmetaread.c gen_udlinks.c getname.c gheap.c hyperslab.c \
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istore.c lheap.c links.c mf.c mount.c mtime.c ntypes.c \
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objcopy.c ohdr.c pool.c reserved.c set_extent.c \
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space_overflow.c stab.c tcheck_version.c $(testhdf5_SOURCES) \
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testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
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ETAGS = etags
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CTAGS = ctags
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am__tty_colors = \
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@ -729,7 +733,8 @@ TEST_PROG = testhdf5 lheap ohdr stab gheap cache cache_api cache_tagging \
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# so do not appear in this list.
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BUILD_ALL_PROGS = gen_bad_ohdr gen_bogus gen_cross gen_deflate gen_filters gen_new_array \
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gen_new_fill gen_new_group gen_new_mtime gen_new_super gen_noencoder \
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gen_nullspace gen_udlinks space_overflow gen_filespace gen_specmetaread
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gen_nullspace gen_udlinks space_overflow gen_filespace gen_specmetaread \
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gen_sizes_lheap
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# The libh5test library provides common support code for the tests.
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@ -959,6 +964,9 @@ gen_noencoder$(EXEEXT): $(gen_noencoder_OBJECTS) $(gen_noencoder_DEPENDENCIES)
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gen_nullspace$(EXEEXT): $(gen_nullspace_OBJECTS) $(gen_nullspace_DEPENDENCIES)
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@rm -f gen_nullspace$(EXEEXT)
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$(LINK) $(gen_nullspace_OBJECTS) $(gen_nullspace_LDADD) $(LIBS)
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gen_sizes_lheap$(EXEEXT): $(gen_sizes_lheap_OBJECTS) $(gen_sizes_lheap_DEPENDENCIES)
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@rm -f gen_sizes_lheap$(EXEEXT)
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$(LINK) $(gen_sizes_lheap_OBJECTS) $(gen_sizes_lheap_LDADD) $(LIBS)
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gen_specmetaread$(EXEEXT): $(gen_specmetaread_OBJECTS) $(gen_specmetaread_DEPENDENCIES)
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@rm -f gen_specmetaread$(EXEEXT)
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$(LINK) $(gen_specmetaread_OBJECTS) $(gen_specmetaread_LDADD) $(LIBS)
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@ -1081,6 +1089,7 @@ distclean-compile:
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gen_new_super.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gen_noencoder.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gen_nullspace.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gen_sizes_lheap.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gen_specmetaread.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gen_udlinks.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/getname.Po@am__quote@
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82
test/gen_sizes_lheap.c
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82
test/gen_sizes_lheap.c
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@ -0,0 +1,82 @@
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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/*
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* Programmer: Neil Fortner <nfortne2@hdfgroup.org>
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* Thursday, July 15, 2010
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*
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* Purpose: Creates a file with non-default sizes of lengths and addresses.
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* This is used to make sure that the local heap code is able to
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* handle this case correctly, even when the heap prefix and data
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* are contiguous.
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*/
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#include "hdf5.h"
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#define TESTFILE "tsizeslheap.h5"
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/*-------------------------------------------------------------------------
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* Function: main
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*
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* Purpose:
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*
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* Return: Success:
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*
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* Failure:
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*
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* Programmer: Neil Fortner
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* Thursday, July 15, 2010
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*
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* Modifications:
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*
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*-------------------------------------------------------------------------
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*/
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int
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main(void)
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{
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hid_t file, space, dset, fcpl;
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/* Create the FCPL */
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fcpl = H5Pcreate(H5P_FILE_CREATE);
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if(fcpl < 0)
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printf("fcpl < 0!\n");
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/* Set sizeof_addr and sizeof_size to be 4 */
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if(H5Pset_sizes(fcpl, 4, 4) < 0)
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printf("H5Pset_sizes < 0!\n");
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/* Create the file */
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file = H5Fcreate(TESTFILE, H5F_ACC_TRUNC, fcpl, H5P_DEFAULT);
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if(file < 0)
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printf("file < 0!\n");
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/* Create the dataspace (for dataset) */
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space = H5Screate(H5S_SCALAR);
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if(space < 0)
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printf("space < 0!\n");
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/* Create the dataset with compound array fields */
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dset = H5Dcreate2(file, "Dataset1", H5T_NATIVE_INT, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
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if(dset < 0)
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printf("dset < 0!\n");
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H5Dclose(dset);
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H5Sclose(space);
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H5Fclose(file);
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H5Pclose(fcpl);
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return 0;
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}
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26
test/lheap.c
26
test/lheap.c
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* Purpose: Test local heaps used by symbol tables (groups).
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*/
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#include "h5test.h"
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#include "H5srcdir.h"
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#include "H5ACprivate.h"
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#include "H5HLprivate.h"
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#include "H5Iprivate.h"
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@ -29,6 +30,8 @@ const char *FILENAME[] = {
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NULL
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};
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#define TESTFILE "tsizeslheap.h5"
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#define NOBJS 40
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@ -170,6 +173,29 @@ main(void)
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if (H5Fclose(file)<0) goto error;
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PASSED();
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/* Check opening existing file non-default sizes of lengths and addresses */
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TESTING("opening pre-created file with non-default sizes");
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{
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const char *testfile = H5_get_srcdir_filename(TESTFILE); /* Corrected test file name */
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hid_t dset = -1;
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file = H5Fopen(testfile, H5F_ACC_RDONLY, H5P_DEFAULT);
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if(file >= 0){
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if((dset = H5Dopen2(file, "/Dataset1", H5P_DEFAULT)) < 0)
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TEST_ERROR
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if(H5Dclose(dset) < 0) TEST_ERROR
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if(H5Fclose(file) < 0) TEST_ERROR
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}
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else {
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H5_FAILED();
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printf("***cannot open the pre-created non-default sizes test file (%s)\n",
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testfile);
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goto error;
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} /* end else */
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}
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PASSED();
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puts("All local heap tests passed.");
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h5_cleanup(FILENAME, fapl);
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BIN
test/tsizeslheap.h5
Normal file
BIN
test/tsizeslheap.h5
Normal file
Binary file not shown.
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