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[svn-r21870] Purpose:

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Fix for HDFFV-7840 h5repack: memory leak over one of the h5diff test file

Description:
  Turned out that there were two causes of memory leaks.
  1. for handling variable length string in attribute. 
  2. for handling compound type with non-reference members.  
  The first issue is fixed in copy_attr() which is updated to use h5tools_detect_vlen to take care of vlen string as well as vlen data. 
  The second is fixed in copy_refs_attr() of compound handling code.
  Merged from HDF5 trunk r21869.
  
Tested:
 jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE),  Windows (32-LE cmake), Cmake (jam)
This commit is contained in:
Jonathan Kim
2012-01-10 11:23:38 -05:00
parent da199c11f4
commit 5540ecb72d
5 changed files with 90 additions and 58 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
release_docs/RELEASE.txt
View File

@@ -112,6 +112,8 @@ Bug Fixes since HDF5-1.8.8
Tools
-----
- h5repack: fixed memory leak for handling variable length string in
attribute. HDFFV-7840 (JKM 2012/01/10)
- h5ls: fixed segfault when access region reference data in an
attribute. HDFFV-7838 (JKM 2012/01/06)

110
tools/h5repack/CMakeLists.txt
View File

@@ -81,68 +81,64 @@ IF (BUILD_TESTING)
ENDIF (HDF5_TEST_VFD)
# --------------------------------------------------------------------
# Copy all the HDF5 files from the test directory into the source directory
# Copy all the HDF5 files from the source directory into the test directory
# --------------------------------------------------------------------
SET (HDF5_REFERENCE_TEST_FILES
h5repack_ext.bin
ublock.bin
h5repack.info
h5repack_attr.h5
h5repack_deflate.h5
h5repack_early.h5
h5repack_ext.h5
h5repack_fill.h5
h5repack_filters.h5
h5repack_fletcher.h5
h5repack_hlink.h5
h5repack_layout.h5
h5repack_layouto.h5
h5repack_layout2.h5
h5repack_named_dtypes.h5
h5repack_nbit.h5
h5repack_objs.h5
h5repack_refs.h5
h5repack_shuffle.h5
h5repack_soffset.h5
h5repack_szip.h5
)
SET (HDF5_COMMON_TEST_FILES
tfamily00000.h5
tfamily00001.h5
tfamily00002.h5
tfamily00003.h5
tfamily00004.h5
tfamily00005.h5
tfamily00006.h5
tfamily00007.h5
tfamily00008.h5
tfamily00009.h5
tfamily00010.h5
h5repack_filters.h5.ddl
SET (LIST_HDF5_TEST_FILES
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_attr.h5
#${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_attr_refs.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_deflate.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_early.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_ext.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_fill.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_filters.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_fletcher.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_hlink.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layouto.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout2.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_named_dtypes.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_nbit.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_objs.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_refs.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_shuffle.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_soffset.h5
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_szip.h5
# h5diff/testfile
${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_attr1.h5
# tools/testfiles
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00000.h5
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00001.h5
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00002.h5
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00003.h5
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00004.h5
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00005.h5
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00006.h5
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00007.h5
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00008.h5
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00009.h5
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00010.h5
)
FOREACH (h5_file ${HDF5_REFERENCE_TEST_FILES})
SET (dest "${PROJECT_BINARY_DIR}/testfiles/${h5_file}")
SET (LIST_OTHER_TEST_FILES
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_ext.bin
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/ublock.bin
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack.info
# tools/testfiles
${HDF5_TOOLS_SRC_DIR}/testfiles/h5repack_filters.h5.ddl
)
FOREACH (h5_file ${LIST_HDF5_TEST_FILES} ${LIST_OTHER_TEST_FILES})
GET_FILENAME_COMPONENT(fname "${h5_file}" NAME)
SET (dest "${PROJECT_BINARY_DIR}/testfiles/${fname}")
#MESSAGE (STATUS " Copying ${h5_file}")
ADD_CUSTOM_COMMAND (
TARGET h5repack
POST_BUILD
COMMAND ${CMAKE_COMMAND}
ARGS -E copy_if_different ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/${h5_file} ${dest}
ARGS -E copy_if_different ${h5_file} ${dest}
)
ENDFOREACH (h5_file ${HDF5_REFERENCE_TEST_FILES})
ENDFOREACH (h5_file ${LIST_HDF5_TEST_FILES} ${LIST_OTHER_TEST_FILES})
FOREACH (h5c_file ${HDF5_COMMON_TEST_FILES})
SET (dest "${PROJECT_BINARY_DIR}/testfiles/${h5c_file}")
#MESSAGE (STATUS " Copying ${h5_file}")
ADD_CUSTOM_COMMAND (
TARGET h5repack
POST_BUILD
COMMAND ${CMAKE_COMMAND}
ARGS -E copy_if_different ${HDF5_TOOLS_SRC_DIR}/testfiles/${h5c_file} ${dest}
)
ENDFOREACH (h5c_file ${HDF5_COMMON_TEST_FILES})
##############################################################################
##############################################################################
### T H E T E S T S M A C R O S ###
@@ -334,6 +330,7 @@ IF (BUILD_TESTING)
h5repack_szip_out.h5
h5repack_ub.h5
h5repack_ub_out.h5
h5diff_attr1_out.h5
)
IF (NOT "${last_test}" STREQUAL "")
SET_TESTS_PROPERTIES (H5REPACK-clearall-objects PROPERTIES DEPENDS ${last_test})
@@ -783,9 +780,16 @@ IF (BUILD_TESTING)
# tests family driver (file is located in common testfiles folder, uses TOOLTEST1
# ADD_H5_TEST ( family "FAMILY" ${FILE16})
# test various references (bug 1814)
# test various references (bug 1814 and 1726)
ADD_H5_TEST (bug1814 "TEST" ${FILE_REF})
# Add test for memory leak in attirbute. This test is verified by CTEST.
# 1. leak from vlen string
# 2. leak from compound type without reference member
# (HDFFV-7840, )
# Note: this test is experimental for sharing test file among tools
ADD_H5_TEST (HDFFV-7840 "TEST" h5diff_attr1.h5)
IF (HDF5_TEST_VFD)
# Run test with different Virtual File Driver
FOREACH (vfd ${VFD_LIST})

10
tools/h5repack/h5repack.c
View File

@@ -541,9 +541,9 @@ int copy_attr(hid_t loc_in,
if(H5Aclose(attr_out) < 0)
goto error;
/* Check if we have VL data in the attribute's datatype that must
/* Check if we have VL data and string in the attribute's datatype that must
* be reclaimed */
if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
if (TRUE == h5tools_detect_vlen(wtype_id))
H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
HDfree(buf);
buf = NULL;
@@ -573,13 +573,13 @@ int copy_attr(hid_t loc_in,
error:
H5E_BEGIN_TRY {
if(buf) {
/* Check if we have VL data in the attribute's datatype that must
/* Check if we have VL data and string in the attribute's datatype that must
* be reclaimed */
if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
if (TRUE == h5tools_detect_vlen(wtype_id))
H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
/* Free buf */
free(buf);
HDfree(buf);
} /* end if */
H5Tclose(ftype_id);

9
tools/h5repack/h5repack.sh.in
View File

@@ -101,6 +101,7 @@ $SRC_H5REPACK_TESTFILES/h5repack_refs.h5
$SRC_H5REPACK_TESTFILES/h5repack_shuffle.h5
$SRC_H5REPACK_TESTFILES/h5repack_soffset.h5
$SRC_H5REPACK_TESTFILES/h5repack_szip.h5
$SRC_H5DIFF_TESTFILES/h5diff_attr1.h5
$SRC_TOOLS_TESTFILES/tfamily00000.h5
$SRC_TOOLS_TESTFILES/tfamily00001.h5
$SRC_TOOLS_TESTFILES/tfamily00002.h5
@@ -800,6 +801,14 @@ TOOLTEST h5repack_refs.h5
# the references in attribute of compund or vlen datatype
TOOLTEST h5repack_attr_refs.h5
# Add test for memory leak in attirbute. This test is verified by CTEST.
# 1. leak from vlen string
# 2. leak from compound type without reference member
# (HDFFV-7840, )
# Note: this test is experimental for sharing test file among tools
TOOLTEST h5diff_attr1.h5
if test $nerrors -eq 0 ; then
echo "All $TESTNAME tests passed."
exit $EXIT_SUCCESS

17
tools/h5repack/h5repack_refs.c
View File

@@ -533,6 +533,23 @@ static int copy_refs_attr(hid_t loc_in,
}
H5Tclose(mtid);
}
/* if don't contain reference type, free malloc for continue
* and malloc again later */
if (!ref_comp_field_n)
{
if (ref_comp_index)
{
HDfree(ref_comp_index);
ref_comp_index = NULL;
}
if (ref_comp_size)
{
HDfree(ref_comp_size);
ref_comp_size = NULL;
}
}
}
is_ref_comp = (ref_comp_field_n > 0);