diff options
| -rw-r--r-- | MANIFEST | 3 | ||||
| -rw-r--r-- | configure.ac | 2 | ||||
| -rw-r--r-- | release_docs/RELEASE.txt | 13 | ||||
| -rw-r--r-- | src/H5Adense.c | 35 | ||||
| -rw-r--r-- | test/CMakeLists.txt | 1 | ||||
| -rw-r--r-- | test/CMakeTests.cmake | 21 | ||||
| -rw-r--r-- | test/Makefile.am | 16 | ||||
| -rw-r--r-- | test/ShellTests.cmake | 3 | ||||
| -rw-r--r-- | test/del_many_dense_attrs.c | 203 | ||||
| -rw-r--r-- | test/testabort_fail.sh.in (renamed from test/test_filenotclosed.sh.in) | 39 |
10 files changed, 316 insertions, 20 deletions
@@ -948,6 +948,7 @@ ./test/cross_read.c ./test/dangle.c ./test/deflate.h5 +./test/del_many_dense_attrs.c ./test/direct_chunk.c ./test/dsets.c ./test/dt_arith.c @@ -1079,10 +1080,10 @@ ./test/tcheck_version.c ./test/tconfig.c ./test/tcoords.c +./test/testabort_fail.sh.in ./test/testcheck_version.sh.in ./test/testerror.sh.in ./test/testlinks_env.sh.in -./test/test_filenotclosed.sh.in ./test/test_filter_plugin.sh.in ./test/testflushrefresh.sh.in ./test/testframe.c diff --git a/configure.ac b/configure.ac index 17789d6..e724f06 100644 --- a/configure.ac +++ b/configure.ac @@ -3395,6 +3395,7 @@ AC_CONFIG_FILES([src/libhdf5.settings src/Makefile test/Makefile test/H5srcdir_str.h + test/testabort_fail.sh test/testcheck_version.sh test/testerror.sh test/testflushrefresh.sh @@ -3402,7 +3403,6 @@ AC_CONFIG_FILES([src/libhdf5.settings test/testlinks_env.sh test/testswmr.sh test/testvdsswmr.sh - test/test_filenotclosed.sh test/test_filter_plugin.sh test/test_usecases.sh testpar/Makefile diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index cb1d33a..62ad9ad 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -271,6 +271,19 @@ Bug Fixes since HDF5-1.10.3 release Library ------- + - Deleting attributes in dense storage + + The library aborts with "infinite loop closing library" after + attributes in dense storage are created and then deleted. + + When deleting the attribute nodes from the name index v2 B-tree, + if an attribute is found in the intermediate B-tree nodes, + which may be merged/redistributed in the process, we need to + free the dynamically allocated spaces for the intermediate + decoded attribute. + + (VC - 2018/12/26, HDFFV-10659) + - A bug was discovered in the parallel library where an application would eventually consume all of the available MPI communicators when continually writing to a compressed dataset in parallel. This diff --git a/src/H5Adense.c b/src/H5Adense.c index 3701022..40a7a9a 100644 --- a/src/H5Adense.c +++ b/src/H5Adense.c @@ -302,20 +302,51 @@ static herr_t H5A__dense_fnd_cb(const H5A_t *attr, hbool_t *took_ownership, void *_user_attr) { H5A_t const **user_attr = (H5A_t const **)_user_attr; /* User data from v2 B-tree attribute lookup */ + herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_STATIC_NOERR + FUNC_ENTER_STATIC /* * Check arguments. */ HDassert(attr); HDassert(user_attr); + HDassert(took_ownership); + /* + * If there is an attribute already stored in "user_attr", + * we need to free the dynamially allocated spaces for the + * attribute, otherwise we got infinite loop closing library due to + * outstanding allocation. (HDFFV-10659) + * + * This callback is used by H5A__dense_remove() to close/free the + * attribute stored in "user_attr" (via H5O__msg_free_real()) after + * the attribute node is deleted from the name index v2 B-tree. + * The issue is: + * When deleting the attribute node from the B-tree, + * if the attribute is found in the intermediate B-tree nodes, + * which may be merged/redistributed, we need to free the dynamically + * allocated spaces for the intermediate decoded attribute. + */ + if(*user_attr != NULL) { + H5A_t *old_attr = *user_attr; + if(old_attr->shared) { + /* Free any dynamically allocated items */ + if(H5A__free(old_attr) < 0) + HGOTO_ERROR(H5E_ATTR, H5E_CANTRELEASE, FAIL, "can't release attribute info") + + /* Destroy shared attribute struct */ + old_attr->shared = H5FL_FREE(H5A_shared_t, old_attr->shared); + } /* end if */ + + old_attr = H5FL_FREE(H5A_t, old_attr); + } /* end if */ /* Take over attribute ownership */ *user_attr = attr; *took_ownership = TRUE; - FUNC_LEAVE_NOAPI(SUCCEED) +done: + FUNC_LEAVE_NOAPI(ret_value) } /* end H5A__dense_fnd_cb() */ diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index ce39506..fa303ed 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -342,6 +342,7 @@ set (H5_CHECK_TESTS atomic_reader links_env filenotclosed + del_many_dense_attrs flushrefresh ) diff --git a/test/CMakeTests.cmake b/test/CMakeTests.cmake index ba64964..881bdb8 100644 --- a/test/CMakeTests.cmake +++ b/test/CMakeTests.cmake @@ -520,6 +520,7 @@ set (test_CLEANFILES flushrefresh_VERIFICATION_CHECKPOINT2 flushrefresh_VERIFICATION_DONE filenotclosed.h5 + del_many_dense_attrs.h5 atomic_data accum_swmr_big.h5 ohdr_swmr.h5 @@ -795,6 +796,7 @@ set_tests_properties (H5TEST-tcheck_version-release PROPERTIES # atomic_reader # links_env # filenotclosed +# del_many_dense_attrs # flushrefresh ############################################################################## # autotools script tests @@ -802,7 +804,7 @@ set_tests_properties (H5TEST-tcheck_version-release PROPERTIES # NOT CONVERTED accum_swmr_reader is used by accum.c. # NOT CONVERTED atomic_writer and atomic_reader are standalone programs. # links_env is used by testlinks_env.sh -# filenotclosed is used by test_filenotclosed.sh +# filenotclosed and del_many_dense_attrs are used by testabort_fail.sh # NOT CONVERTED flushrefresh is used by testflushrefresh.sh. # NOT CONVERTED use_append_chunk, use_append_mchunks and use_disable_mdc_flushes are used by test_usecases.sh # NOT CONVERTED swmr_* files (besides swmr.c) are used by testswmr.sh. @@ -829,6 +831,23 @@ set_tests_properties (H5TEST-filenotclosed PROPERTIES WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/H5TEST ) +#-- Adding test for del_many_dense_attrs +add_test ( + NAME H5TEST-clear-del_many_dense_attrs-objects + COMMAND ${CMAKE_COMMAND} + -E remove + del_many_dense_attrs.h5 + WORKING_DIRECTORY + ${HDF5_TEST_BINARY_DIR}/H5TEST +) +set_tests_properties (H5TEST-clear-del_many_dense_attrs-objects PROPERTIES FIXTURES_SETUP del_many_dense_attrs_clear_objects) +add_test (NAME H5TEST-del_many_dense_attrs COMMAND $<TARGET_FILE:del_many_dense_attrs>) +set_tests_properties (H5TEST-del_many_dense_attrs PROPERTIES + FIXTURES_REQUIRED del_many_dense_attrs_clear_objects + ENVIRONMENT "srcdir=${HDF5_TEST_BINARY_DIR}/H5TEST" + WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/H5TEST +) + #-- Adding test for err_compat if (HDF5_ENABLE_DEPRECATED_SYMBOLS) add_test (NAME H5TEST-clear-err_compat-objects diff --git a/test/Makefile.am b/test/Makefile.am index 6a057c1..c4fb876 100644 --- a/test/Makefile.am +++ b/test/Makefile.am @@ -29,12 +29,13 @@ AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_builddir)/src # testflushrefresh.sh: flushrefresh # testswmr.sh: swmr* # testvdsswmr.sh: vds_swmr* -# test_filenotclosed.sh: filenotclosed.c +# testabort_fail.sh: filenotclosed.c and del_many_dense_attrs.c # test_filter_plugin.sh: filter_plugin.c # test_usecases.sh: use_append_chunk, use_append_mchunks, use_disable_mdc_flushes -TEST_SCRIPT = testerror.sh testlibinfo.sh testcheck_version.sh testlinks_env.sh test_filenotclosed.sh\ - testswmr.sh testvdsswmr.sh testflushrefresh.sh test_usecases.sh -SCRIPT_DEPEND = error_test$(EXEEXT) err_compat$(EXEEXT) links_env$(EXEEXT) filenotclosed$(EXEEXT) \ +TEST_SCRIPT = testerror.sh testlibinfo.sh testcheck_version.sh testlinks_env.sh \ + testswmr.sh testvdsswmr.sh testflushrefresh.sh test_usecases.sh testabort_fail.sh +SCRIPT_DEPEND = error_test$(EXEEXT) err_compat$(EXEEXT) links_env$(EXEEXT) \ + filenotclosed$(EXEEXT) del_many_dense_attrs$(EXEEXT) \ flushrefresh$(EXEEXT) use_append_chunk$(EXEEXT) use_append_mchunks$(EXEEXT) use_disable_mdc_flushes$(EXEEXT) \ swmr_generator$(EXEEXT) swmr_reader$(EXEEXT) swmr_writer$(EXEEXT) \ swmr_remove_reader$(EXEEXT) swmr_remove_writer$(EXEEXT) swmr_addrem_writer$(EXEEXT) \ @@ -68,7 +69,7 @@ TEST_PROG= testhdf5 \ # accum_swmr_reader is used by accum.c. # atomic_writer and atomic_reader are standalone programs. # links_env is used by testlinks_env.sh -# filenotclosed is used by test_filenotclosed.sh +# filenotclosed and del_many_dense_attrs are used by testabort_fail.sh # flushrefresh is used by testflushrefresh.sh. # use_append_chunk, use_append_mchunks and use_disable_mdc_flushes are used by test_usecases.sh # swmr_* files (besides swmr.c) are used by testswmr.sh. @@ -78,7 +79,8 @@ TEST_PROG= testhdf5 \ # and this lets automake keep all its test programs in one place. check_PROGRAMS=$(TEST_PROG) error_test err_compat tcheck_version \ testmeta accum_swmr_reader atomic_writer atomic_reader \ - links_env filenotclosed flushrefresh use_append_chunk use_append_mchunks use_disable_mdc_flushes \ + links_env filenotclosed del_many_dense_attrs flushrefresh \ + use_append_chunk use_append_mchunks use_disable_mdc_flushes \ swmr_generator swmr_start_write swmr_reader swmr_writer swmr_remove_reader \ swmr_remove_writer swmr_addrem_writer swmr_sparse_reader swmr_sparse_writer \ swmr_check_compat_vfd vds_swmr_gen vds_swmr_reader vds_swmr_writer @@ -209,6 +211,6 @@ use_disable_mdc_flushes_SOURCES=use_disable_mdc_flushes.c # Temporary files. DISTCLEANFILES=testerror.sh testlibinfo.sh testcheck_version.sh testlinks_env.sh test_filter_plugin.sh \ - testswmr.sh testvdsswmr.sh test_usecases.sh testflushrefresh.sh test_filenotclosed.sh + testswmr.sh testvdsswmr.sh test_usecases.sh testflushrefresh.sh testabort_fail.sh include $(top_srcdir)/config/conclude.am diff --git a/test/ShellTests.cmake b/test/ShellTests.cmake index 58dc85d..98f3daf 100644 --- a/test/ShellTests.cmake +++ b/test/ShellTests.cmake @@ -171,6 +171,7 @@ if (UNIX) # atomic_writer # atomic_reader # filenotclosed + # del_many_dense_attrs # flushrefresh ############################################################################## # autotools script tests @@ -178,7 +179,7 @@ if (UNIX) # NOT CONVERTED accum_swmr_reader is used by accum.c. # NOT CONVERTED atomic_writer and atomic_reader are standalone programs. # links_env is used by testlinks_env.sh - # filenotclosed is used by test_filenotclosed.sh + # filenotclosed and del_many_dense_attrs are used by testabort_fail.sh # NOT CONVERTED flushrefresh is used by testflushrefresh.sh. # NOT CONVERTED use_append_chunk, use_append_mchunks and use_disable_mdc_flushes are used by test_usecases.sh # NOT CONVERTED swmr_* files (besides swmr.c) are used by testswmr.sh. diff --git a/test/del_many_dense_attrs.c b/test/del_many_dense_attrs.c new file mode 100644 index 0000000..d88045c --- /dev/null +++ b/test/del_many_dense_attrs.c @@ -0,0 +1,203 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * Purpose: Test to verify that the infinite loop closing library/abort failure + * is fixed when the application creates and removes dense attributes + * (See HDFFV-10659). + */ + + +#include "h5test.h" + +/* The test file name */ +const char *FILENAME[] = { + "del_many_dense_attrs", + NULL +}; + +#define ATTR_COUNT 64 /* The number of attributes */ + +/*------------------------------------------------------------------------- + * Function: catch_signal + * + * Purpose: The signal handler to catch the SIGABRT signal. + * + * Return: No return + * + * Programmer: Vailin Choi + * + *------------------------------------------------------------------------- + */ +static void catch_signal(int H5_ATTR_UNUSED signo) +{ + HDexit(1); +} /* catch_signal() */ + + +/*------------------------------------------------------------------------- + * Function: main + * + * Purpose: Test to verify that the infinite loop closing library/abort failure + * is fixed when the application creates and removes dense attributes + * (See HDFFV-10659). + * + * Return: Success: exit(EXIT_SUCCESS) + * Failure: exit(EXIT_FAILURE) + * + * Programmer: Vailin Choi; Dec 2018 + * + *------------------------------------------------------------------------- + */ +int +main(void) +{ + hid_t fid = -1; /* HDF5 File ID */ + hid_t gid = -1; /* Group ID */ + hid_t sid = -1; /* Dataspace ID */ + hid_t aid = -1; /* Attribute ID */ + hid_t tid = -1; /* Datatype ID */ + hid_t fapl = -1; /* File access property lists */ + hid_t gcpl = -1; /* Group creation property list */ + char aname[50]; /* Name of attribute */ + char *basename="attr"; /* Name prefix for attribute */ + char filename[100]; /* File name */ + int i; /* Local index variable */ + + /* Testing setup */ + h5_reset(); + + /* To exit from the file for SIGABRT signal */ + if(HDsignal(SIGABRT, catch_signal) == SIG_ERR) + TEST_ERROR + + fapl = h5_fileaccess(); + h5_fixname(FILENAME[0], fapl, filename, sizeof(filename)); + + /* Set to latest format */ + if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) + TEST_ERROR + + /* Create the file */ + if((fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0) + TEST_ERROR + + /* Close the file */ + if(H5Fclose(fid) < 0) + TEST_ERROR + + /* Re-open the file */ + if((fid = H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0) + TEST_ERROR + + /* Create the group creation property list */ + if((gcpl = H5Pcreate(H5P_GROUP_CREATE)) < 0) + TEST_ERROR + + /* Set to use dense storage for all attributes on the group */ + if(H5Pset_attr_phase_change(gcpl, 0, 0) < 0) + TEST_ERROR + + /* Create the group in the file */ + if((gid = H5Gcreate2(fid, "group", H5P_DEFAULT, gcpl, H5P_DEFAULT)) < 0) + TEST_ERROR + + /* Create dataspace */ + if((sid = H5Screate(H5S_SCALAR)) < 0) + TEST_ERROR + + /* Get a copy of the datatype */ + if((tid = H5Tcopy(H5T_NATIVE_FLOAT)) < 0) + TEST_ERROR + + /* Create attributes in the group */ + for(i = ATTR_COUNT; i >= 0; i--) { + /* Set up the attribute name */ + HDsprintf(aname, "%s%d", basename, i); + + /* Create the attribute */ + if((aid = H5Acreate2(gid, aname, tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) + TEST_ERROR + + /* Write to the attribute */ + if(H5Awrite(aid, tid, &i) < 0) + TEST_ERROR + + /* Close the attribute */ + if(H5Aclose(aid) < 0) + TEST_ERROR + } + + /* Close the datatype */ + if(H5Tclose(tid) < 0) + TEST_ERROR + + /* Close the dataspace */ + if(H5Sclose(sid) < 0) + TEST_ERROR + + /* Close the group */ + if(H5Gclose(gid) < 0) + TEST_ERROR + + /* Close the group creation property list */ + if(H5Pclose(gcpl) < 0) + TEST_ERROR + + /* Close the file */ + if(H5Fclose(fid) < 0) + TEST_ERROR + + /* Re-open the file */ + if((fid = H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0) + TEST_ERROR + + /* Open the group */ + if((gid = H5Gopen2(fid, "group", H5P_DEFAULT)) < 0) + TEST_ERROR + + /* Delete the attributes */ + for (i = 0; i <= ATTR_COUNT; i++) { + /* Set up the attribute name */ + HDsprintf(aname, "%s%d", basename, i); + + /* Delete the attribute */ + if(H5Adelete(gid, aname) < 0) + TEST_ERROR + } /* end for */ + + /* Close the group */ + if(H5Gclose(gid) < 0) + TEST_ERROR + + /* Close the file */ + if(H5Fclose(fid) < 0) + TEST_ERROR + + h5_cleanup(FILENAME, fapl); + + return(EXIT_SUCCESS); + +error: + H5E_BEGIN_TRY { + H5Gclose(gid); + H5Sclose(sid); + H5Tclose(tid); + H5Aclose(aid); + H5Fclose(fid); + H5Pclose(gcpl); + H5Pclose(fapl); + } H5E_END_TRY + + return EXIT_FAILURE; +} diff --git a/test/test_filenotclosed.sh.in b/test/testabort_fail.sh.in index 0b43c5b..925d8a4 100644 --- a/test/test_filenotclosed.sh.in +++ b/test/testabort_fail.sh.in @@ -13,6 +13,9 @@ # # Test to verify that the assertion/abort failure is fixed when the application # does not close the file. (See HDFFV-10160) +# +# Test to verify that the infinite loop closing library/abort failure is fixed +# when the application creates and removes dense attributes (See HDFFV-10659) srcdir=@srcdir@ @@ -20,22 +23,44 @@ nerrors=0 ############################################################################## ############################################################################## -### T H E T E S T ### +### T H E T E S T S ### ############################################################################## ############################################################################## - +# +# echo "Testing file not closed assertion/abort failure" TEST_NAME=filenotclosed # The test name -TEST_BIN=`pwd`/$TEST_NAME # The path of the test binary +TEST_BIN=`pwd`/$TEST_NAME # The path of the test binary # # Run the test -#$RUNSERIAL $TEST_BIN >/dev/null 2>&1 -$RUNSERIAL $TEST_BIN 2>&1 +$RUNSERIAL $TEST_BIN >/dev/null 2>&1 exitcode=$? if [ $exitcode -eq 0 ]; then echo "Test PASSED" else + echo "Test FAILED" nerrors="`expr $nerrors + 1`" - echo "***Error encountered***" fi -exit $nerrors +# +# +echo "Testing infinite loop closing library/abort failure" +TEST_NAME=del_many_dense_attrs # The test name +TEST_BIN=`pwd`/$TEST_NAME # The path of the test binary +# Run the test +$RUNSERIAL $TEST_BIN >/dev/null 2>&1 +exitcode=$? +if [ $exitcode -eq 0 ]; then + echo "Test PASSED" +else + echo "Test FAILED" + nerrors="`expr $nerrors + 1`" +fi +# +# +if test $nerrors -eq 0 ; then + echo "All tests for abort failure passed." + exit 0 +else + echo "Tests for abort failure failed with $nerrors errors." + exit 1 +fi |