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can't load HDF5 files: msg#00021

gnu.octave.bugs

Subject: can't load HDF5 files

--------
Bug report for Octave 2.1.57 configured for i386-pc-linux-gnu

Description:
-----------

I am unable to load files in HDF5 format, even sample files from
http://hdf.ncsa.uiuc.edu/HDF5/


Repeat-By:
---------

Below is a transcript of the error message, I hope it helps.

octave:38> load nov03.h5m2
HDF5-DIAG: Error detected in HDF5 library version: 1.6.2 thread
1096206784. Back trace follows.
#000: ../../../src/H5D.c line 1080 in H5Dopen(): not found
major(15): Dataset interface
minor(40): Object not found
#001: ../../../src/H5G.c line 2164 in H5G_find(): object not found
major(10): Symbol table layer
minor(40): Object not found
#002: ../../../src/H5G.c line 1499 in H5G_namei(): component not found
major(10): Symbol table layer
minor(40): Object not found
#003: ../../../src/H5Gstab.c line 172 in H5G_stab_find(): not found
major(10): Symbol table layer
minor(40): Object not found
#004: ../../../src/H5B.c line 649 in H5B_find(): B-tree key not found
major(09): B-tree layer
minor(40): Object not found
HDF5-DIAG: Error detected in HDF5 library version: 1.6.2 thread
1096206784. Back trace follows.
#000: ../../../src/H5D.c line 1170 in H5Dget_space(): not a dataset
major(01): Function arguments
minor(03): Inappropriate type
HDF5-DIAG: Error detected in HDF5 library version: 1.6.2 thread
1096206784. Back trace follows.
#000: ../../../src/H5S.c line 895 in H5Sget_simple_extent_ndims(): not
a data space
major(01): Function arguments
minor(03): Inappropriate type
HDF5-DIAG: Error detected in HDF5 library version: 1.6.2 thread
1096206784. Back trace follows.
#000: ../../../src/H5D.c line 1122 in H5Dclose(): not a dataset
major(01): Function arguments
minor(03): Inappropriate type
error: load: error while reading hdf5 item HDF4_DIMGROUP


Configuration (please do not edit this section):
-----------------------------------------------

uname output: Linux envpg75 2.6.8.1-3-386 #1 Thu Nov 18 11:47:33 UTC
2004 i686 GNU/Linux
configure opts: '--prefix=/usr' '--datadir=/usr/share'
'--libdir=/usr/lib' '--libexecdir=/usr/lib' '--infodir=/usr/share/info'
'--mandir=/usr/share/man' '--with-blas=/usr/lib/libblas-3.so'
'--with-lapack=/usr/lib/liblapack-3.so' '--with-hdf5' '--with-fftw'
'--with-f77=/usr/bin/g77' '--enable-shared' '--enable-rpath'
'--disable-static' '--build' 'i386-linux' 'CC=/usr/bin/gcc'
'CXX=/usr/bin/g++' 'F77=/usr/bin/g77' 'build_alias=i386-linux'
Fortran compiler: /usr/bin/g77
FFLAGS: -O2
F2C:
F2CFLAGS:
FLIBS: -L/usr/lib/gcc-lib/i486-linux/3.3.4
-L/usr/lib/gcc-lib/i486-linux/3.3.4/../../.. -lhdf5 -lz -lfrtbegin -lg2c
-lm -lgcc_s
CPPFLAGS:
INCFLAGS: -I. -I. -I./liboctave -I./src -I./libcruft/misc
-I./glob -I./glob
C compiler: /usr/bin/gcc, version 3.3.4 (Debian 1:3.3.4-5ubuntu2)
CFLAGS: -O2
CPICFLAG: -fPIC
C++ compiler: /usr/bin/g++, version 3.3.4
CXXFLAGS: -O2
CXXPICFLAG: -fPIC
LD_CXX: /usr/bin/g++
LDFLAGS: -s
LIBFLAGS: -L.
RLD_FLAG: -Wl,-rpath -Wl,/usr/lib/octave-2.1.57
BLAS_LIBS: /usr/lib/liblapack-3.so /usr/lib/libblas-3.so
FFTW_LIBS: -lfftw3
LIBS: -lreadline -lncurses -ldl -lhdf5 -lz -lm
LEXLIB:
LIBPLPLOT:
LIBDLFCN:
LIBGLOB: ./glob/glob.o ./glob/fnmatch.o
SED: /bin/sed
DEFS:

-DPACKAGE_NAME="" -DPACKAGE_TARNAME="" -DPACKAGE_VERSION=""
-DPACKAGE_STRING="" -DPACKAGE_BUGREPORT="" -DOCTAVE_SOURCE=1
-DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1
-DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSEPCHAR=1
-DSEPCHAR_STR=":" -D__NO_MATH_INLINES=1
-DCXX_NEW_FRIEND_TEMPLATE_DECL=1
-DCXX_ISO_COMPLIANT_LIBRARY=1 -DCXX_ABI=gnu_v3 -DHAVE_LIBM=1
-DHAVE_HDF5_H=1 -DHAVE_HDF5=1 -DHAVE_H5GGET_NUM_OBJS=1 -DHAVE_FFTW3=1
-DF77_FUNC(name,NAME)=name ## _ -DF77_FUNC_(name,NAME)=name ## __
-DHAVE_BLAS=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPWNAM=1 -DHAVE_DEV_T=1
-DHAVE_INO_T=1 -DHAVE_NLINK_T=1 -DHAVE_NLINK_T=1
-DHAVE_LONG_LONG_INT=1
-DHAVE_UNSIGNED_LONG_LONG_INT=1 -DHAVE_SIGSET_T=1
-DHAVE_SIG_ATOMIC_T=1
-DSIZEOF_SHORT=2 -DSIZEOF_INT=4 -DSIZEOF_LONG=4 -DSIZEOF_LONG_LONG=8
-DHAVE_ALLOCA_H=1 -DHAVE_ALLOCA=1 -DNPOS=std::string::npos
-DHAVE_PLACEMENT_DELETE=1 -DHAVE_DYNAMIC_AUTO_ARRAYS=1
-DSTDC_HEADERS=1
-DHAVE_DIRENT_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_SYS_WAIT_H=1
-DHAVE_ASSERT_H=1 -DHAVE_CURSES_H=1 -DHAVE_DLFCN_H=1 -DHAVE_FCNTL_H=1
-DHAVE_FLOAT_H=1 -DHAVE_GRP_H=1 -DHAVE_LIMITS_H=1 -DHAVE_MEMORY_H=1
-DHAVE_NCURSES_H=1 -DHAVE_POLL_H=1 -DHAVE_PWD_H=1 -DHAVE_STDLIB_H=1
-DHAVE_STRING_H=1 -DHAVE_SYS_IOCTL_H=1 -DHAVE_SYS_PARAM_H=1
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-DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_SYS_TIMES_H=1
-DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_UTSNAME_H=1 -DHAVE_TERMCAP_H=1
-DHAVE_UNISTD_H=1 -DHAVE_SSTREAM=1 -DHAVE_TERMIO_H=1 -DHAVE_SGTTY_H=1
-DHAVE_GLOB_H=1 -DHAVE_FNMATCH_H=1 -DHAVE_ATEXIT=1 -DHAVE_BASENAME=1
-DHAVE_BCOPY=1 -DHAVE_BZERO=1 -DHAVE_DUP2=1 -DHAVE_ENDGRENT=1
-DHAVE_ENDPWENT=1 -DHAVE_EXECVP=1 -DHAVE_FCNTL=1 -DHAVE_FORK=1
-DHAVE_GETCWD=1 -DHAVE_GETEGID=1 -DHAVE_GETEUID=1 -DHAVE_GETGID=1
-DHAVE_GETGRENT=1 -DHAVE_GETGRGID=1 -DHAVE_GETGRNAM=1 -DHAVE_GETPGRP=1
-DHAVE_GETPID=1 -DHAVE_GETPPID=1 -DHAVE_GETPWENT=1 -DHAVE_GETPWUID=1
-DHAVE_GETTIMEOFDAY=1 -DHAVE_GETUID=1 -DHAVE_GETWD=1 -DHAVE_KILL=1
-DHAVE_LINK=1 -DHAVE_LOCALTIME_R=1 -DHAVE_LSTAT=1 -DHAVE_MEMMOVE=1
-DHAVE_MKDIR=1 -DHAVE_MKFIFO=1 -DHAVE_MKSTEMP=1 -DHAVE_ON_EXIT=1
-DHAVE_PIPE=1 -DHAVE_POLL=1 -DHAVE_PUTENV=1 -DHAVE_RAISE=1
-DHAVE_READLINK=1 -DHAVE_RENAME=1 -DHAVE_RINDEX=1 -DHAVE_RMDIR=1
-DHAVE_SELECT=1 -DHAVE_SETGRENT=1 -DHAVE_SETPWENT=1 -DHAVE_SETVBUF=1
-DHAVE_SIGACTION=1 -DHAVE_SIGLONGJMP=1 -DHAVE_SIGPENDING=1
-DHAVE_SIGPROCMASK=1 -DHAVE_SIGSUSPEND=1 -DHAVE_STAT=1
-DHAVE_STRCASECMP=1
-DHAVE_STRDUP=1 -DHAVE_STRERROR=1 -DHAVE_STRFTIME=1
-DHAVE_STRNCASECMP=1
-DHAVE_STRPTIME=1 -DHAVE_SYMLINK=1 -DHAVE_TEMPNAM=1 -DHAVE_UMASK=1
-DHAVE_UNLINK=1 -DHAVE_USLEEP=1 -DHAVE_VFPRINTF=1 -DHAVE_VSPRINTF=1
-DHAVE_VSNPRINTF=1 -DHAVE_WAITPID=1 -DHAVE_LIBDL=1 -DHAVE_DLOPEN=1
-DHAVE_DLSYM=1 -DHAVE_DLERROR=1 -DHAVE_DLCLOSE=1 -DHAVE_DLOPEN_API=1
-DENABLE_DYNAMIC_LINKING=1 -DHAVE_TIMEVAL=1 -DHAVE_FINITE=1
-DHAVE_ISNAN=1
-DHAVE_ISINF=1 -DHAVE_COPYSIGN=1 -DHAVE_ACOSH=1 -DHAVE_ASINH=1
-DHAVE_ATANH=1 -DHAVE_ERF=1 -DHAVE_ERFC=1
-DHAVE_STRUCT_STAT_ST_BLKSIZE=1
-DHAVE_STRUCT_STAT_ST_BLOCKS=1 -DHAVE_STRUCT_STAT_ST_RDEV=1
-DHAVE_STRUCT_TM_TM_ZONE=1 -DHAVE_TM_ZONE=1 -DUSE_READLINE=1
-DEXCEPTION_IN_MATH=1 -DRETSIGTYPE=void -DSYS_SIGLIST_DECLARED=1
-DHAVE_SYS_SIGLIST=1 -DHAVE_POSIX_SIGNALS=1 -DHAVE_GETRUSAGE=1
-DHAVE_TIMES=1 -DGNUPLOT_BINARY="gnuplot" -DGNUPLOT_HAS_FRAMES=

User-preferences (please do not edit this section):
--------------------------------------------------

DEFAULT_EXEC_PATH =
"/usr/lib/octave/2.1.57/site/exec/i386-pc-linux-gnu:/usr/lib/octave/site/exec/i386-pc-linux-gnu:/usr/lib/octave/2.1.57/exec/i386-pc-linux-gnu:/usr/bin"
DEFAULT_LOADPATH =
".:/usr/lib/octave/2.1.57/site/oct/i386-pc-linux-gnu//:/usr/lib/octave/site/oct/api-v8/i386-pc-linux-gnu//:/usr/lib/octave/site/oct/i386-pc-linux-gnu//:/usr/share/octave/2.1.57/site/m//:/usr/share/octave/site/api-v8/m//:/usr/share/octave/site/m//:/usr/lib/octave/2.1.57/oct/i386-pc-linux-gnu//:/usr/share/octave/2.1.57/m//"
EDITOR = "emacs"
EXEC_PATH =
":/home/sw7/matlab140/bin:/usr/local/bin:/usr/local/sbin:/sbin:/usr/sbin:/bin:/usr/bin:/usr/bin/X11:/usr/games"
IMAGEPATH = ".:/usr/share/octave/2.1.57/imagelib//"
INFO_FILE = "/usr/share/info/octave.info"
INFO_PROGRAM = "info"
LOADPATH = ":/usr/local/share/octave/site-m//:"
PAGER = "pager"
PS1 = "\\s:\\#> "
PS2 = "> "
PS4 = "+ "
automatic_replot = 1
beep_on_error = 0
completion_append_char = " "
crash_dumps_octave_core = 1
default_save_format = "ascii"
echo_executing_commands = 0
fixed_point_format = 0
gnuplot_binary = "gnuplot"
gnuplot_command_end = "\n"
gnuplot_command_plot = "pl"
gnuplot_command_replot = "rep"
gnuplot_command_splot = "sp"
gnuplot_command_title = "t"
gnuplot_command_using = "u"
gnuplot_command_with = "w"
gnuplot_has_frames = 1
history_file = "/local/nuno/.octave_hist"
history_size = 1024
ignore_function_time_stamp = "system"
max_recursion_depth = 256
output_max_field_width = 10
output_precision = 5
page_output_immediately = 0
page_screen_output = 1
print_answer_id_name = 1
print_empty_dimensions = 1
print_rhs_assign_val = 0
# return_last_computed_value = <no value or error in displaying it>
save_precision = 15
saving_history = 1
sighup_dumps_octave_core = 1
sigterm_dumps_octave_core = 1
silent_functions = 0
split_long_rows = 1
string_fill_char = " "
struct_levels_to_print = 2
suppress_verbose_help_message = 0
warn_assign_as_truth_value = 1
warn_divide_by_zero = 1
warn_empty_list_elements = 0
warn_fortran_indexing = 0
warn_function_name_clash = 1
warn_future_time_stamp = 1
warn_imag_to_real = 0
warn_missing_semicolon = 0
warn_neg_dim_as_zero = 0
warn_num_to_str = 1
warn_resize_on_range_error = 0
warn_separator_insert = 0
warn_single_quote_string = 0
warn_str_to_num = 0
warn_undefined_return_values = 1
warn_variable_switch_label = 0



-------------------------------------------------------------
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