Error in test_ds on PPC OS X

mike.jackson · December 2, 2009, 8:17pm

I was running some tests on an OS X 10.4.11 PPC G4 box. I used the standard source download from the normal site and ./configure'd and "make". I then ran the "test_ds" which is part of the High Level library set. I came across some tests that are not passing. The following is the output from the test.

Just wondering if this test has been seen before? Is it known not to work on OS X PPC hardware? The same failure happens on a G5 built as a 64 Bit binary. I came across this error as I was trying to diagnose the same issue with the CMake build system. Nice to know that the CMake build system can replicate the same errors.

#------------- OUTPUT ------------------------------------
Testing test_numberofscales PASSED
Testing test_long_attachscales PASSED
Testing test_duplicatelong_attachscales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
   #000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
     major: References
     minor: Unable to initialize object
   #001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
     major: References
     minor: Bad object header link count
   #002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
     major: Object header
     minor: Unable to load metadata into cache
   #003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
     major: Object cache
     minor: Unable to protect metadata
   #004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
     major: Object cache
     minor: Unable to load metadata into cache
   #005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
     major: Object cache
     minor: Unable to load metadata into cache
   #006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
     major: Object header
     minor: Read failed
   #007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
     major: Low-level I/O
     minor: Read failed
   #008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
     major: Low-level I/O
     minor: Read failed
   #009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
     major: Virtual File Layer
     minor: Read failed
   #010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
     major: Invalid arguments to routine
     minor: Address overflowed
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
   #000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
     major: References
     minor: Unable to initialize object
   #001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
     major: References
     minor: Bad object header link count
   #002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
     major: Object header
     minor: Unable to load metadata into cache
   #003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
     major: Object cache
     minor: Unable to protect metadata
   #004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
     major: Object cache
     minor: Unable to load metadata into cache
   #005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
     major: Object cache
     minor: Unable to load metadata into cache
   #006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
     major: Object header
     minor: Read failed
   #007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
     major: Low-level I/O
     minor: Read failed
   #008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
     major: Low-level I/O
     minor: Read failed
   #009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
     major: Virtual File Layer
     minor: Read failed
   #010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
     major: Invalid arguments to routine
     minor: Address overflowed
*FAILED*
Testing set same long scale/cmp scale name HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
   #000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
     major: References
     minor: Unable to initialize object
   #001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
     major: References
     minor: Bad object header link count
   #002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
     major: Object header
     minor: Unable to load metadata into cache
   #003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
     major: Object cache
     minor: Unable to protect metadata
   #004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
     major: Object cache
     minor: Unable to load metadata into cache
   #005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
     major: Object cache
     minor: Unable to load metadata into cache
   #006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
     major: Object header
     minor: Read failed
   #007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
     major: Low-level I/O
     minor: Read failed
   #008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
     major: Low-level I/O
     minor: Read failed
   #009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
     major: Virtual File Layer
     minor: Read failed
   #010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
     major: Invalid arguments to routine
     minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
   #000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
     major: References
     minor: Unable to initialize object
   #001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
     major: References
     minor: Bad object header link count
   #002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
     major: Object header
     minor: Unable to load metadata into cache
   #003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
     major: Object cache
     minor: Unable to protect metadata
   #004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
     major: Object cache
     minor: Unable to load metadata into cache
   #005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
     major: Object cache
     minor: Unable to load metadata into cache
   #006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
     major: Object header
     minor: Read failed
   #007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
     major: Low-level I/O
     minor: Read failed
   #008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
     major: Low-level I/O
     minor: Read failed
   #009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
     major: Virtual File Layer
     minor: Read failed
   #010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
     major: Invalid arguments to routine
     minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
   #000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
     major: References
     minor: Unable to initialize object
   #001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
     major: References
     minor: Bad object header link count
   #002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
     major: Object header
     minor: Unable to load metadata into cache
   #003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
     major: Object cache
     minor: Unable to protect metadata
   #004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
     major: Object cache
     minor: Unable to load metadata into cache
   #005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
     major: Object cache
     minor: Unable to load metadata into cache
   #006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
     major: Object header
     minor: Read failed
   #007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
     major: Low-level I/O
     minor: Read failed
   #008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
     major: Low-level I/O
     minor: Read failed
   #009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
     major: Virtual File Layer
     minor: Read failed
   #010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
     major: Invalid arguments to routine
     minor: Address overflowed
*FAILED*
Testing API functions
Testing detach scales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
   #000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
     major: References
     minor: Unable to initialize object
   #001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
     major: References
     minor: Bad object header link count
   #002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
     major: Object header
     minor: Unable to load metadata into cache
   #003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
     major: Object cache
     minor: Unable to protect metadata
   #004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
     major: Object cache
     minor: Unable to load metadata into cache
   #005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
     major: Object cache
     minor: Unable to load metadata into cache
   #006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
     major: Object header
     minor: Read failed
   #007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
     major: Low-level I/O
     minor: Read failed
   #008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
     major: Low-level I/O
     minor: Read failed
   #009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
     major: Virtual File Layer
     minor: Read failed
   #010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
     major: Invalid arguments to routine
     minor: Address overflowed
*FAILED*
Testing error conditions
Testing attach a dataset to itself PASSED
Testing attach a group with a dataset PASSED

···

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

epourmal · December 3, 2009, 2:52am

Hi Mike,

Hmm... Is PPC G4 32-bit big-endian? I don't think we saw that error before on the platforms we test. I guess something is not configured correctly....Any chance to give us access to a machine where we can reproduce the failure?

Thank you!

Elena

···

On Dec 2, 2009, at 2:17 PM, Michael Jackson wrote:

I was running some tests on an OS X 10.4.11 PPC G4 box. I used the standard source download from the normal site and ./configure'd and "make". I then ran the "test_ds" which is part of the High Level library set. I came across some tests that are not passing. The following is the output from the test.

Just wondering if this test has been seen before? Is it known not to work on OS X PPC hardware? The same failure happens on a G5 built as a 64 Bit binary. I came across this error as I was trying to diagnose the same issue with the CMake build system. Nice to know that the CMake build system can replicate the same errors.

#------------- OUTPUT ------------------------------------
Testing test_numberofscales PASSED
Testing test_long_attachscales PASSED
Testing test_duplicatelong_attachscales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing set same long scale/cmp scale name HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing API functions
Testing detach scales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing error conditions
Testing attach a dataset to itself PASSED
Testing attach a group with a dataset PASSED

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

pedro.vicente · December 3, 2009, 5:24am

Hello, Mike

Yes, that error happens on the PPC G4, I'll give it a try to see if I can find what's happening.

I have been reading your thread regarding CMake.

I have been experimenting with another build system, Qmake

http://qt.nokia.com/

I have a working project that uses QtCreator to build HDF5, so it's going to be handy to debug it, QtCreator it's an excellent IDE.
The good thing about it is that it's cross platform (Linux, Mac, Windows, Symbian OS).

Pedro

···

----------------------
Pedro Vicente
pedro.vicente@space-research.org
http://www.space-research.org/
1004 E. Mumford 61801 Urbana IL
(217) 898-9356
http://www.linkedin.com/in/pedrosilvavicente

----- Original Message ----- From: "Michael Jackson" <mike.jackson@bluequartz.net>
To: "hdf-forum forum" <hdf-forum@hdfgroup.org>
Sent: Wednesday, December 02, 2009 2:17 PM
Subject: [Hdf-forum] Error in test_ds on PPC OS X

I was running some tests on an OS X 10.4.11 PPC G4 box. I used the standard source download from the normal site and ./configure'd and "make". I then ran the "test_ds" which is part of the High Level library set. I came across some tests that are not passing. The following is the output from the test.

Just wondering if this test has been seen before? Is it known not to work on OS X PPC hardware? The same failure happens on a G5 built as a 64 Bit binary. I came across this error as I was trying to diagnose the same issue with the CMake build system. Nice to know that the CMake build system can replicate the same errors.

#------------- OUTPUT ------------------------------------
Testing test_numberofscales PASSED
Testing test_long_attachscales PASSED
Testing test_duplicatelong_attachscales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
  #000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
    major: References
    minor: Unable to initialize object
  #001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
    major: References
    minor: Bad object header link count
  #002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
    major: Object header
    minor: Unable to load metadata into cache
  #003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
    major: Object cache
    minor: Unable to protect metadata
  #004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
    major: Object header
    minor: Read failed
  #007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
    major: Low-level I/O
    minor: Read failed
  #008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
    major: Low-level I/O
    minor: Read failed
  #009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
    major: Virtual File Layer
    minor: Read failed
  #010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
    major: Invalid arguments to routine
    minor: Address overflowed
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
  #000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
    major: References
    minor: Unable to initialize object
  #001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
    major: References
    minor: Bad object header link count
  #002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
    major: Object header
    minor: Unable to load metadata into cache
  #003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
    major: Object cache
    minor: Unable to protect metadata
  #004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
    major: Object header
    minor: Read failed
  #007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
    major: Low-level I/O
    minor: Read failed
  #008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
    major: Low-level I/O
    minor: Read failed
  #009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
    major: Virtual File Layer
    minor: Read failed
  #010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
    major: Invalid arguments to routine
    minor: Address overflowed
*FAILED*
Testing set same long scale/cmp scale name HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
  #000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
    major: References
    minor: Unable to initialize object
  #001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
    major: References
    minor: Bad object header link count
  #002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
    major: Object header
    minor: Unable to load metadata into cache
  #003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
    major: Object cache
    minor: Unable to protect metadata
  #004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
    major: Object header
    minor: Read failed
  #007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
    major: Low-level I/O
    minor: Read failed
  #008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
    major: Low-level I/O
    minor: Read failed
  #009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
    major: Virtual File Layer
    minor: Read failed
  #010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
    major: Invalid arguments to routine
    minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
  #000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
    major: References
    minor: Unable to initialize object
  #001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
    major: References
    minor: Bad object header link count
  #002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
    major: Object header
    minor: Unable to load metadata into cache
  #003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
    major: Object cache
    minor: Unable to protect metadata
  #004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
    major: Object header
    minor: Read failed
  #007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
    major: Low-level I/O
    minor: Read failed
  #008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
    major: Low-level I/O
    minor: Read failed
  #009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
    major: Virtual File Layer
    minor: Read failed
  #010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
    major: Invalid arguments to routine
    minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
  #000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
    major: References
    minor: Unable to initialize object
  #001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
    major: References
    minor: Bad object header link count
  #002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
    major: Object header
    minor: Unable to load metadata into cache
  #003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
    major: Object cache
    minor: Unable to protect metadata
  #004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
    major: Object header
    minor: Read failed
  #007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
    major: Low-level I/O
    minor: Read failed
  #008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
    major: Low-level I/O
    minor: Read failed
  #009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
    major: Virtual File Layer
    minor: Read failed
  #010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
    major: Invalid arguments to routine
    minor: Address overflowed
*FAILED*
Testing API functions
Testing detach scales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
  #000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
    major: References
    minor: Unable to initialize object
  #001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
    major: References
    minor: Bad object header link count
  #002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
    major: Object header
    minor: Unable to load metadata into cache
  #003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
    major: Object cache
    minor: Unable to protect metadata
  #004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
    major: Object header
    minor: Read failed
  #007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
    major: Low-level I/O
    minor: Read failed
  #008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
    major: Low-level I/O
    minor: Read failed
  #009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
    major: Virtual File Layer
    minor: Read failed
  #010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
    major: Invalid arguments to routine
    minor: Address overflowed
*FAILED*
Testing error conditions
Testing attach a dataset to itself PASSED
Testing attach a group with a dataset PASSED

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

mike.jackson · December 3, 2009, 3:49pm

I looked into qmake a while back for my projects but CMake seemed to have better support for the systems, configurations and packaging that I was doing. Now with the addition of CTest and a CDash server automated testing and reporting is pretty straight forward.

The CMake system is pretty far along. There is support for C, High Level, C++, Tools, Examples and Fortran (Windows tested only currently). There are about 62 executable tests that are run which when combined have about 3,000 to 5,000 individual tests performed. I can get OS X 32 and 64 bit Intel to pass all of them. I can get Visual Studio 2008 to build in 32 and 64 bit and pass all the tests now. There is a WinXP client doing some testing also.

John B. and I are working on cleaning up the CMake files with comments/documentation so the HDF Team has an easier time of things if/when they transition.

The biggest problem currently is that the "Free" version of the CDash server that we post test results to only allows 10 submissions per day. We have to be very frugal about what we test and when we submit.

Currently here are the systems that We can cover:

  OS X 10.5.8 Intel 32 and 64 Bit (C,C++, HL) (2 Submissions)
  OS X 10.4/10.5 PPC 32 and 64 Bit (C,C++, HL) (2 Submissions)
  Windows (xp) VS 9 32Bit (C and Fortran) (1 Submission)
  Windows (7) VS 9 32 and 64 Bit (C,C++, HL) (2 Submissions)

Would be nice to get a Linux Build running. I can get a virtual machine together for Linux if needed.
Also maybe an OpenSolaris box would be nice.

If you can track down the bug in the PPC code for the test_ds please do submit a patch.

You can follow the HDF5 V1.8.4 CMake branch at <http://www.gitorious.com/hdf5/hdf5-v18

···

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

On Dec 3, 2009, at 12:24 AM, Pedro Vicente wrote:

Hello, Mike

Yes, that error happens on the PPC G4, I'll give it a try to see if I can find what's happening.

I have been reading your thread regarding CMake.

I have been experimenting with another build system, Qmake

http://qt.nokia.com/

I have a working project that uses QtCreator to build HDF5, so it's going to be handy to debug it, QtCreator it's an excellent IDE.
The good thing about it is that it's cross platform (Linux, Mac, Windows, Symbian OS).

Pedro

----------------------
Pedro Vicente
pedro.vicente@space-research.org
http://www.space-research.org/
1004 E. Mumford 61801 Urbana IL
(217) 898-9356
http://www.linkedin.com/in/pedrosilvavicente

----- Original Message ----- From: "Michael Jackson" <mike.jackson@bluequartz.net>
To: "hdf-forum forum" <hdf-forum@hdfgroup.org>
Sent: Wednesday, December 02, 2009 2:17 PM
Subject: [Hdf-forum] Error in test_ds on PPC OS X

I was running some tests on an OS X 10.4.11 PPC G4 box. I used the standard source download from the normal site and ./configure'd and "make". I then ran the "test_ds" which is part of the High Level library set. I came across some tests that are not passing. The following is the output from the test.

Just wondering if this test has been seen before? Is it known not to work on OS X PPC hardware? The same failure happens on a G5 built as a 64 Bit binary. I came across this error as I was trying to diagnose the same issue with the CMake build system. Nice to know that the CMake build system can replicate the same errors.

#------------- OUTPUT ------------------------------------
Testing test_numberofscales PASSED
Testing test_long_attachscales PASSED
Testing test_duplicatelong_attachscales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing set same long scale/cmp scale name HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing API functions
Testing detach scales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing error conditions
Testing attach a dataset to itself PASSED
Testing attach a group with a dataset PASSED

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

sean · December 3, 2009, 4:23pm

Yes.

···

On 12/2/09 8:52 PM, Elena Pourmal said:

Hmm... Is PPC G4 32-bit big-endian?

--
____________________________________________________________
Sean McBride, B. Eng sean@rogue-research.com
Rogue Research www.rogue-research.com
Mac Software Developer Montréal, Québec, Canada

pedro.vicente · December 4, 2009, 3:46pm

Hello, Mike

CMake looks like an interesting system for cross platform building, but in my case I use Qt more because it has an API and a graphical debugger for user interface development in Windows, Linux/X11 and Mac (same code runs everywhere), kind of the holy grail for cross platform development.

That error in test_ds happens because one array that contains information regarding the Dimension Scales API (read from H5Dread in the H5DSis_attached function) has some garbage values at an element position, values that are used in a call to H5Rdereference.

Pedro

···

----- Original Message ----- From: "Michael Jackson" <mike.jackson@bluequartz.net>
To: <hdf-forum@hdfgroup.org>
Sent: Thursday, December 03, 2009 9:49 AM
Subject: Re: [Hdf-forum] Error in test_ds on PPC OS X

I looked into qmake a while back for my projects but CMake seemed to have better support for the systems, configurations and packaging that I was doing. Now with the addition of CTest and a CDash server automated testing and reporting is pretty straight forward.

  The CMake system is pretty far along. There is support for C, High Level, C++, Tools, Examples and Fortran (Windows tested only currently). There are about 62 executable tests that are run which when combined have about 3,000 to 5,000 individual tests performed. I can get OS X 32 and 64 bit Intel to pass all of them. I can get Visual Studio 2008 to build in 32 and 64 bit and pass all the tests now. There is a WinXP client doing some testing also.

  John B. and I are working on cleaning up the CMake files with comments/documentation so the HDF Team has an easier time of things if/ when they transition.

  The biggest problem currently is that the "Free" version of the CDash server that we post test results to only allows 10 submissions per day. We have to be very frugal about what we test and when we submit.

Currently here are the systems that We can cover:

OS X 10.5.8 Intel 32 and 64 Bit (C,C++, HL) (2 Submissions)
OS X 10.4/10.5 PPC 32 and 64 Bit (C,C++, HL) (2 Submissions)
Windows (xp) VS 9 32Bit (C and Fortran) (1 Submission)
Windows (7) VS 9 32 and 64 Bit (C,C++, HL) (2 Submissions)

Would be nice to get a Linux Build running. I can get a virtual machine together for Linux if needed.
Also maybe an OpenSolaris box would be nice.

If you can track down the bug in the PPC code for the test_ds please do submit a patch.

You can follow the HDF5 V1.8.4 CMake branch at <http://www.gitorious.com/hdf5/hdf5-v18
>
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

On Dec 3, 2009, at 12:24 AM, Pedro Vicente wrote:

Hello, Mike

Yes, that error happens on the PPC G4, I'll give it a try to see if I can find what's happening.

I have been reading your thread regarding CMake.

I have been experimenting with another build system, Qmake

http://qt.nokia.com/

I have a working project that uses QtCreator to build HDF5, so it's going to be handy to debug it, QtCreator it's an excellent IDE.
The good thing about it is that it's cross platform (Linux, Mac, Windows, Symbian OS).

Pedro

----------------------
Pedro Vicente
pedro.vicente@space-research.org
http://www.space-research.org/
1004 E. Mumford 61801 Urbana IL
(217) 898-9356
http://www.linkedin.com/in/pedrosilvavicente

----- Original Message ----- From: "Michael Jackson" <mike.jackson@bluequartz.net
>
To: "hdf-forum forum" <hdf-forum@hdfgroup.org>
Sent: Wednesday, December 02, 2009 2:17 PM
Subject: [Hdf-forum] Error in test_ds on PPC OS X

I was running some tests on an OS X 10.4.11 PPC G4 box. I used the standard source download from the normal site and ./configure'd and "make". I then ran the "test_ds" which is part of the High Level library set. I came across some tests that are not passing. The following is the output from the test.

Just wondering if this test has been seen before? Is it known not to work on OS X PPC hardware? The same failure happens on a G5 built as a 64 Bit binary. I came across this error as I was trying to diagnose the same issue with the CMake build system. Nice to know that the CMake build system can replicate the same errors.

#------------- OUTPUT ------------------------------------
Testing test_numberofscales PASSED
Testing test_long_attachscales PASSED
Testing test_duplicatelong_attachscales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing set same long scale/cmp scale name HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing API functions
Testing detach scales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
   major: References
   minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
   major: References
   minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
   major: Object header
   minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
   major: Object cache
   minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
   major: Object cache
   minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
   major: Object cache
   minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
   major: Object header
   minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
   major: Low-level I/O
   minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
   major: Low-level I/O
   minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
   major: Virtual File Layer
   minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
   major: Invalid arguments to routine
   minor: Address overflowed
*FAILED*
Testing error conditions
Testing attach a dataset to itself PASSED
Testing attach a group with a dataset PASSED

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

mike.jackson · December 4, 2009, 4:00pm

CMake is used to generate your preferred build system: Makefiles, Visual Studio Solutions, Xcode projects.

Qt is a Cross platform C++ development framework. They are different completely. CMake is used all the time with Qt. I think you are getting Qt and qmake confused. QMake comes with Qt and very similar to CMake. For both qmake and CMake the user writes a "Script" file that is used to generate the platform specific build files. If you have a qmake files for HDF5 that is great. Use what ever works for you. John B. and I have decided to pool our resources to update the CMake build system that I had for HDF5 Version 1.6.9 to HDF5 Version 1.8.4 since a lot of projects are requesting that capability.

So, do you have a patch for the code by any chance? I came to the same conclusion but I have no idea how the garbage is getting in there. My guess is that the array was not properly initialized on the PPC platform but again, not knowing the HDF5 code base well enough, I have no idea where to begin looking for the bug.

Thanks for the effort of diagnosing the bug. Hopefully we can get a patch into the HDF5 source tree so all the tests will pass.

···

---
Mike Jackson www.bluequartz.net

On Dec 4, 2009, at 10:46 AM, Pedro Vicente wrote:

Hello, Mike

CMake looks like an interesting system for cross platform building, but in my case I use Qt more because it has an API and a graphical debugger for user interface development in Windows, Linux/X11 and Mac (same code runs everywhere), kind of the holy grail for cross platform development.

That error in test_ds happens because one array that contains information regarding the Dimension Scales API (read from H5Dread in the H5DSis_attached function) has some garbage values at an element position, values that are used in a call to H5Rdereference.

Pedro

----- Original Message ----- From: "Michael Jackson" <mike.jackson@bluequartz.net>
To: <hdf-forum@hdfgroup.org>
Sent: Thursday, December 03, 2009 9:49 AM
Subject: Re: [Hdf-forum] Error in test_ds on PPC OS X

I looked into qmake a while back for my projects but CMake seemed to have better support for the systems, configurations and packaging that I was doing. Now with the addition of CTest and a CDash server automated testing and reporting is pretty straight forward.

The CMake system is pretty far along. There is support for C, High Level, C++, Tools, Examples and Fortran (Windows tested only currently). There are about 62 executable tests that are run which when combined have about 3,000 to 5,000 individual tests performed. I can get OS X 32 and 64 bit Intel to pass all of them. I can get Visual Studio 2008 to build in 32 and 64 bit and pass all the tests now. There is a WinXP client doing some testing also.

John B. and I are working on cleaning up the CMake files with comments/documentation so the HDF Team has an easier time of things if/ when they transition.

The biggest problem currently is that the "Free" version of the CDash server that we post test results to only allows 10 submissions per day. We have to be very frugal about what we test and when we submit.

Currently here are the systems that We can cover:

OS X 10.5.8 Intel 32 and 64 Bit (C,C++, HL) (2 Submissions)
OS X 10.4/10.5 PPC 32 and 64 Bit (C,C++, HL) (2 Submissions)
Windows (xp) VS 9 32Bit (C and Fortran) (1 Submission)
Windows (7) VS 9 32 and 64 Bit (C,C++, HL) (2 Submissions)

Would be nice to get a Linux Build running. I can get a virtual machine together for Linux if needed.
Also maybe an OpenSolaris box would be nice.

If you can track down the bug in the PPC code for the test_ds please do submit a patch.

You can follow the HDF5 V1.8.4 CMake branch at <http://www.gitorious.com/hdf5/hdf5-v18
>
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

On Dec 3, 2009, at 12:24 AM, Pedro Vicente wrote:

Hello, Mike

Yes, that error happens on the PPC G4, I'll give it a try to see if I can find what's happening.

I have been reading your thread regarding CMake.

I have been experimenting with another build system, Qmake

http://qt.nokia.com/

I have a working project that uses QtCreator to build HDF5, so it's going to be handy to debug it, QtCreator it's an excellent IDE.
The good thing about it is that it's cross platform (Linux, Mac, Windows, Symbian OS).

Pedro

----------------------
Pedro Vicente
pedro.vicente@space-research.org
http://www.space-research.org/
1004 E. Mumford 61801 Urbana IL
(217) 898-9356
http://www.linkedin.com/in/pedrosilvavicente

----- Original Message ----- From: "Michael Jackson" <mike.jackson@bluequartz.net
>
To: "hdf-forum forum" <hdf-forum@hdfgroup.org>
Sent: Wednesday, December 02, 2009 2:17 PM
Subject: [Hdf-forum] Error in test_ds on PPC OS X

I was running some tests on an OS X 10.4.11 PPC G4 box. I used the standard source download from the normal site and ./configure'd and "make". I then ran the "test_ds" which is part of the High Level library set. I came across some tests that are not passing. The following is the output from the test.

Just wondering if this test has been seen before? Is it known not to work on OS X PPC hardware? The same failure happens on a G5 built as a 64 Bit binary. I came across this error as I was trying to diagnose the same issue with the CMake build system. Nice to know that the CMake build system can replicate the same errors.

#------------- OUTPUT ------------------------------------
Testing test_numberofscales PASSED
Testing test_long_attachscales PASSED
Testing test_duplicatelong_attachscales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
  major: References
  minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
  major: References
  minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
  major: Object header
  minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
  major: Object cache
  minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
  major: Object cache
  minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
  major: Object cache
  minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
  major: Object header
  minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
  major: Low-level I/O
  minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
  major: Low-level I/O
  minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
  major: Virtual File Layer
  minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
  major: Invalid arguments to routine
  minor: Address overflowed
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
  major: References
  minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
  major: References
  minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
  major: Object header
  minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
  major: Object cache
  minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
  major: Object cache
  minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
  major: Object cache
  minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
  major: Object header
  minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
  major: Low-level I/O
  minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
  major: Low-level I/O
  minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
  major: Virtual File Layer
  minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
  major: Invalid arguments to routine
  minor: Address overflowed
*FAILED*
Testing set same long scale/cmp scale name HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
  major: References
  minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
  major: References
  minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
  major: Object header
  minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
  major: Object cache
  minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
  major: Object cache
  minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
  major: Object cache
  minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
  major: Object header
  minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
  major: Low-level I/O
  minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
  major: Low-level I/O
  minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
  major: Virtual File Layer
  minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
  major: Invalid arguments to routine
  minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
  major: References
  minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
  major: References
  minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
  major: Object header
  minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
  major: Object cache
  minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
  major: Object cache
  minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
  major: Object cache
  minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
  major: Object header
  minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
  major: Low-level I/O
  minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
  major: Low-level I/O
  minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
  major: Virtual File Layer
  minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
  major: Invalid arguments to routine
  minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
  major: References
  minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
  major: References
  minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
  major: Object header
  minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
  major: Object cache
  minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
  major: Object cache
  minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
  major: Object cache
  minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
  major: Object header
  minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
  major: Low-level I/O
  minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
  major: Low-level I/O
  minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
  major: Virtual File Layer
  minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
  major: Invalid arguments to routine
  minor: Address overflowed
*FAILED*
Testing API functions
Testing detach scales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
  major: References
  minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
  major: References
  minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
  major: Object header
  minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
  major: Object cache
  minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
  major: Object cache
  minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
  major: Object cache
  minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
  major: Object header
  minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
  major: Low-level I/O
  minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
  major: Low-level I/O
  minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
  major: Virtual File Layer
  minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
  major: Invalid arguments to routine
  minor: Address overflowed
*FAILED*
Testing error conditions
Testing attach a dataset to itself PASSED
Testing attach a group with a dataset PASSED

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

sean · December 4, 2009, 4:28pm

Mike,

You might have success using valgrind to catch this. valgrind works on
10.5 with 32 bit apps (but not in 10.6, not with 64 bit apps, and not
with GC apps-- none of which matter in this case).

···

On 12/4/09 9:46 AM, Pedro Vicente said:

That error in test_ds happens because one array that contains information
regarding the Dimension Scales API (read from H5Dread in the H5DSis_attached
function) has some garbage values at an element position, values that are
used in a call to H5Rdereference.

--
____________________________________________________________
Sean McBride, B. Eng sean@rogue-research.com
Rogue Research www.rogue-research.com
Mac Software Developer Montréal, Québec, Canada

pedro.vicente · December 4, 2009, 4:11pm

> So, do you have a patch for the code by any chance? I came to the same
conclusion but I have no idea how the garbage is getting in there

No patch yet, I also don't know why the array gets corrupted.

> Thanks for the effort of diagnosing the bug

You're welcome.

Pedro

···

----- Original Message ----- From: "Michael Jackson" <mike.jackson@bluequartz.net>
To: <hdf-forum@hdfgroup.org>
Sent: Friday, December 04, 2009 10:00 AM
Subject: Re: [Hdf-forum] Error in test_ds on PPC OS X

CMake is used to generate your preferred build system: Makefiles, Visual Studio Solutions, Xcode projects.

Qt is a Cross platform C++ development framework. They are different completely. CMake is used all the time with Qt. I think you are getting Qt and qmake confused. QMake comes with Qt and very similar to CMake. For both qmake and CMake the user writes a "Script" file that is used to generate the platform specific build files. If you have a qmake files for HDF5 that is great. Use what ever works for you. John B. and I have decided to pool our resources to update the CMake build system that I had for HDF5 Version 1.6.9 to HDF5 Version 1.8.4 since a lot of projects are requesting that capability.

So, do you have a patch for the code by any chance? I came to the same conclusion but I have no idea how the garbage is getting in there. My guess is that the array was not properly initialized on the PPC platform but again, not knowing the HDF5 code base well enough, I have no idea where to begin looking for the bug.

Thanks for the effort of diagnosing the bug. Hopefully we can get a patch into the HDF5 source tree so all the tests will pass.

---
Mike Jackson www.bluequartz.net

On Dec 4, 2009, at 10:46 AM, Pedro Vicente wrote:

Hello, Mike

CMake looks like an interesting system for cross platform building, but in my case I use Qt more because it has an API and a graphical debugger for user interface development in Windows, Linux/X11 and Mac (same code runs everywhere), kind of the holy grail for cross platform development.

That error in test_ds happens because one array that contains information regarding the Dimension Scales API (read from H5Dread in the H5DSis_attached function) has some garbage values at an element position, values that are used in a call to H5Rdereference.

Pedro

----- Original Message ----- From: "Michael Jackson" <mike.jackson@bluequartz.net
>
To: <hdf-forum@hdfgroup.org>
Sent: Thursday, December 03, 2009 9:49 AM
Subject: Re: [Hdf-forum] Error in test_ds on PPC OS X

I looked into qmake a while back for my projects but CMake seemed to have better support for the systems, configurations and packaging that I was doing. Now with the addition of CTest and a CDash server automated testing and reporting is pretty straight forward.

The CMake system is pretty far along. There is support for C, High Level, C++, Tools, Examples and Fortran (Windows tested only currently). There are about 62 executable tests that are run which when combined have about 3,000 to 5,000 individual tests performed. I can get OS X 32 and 64 bit Intel to pass all of them. I can get Visual Studio 2008 to build in 32 and 64 bit and pass all the tests now. There is a WinXP client doing some testing also.

John B. and I are working on cleaning up the CMake files with comments/documentation so the HDF Team has an easier time of things if/ when they transition.

The biggest problem currently is that the "Free" version of the CDash server that we post test results to only allows 10 submissions per day. We have to be very frugal about what we test and when we submit.

Currently here are the systems that We can cover:

OS X 10.5.8 Intel 32 and 64 Bit (C,C++, HL) (2 Submissions)
OS X 10.4/10.5 PPC 32 and 64 Bit (C,C++, HL) (2 Submissions)
Windows (xp) VS 9 32Bit (C and Fortran) (1 Submission)
Windows (7) VS 9 32 and 64 Bit (C,C++, HL) (2 Submissions)

Would be nice to get a Linux Build running. I can get a virtual machine together for Linux if needed.
Also maybe an OpenSolaris box would be nice.

If you can track down the bug in the PPC code for the test_ds please do submit a patch.

You can follow the HDF5 V1.8.4 CMake branch at <http://www.gitorious.com/hdf5/hdf5-v18
>
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

On Dec 3, 2009, at 12:24 AM, Pedro Vicente wrote:

Hello, Mike

Yes, that error happens on the PPC G4, I'll give it a try to see if I can find what's happening.

I have been reading your thread regarding CMake.

I have been experimenting with another build system, Qmake

http://qt.nokia.com/

I have a working project that uses QtCreator to build HDF5, so it's going to be handy to debug it, QtCreator it's an excellent IDE.
The good thing about it is that it's cross platform (Linux, Mac, Windows, Symbian OS).

Pedro

----------------------
Pedro Vicente
pedro.vicente@space-research.org
http://www.space-research.org/
1004 E. Mumford 61801 Urbana IL
(217) 898-9356
http://www.linkedin.com/in/pedrosilvavicente

----- Original Message ----- From: "Michael Jackson" <mike.jackson@bluequartz.net
>
To: "hdf-forum forum" <hdf-forum@hdfgroup.org>
Sent: Wednesday, December 02, 2009 2:17 PM
Subject: [Hdf-forum] Error in test_ds on PPC OS X

I was running some tests on an OS X 10.4.11 PPC G4 box. I used the standard source download from the normal site and ./ configure'd and "make". I then ran the "test_ds" which is part of the High Level library set. I came across some tests that are not passing. The following is the output from the test.

Just wondering if this test has been seen before? Is it known not to work on OS X PPC hardware? The same failure happens on a G5 built as a 64 Bit binary. I came across this error as I was trying to diagnose the same issue with the CMake build system. Nice to know that the CMake build system can replicate the same errors.

#------------- OUTPUT ------------------------------------
Testing test_numberofscales PASSED
Testing test_long_attachscales PASSED
Testing test_duplicatelong_attachscales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
  major: References
  minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
  major: References
  minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
  major: Object header
  minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
  major: Object cache
  minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
  major: Object cache
  minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
  major: Object cache
  minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
  major: Object header
  minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
  major: Low-level I/O
  minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
  major: Low-level I/O
  minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
  major: Virtual File Layer
  minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
  major: Invalid arguments to routine
  minor: Address overflowed
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
  major: References
  minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
  major: References
  minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
  major: Object header
  minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
  major: Object cache
  minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
  major: Object cache
  minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
  major: Object cache
  minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
  major: Object header
  minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
  major: Low-level I/O
  minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
  major: Low-level I/O
  minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
  major: Virtual File Layer
  minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
  major: Invalid arguments to routine
  minor: Address overflowed
*FAILED*
Testing set same long scale/cmp scale name HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
  major: References
  minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
  major: References
  minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
  major: Object header
  minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
  major: Object cache
  minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
  major: Object cache
  minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
  major: Object cache
  minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
  major: Object header
  minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
  major: Low-level I/O
  minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
  major: Low-level I/O
  minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
  major: Virtual File Layer
  minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
  major: Invalid arguments to routine
  minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
  major: References
  minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
  major: References
  minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
  major: Object header
  minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
  major: Object cache
  minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
  major: Object cache
  minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
  major: Object cache
  minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
  major: Object header
  minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
  major: Low-level I/O
  minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
  major: Low-level I/O
  minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
  major: Virtual File Layer
  minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
  major: Invalid arguments to routine
  minor: Address overflowed
*FAILED*
Testing test_foreign_scaleattached HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
  major: References
  minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
  major: References
  minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
  major: Object header
  minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
  major: Object cache
  minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
  major: Object cache
  minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
  major: Object cache
  minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
  major: Object header
  minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
  major: Low-level I/O
  minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
  major: Low-level I/O
  minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
  major: Virtual File Layer
  minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
  major: Invalid arguments to routine
  minor: Address overflowed
*FAILED*
Testing API functions
Testing detach scales HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 532 in H5Rdereference(): unable dereference object
  major: References
  minor: Unable to initialize object
#001: /Users/mjackson/Workspace/hdf5-v18/src/H5R.c line 418 in H5R_dereference(): dereferencing deleted object
  major: References
  minor: Bad object header link count
#002: /Users/mjackson/Workspace/hdf5-v18/src/H5O.c line 1542 in H5O_link(): unable to load object header
  major: Object header
  minor: Unable to load metadata into cache
#003: /Users/mjackson/Workspace/hdf5-v18/src/H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
  major: Object cache
  minor: Unable to protect metadata
#004: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 6160 in H5C_protect(): can't load entry
  major: Object cache
  minor: Unable to load metadata into cache
#005: /Users/mjackson/Workspace/hdf5-v18/src/H5C.c line 10990 in H5C_load_entry(): unable to load entry
  major: Object cache
  minor: Unable to load metadata into cache
#006: /Users/mjackson/Workspace/hdf5-v18/src/H5Ocache.c line 154 in H5O_load(): unable to read object header
  major: Object header
  minor: Read failed
#007: /Users/mjackson/Workspace/hdf5-v18/src/H5Fio.c line 113 in H5F_block_read(): read from metadata accumulator failed
  major: Low-level I/O
  minor: Read failed
#008: /Users/mjackson/Workspace/hdf5-v18/src/H5Faccum.c line 196 in H5F_accum_read(): driver read request failed
  major: Low-level I/O
  minor: Read failed
#009: /Users/mjackson/Workspace/hdf5-v18/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
  major: Virtual File Layer
  minor: Read failed
#010: /Users/mjackson/Workspace/hdf5-v18/src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
  major: Invalid arguments to routine
  minor: Address overflowed
*FAILED*
Testing error conditions
Testing attach a dataset to itself PASSED
Testing attach a group with a dataset PASSED

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org