Description:
In this bug, H5File doesn't have the ability to create attribute. The
following changes will provide that functionality and several others that
were also missing:
- Added an abstract class H5Location in between IdComponent and H5Object.
- New class structure of IdComponent, H5Location, H5Object, H5File
IdComponent
|
H5Location
/ \
H5Object H5File
- Wrappers in H5Object were moved to H5Location because the related C
functions take either file, group, dataset, or named datatype ID.
- Added wrapper for H5Rget_obj_type2
- Added tests for file attributes and H5Rget_obj_type2 wrapper
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 2.6 (koala)
SunOS 5.10 (linew)
Description:
- Replaced PredType::NotAtexit() with PredType::AtExit(H5CPP_EXITED);
and used PredType::AtExit as a flag to detect when all predefined
types have been destroyed. Then, H5close will be called to terminate
the library after its being re-initiated when the PredType destructors
were activated. This change removed the memory leaks shown by the
user's sample program.
- Added H5CPP_EXITED for PredType::AtExit to use as a flag
- Updated some inaccurate comments
- Removed stream functions from FileAccPropList
- Replaced H5_VMS with appropriate macro in H5IdComponent.cpp
- Corrected many URLs (hdfgroup vs. ncsa) in comments
- Replaced std::string with H5std_string in comments
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 2.6 (amani)
SunOS 5.10 (linew)
Description:
Closed various HDF5 objects in DataSet::getInMemDataSize and
Attribute::getInMemDataSize to remove some memory leaks.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 2.6 (amani)
SunOS 5.10 (linew)
Description:
After a C++ API object is closed, its id should be reset regardless
of the reference count of the underlying HDF5 object. User reported
the bug for Group, but it's applicable to all other objects. Fixed.
Platforms tested:
Linux/32 2.6 (jam)
FreeBSD/64 6.3 (liberty)
SunOS 5.10 (linew)
Description:
- Revised DataSet::write to pass in correct string buffer
- Added member function DataSet::getInMemDataSize() to simplify
getting the dataset's data size in memory.
- Added private functions for reading fixed- and variable-length
string data: p_read_fixed_len and p_read_variable_len.
- Added tests to write/read array of strings to datasets.
Platforms tested:
Linux/32 2.6 (jam)
FreeBSD/64 6.3 (liberty)
SunOS 5.10 (linew)
Added missing wrappers for H5Rdereference.
Also, for these wrappers, improved exception handlings to report specific
overloaded functions, where failure occurs. Will do the same for more
functions later...
Platforms tested:
Linux 2.6 (kagiso)
SunOS 5.10 (linew)
FreeBSD (duty)
Remove trailing whitespace from C/C++ source files, with the following
script:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Tested on:
Mac OS X/32 10.5.5 (amazon)
No need for h5committest, just whitespace changes...
Description:
Changed all subclasses' setId to protected p_setId and put back setId
in IdComponent. p_setId is used in the library where the id provided
by a C API passed on to user's application in the form of a C++ API
object, which will be destroyed properly, and so p_setId does not
call incRefCount. On the other hand, the public version setId is
used by other applications, in which the id passed to setId needs
to be closed properly by the application, so setId must call incRefCount
for the new object to prevent prematurely closing of the id.
Platforms tested:
Linux 2.6 (kagiso)
SunOS 5.10 (linew)
FreeBSD (duty)
the file didn't have the data. It happened because each handle had its own
object structure, and the empty one overwrote the data with fill value. This is
fixed by making some attribute information like the data be shared in the
attribute structure.
Tested on smirom, kagiso, and linew.
Description:
The class hierarchy was revised to address the problem reported in
bugzilla #1068. Classes AbstractDS and Attribute are moved out of
H5Object. Class Attribute now multiply inherits from IdComponent and
AbstractDs and class DataSet from H5Object and AbstractDs.
In addition, data member IdComponent::id was moved into subclasses:
Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList.
Platforms tested:
SunOS 5.10 (linew)
Linux 2.6 (kagiso)
FreeBSD (duty)
Deprecate H5Dextend in favor of H5Dset_extent (without using API
versioning, due to changed behavior) and switch internal usage to H5Dset_extent
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Add H5Rget_obj_type() to the API versioning and switch internal
routines to use H5Rget_obj_type2()
Misc. other code cleanups, etc.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
AIX/32 5.3 (copper)
Solaris/32 2.10 (linew)
Mac OS X/32 10.4.10 (amazon)
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
Description:
Fixed typos and re-arranged some functions to be in sync with 1.6.
Platforms tested:
Linux 2.4 (heping)
SunOS 5.9 (shanti)
AIX 5.1 (copper)
Description:
Shanti compiler destroy unnamed objects later than others, which caused
some reference counting test fail. Revised the test so that destructors
are called at the same time, regardless the differences of compiler
implementation.
Revised some constructors, close, operator=, and destructors to make
sure that all the object ids are handled properly.
Platforms tested:
Linux 2.4 (heping)
SunOS 5.9 (shanti)
HPUX 11.00 (kelgia)
AIX 5.1 (copper)
Description:
Changed to alias string instead of std, i.e. H5std_string instead
of H5std, because the old way wasn't working when std didn't exist.
Platforms tested:
Linux 2.4 (heping)
SunOS 5.8 64-bit (sol)
HPUX 11.00 (kelgia) - this was the problematic platform but I wasn't
able to test before.
Description:
Added alias H5_std so either the global or std namespace can be
used, depending on H5_NO_STD.
Platforms tested:
Linux 2.4 (heping)
SunOS 5.8 64-bit (sol)
AIX 5.1 (copper)
Description:
There was a workaround for predefined types, in the C++ library,
implemented when the C++ library was handling the reference
counting of the object ids on its own. Currently, the C++ library
is using the available APIs from the C library for that purpose,
and there were bugs reported involving that part of the C++ library.
So, I decided to remove the workaround completely.
Also, improved the use of std members.
Platforms tested:
Linux 2.4 (heping)
SunOS 5.8 64-bit (sol)
Linux 2.4 w/PGI (colonelk)
Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Description:
Added wrapper for H5Iget_type.
Added try/catch to many APIs that call private functions so that more
specific information can be provided at failure.
Added IdComponent::inMemFunc to help providing specific info.
Added const to parameters of several functions that missed that.
Platforms tested:
Linux 2.4 (heping)
SunOS 5.8 64-bit (sol)
AIX 5.1 (copper)
IRIX64 with -n32 (modi4)
HPUX 11.00 (kelgia)
Description:
PropList::copyProp has incorrect prototype; although it works,
it does cause users inconvenience.
Solution:
Added another overloaded function with correct prototype. The
old version will be removed in a future release. In the meantime,
"Obsolete" will be displayed in its RM page.
Also, changed several checks on the returned value of a C API from
non-positive to negative because id = 0 is no longer significant,
now that the C++ reference counting had been removed.
Platforms tested:
Linux 2.4 (heping)
IRIX64 with -n32 (modi4)
Linux 2.4 w/PGI (colonelk)
Description:
The use of FileCreatPropList::DEFAULT sometimes caused failure
in the reference counting area. This occurs to all the default
property lists, which also include FileAccPropList::DEFAULT,
DSetCreatPropList::DEFAULT, and DSetMemXferPropList::DEFAULT.
H5P_DEFAULT was used to create these default prop lists and
because its value is 0, the id of these prop lists are 0, which
is rejected by the H5I functions during the reference counting.
Solution:
The main action to fix the above problem was to use
H5P_FILE_CREATE
H5P_FILE_ACCESS
H5P_DATASET_CREATE
H5P_DATASET_XFER
to define the default property lists accordingly. Yet, when this
fix was applied, some bug in reference counting was revealed.
It appeared that some ids were not incremented but were passed in
for decrementing. The following actions were then taken to fix and
improve the current use of reference counting H5I functions.
* added private func IdComponent::p_valid_id to verify that the
id is a valid id and can be passed into an H5I function
* used p_valid_id to validate an id before calling an H5I functions
in the reference-counting member functions incRefCount,
decRefCount, and getCounter
* changed to use member function incRefCount, decRefCount, and
getCounter instead of the C APIs H5Iinc_ref, H5Idec_ref, and
H5Iget_ref throughout IdComponent.
In addition, overloadings were added for incRefCount, decRefCount,
and getCounter to take an id different than the id of the current
instance; they can be convenient during debugging.
Platforms tested:
Linux 2.4 (heping)
SunOS 5.8 64-bit (sol)
AIX 5.1 (copper)
Description:
Doxygen 1.4.2 has a bug that when an \exception immediately
follows a \brief, the exception will be displayed prominently
in the brief section.
Solution:
Temporarily added /// to after \brief to work around this
problem and notified the Doxygen's author.
Platforms tested:
Linux 2.4 (heping) - only in documentation sections
Description:
Added the following to the C++ library
+ overloaded functions:
string CommonFG::getObjnameByIdx(hsize_t idx)
H5T_order_t AtomType::getOrder()
+ wrappers for H5*close
+ wrappers for H5Arename, H5Aget_storage_size, and H5Dget_storage_size
Platforms tested:
Linux 2.4 (heping)
AIX 5.1 (copper)
SunOS 5.8 64-bit (sol)
Description:
Checked return value from C API for failure condition.
Added/Modified some comments appropriately.
Platforms tested:
Linux 2.4 (heping)
AIX 5.1 (copper) - tests passed but there were some old warnings about
duplicate symbols on std::string; I'll check on that.
Description:
Updated various function headers for the RM as reviewing progresses.
Rearranged functions in header files for more sensible look of the RM.
Platforms tested:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
Description:
Removed private functions p_close, that were left over from the
removal of the reference counting mechanism.
Platforms tested:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
Misc. update:
release_docs/RELEASE will be updated soon.
Code cleanup
Description:
DataType::commit had incorrect parameter, H5Object. Changed
it to CommonFG, for H5File and Group.
The change caused additional header files needed for several
other cpp files.
Moved some functions from Group into the base class CommonFG for
H5File too.
Platforms tested:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
Misc. update:
Code update
Description:
Update C++ wrappers to use new ID reference counting mechanisms.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/C++
Too focused to require h5committest
Add/Improve documentation
Description
Added doxygen documentation to H5PredType.cpp and made minor changes
to the others for either correction or clarification.
Platforms:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
Misc. update:
Add more C++ wrapper and documentation - incrementally check-in
Description
Added another overloaded constructor to StrType.
Added doxygen documentation to H5IdComponent.cpp.
Corrected some comments.
This is an incremental check-in to preserve the code, corresponding
tests will follow in a few weeks.
Platforms:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
Misc. update:
Add C++ wrappers - incrementally check-in
Description
Added wrapper for these C APIs:
H5Rcreate
H5Rget_obj_type
H5Rget_region
This is an incremental check-in to preserve the code, corresponding
tests will follow in a few weeks.
Platforms:
Linux 2.4 (eirene)
I'm checking the code out and test on arabica too.
Misc. update:
Add C++ wrappers - incrementally check-in
Description
Added wrapper for these C APIs:
H5Dget_offset
H5Dget_space_status
Platforms:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
Misc. update:
Add more C++ wrapper and documentation - incrementally check-in
Description:
Added doxygen documentation to:
H5DataSet.cpp
H5DataSpace.cpp
H5CommonFG.cpp
and a wrapper for H5Rcreate to H5Object.* with tests will be added
later.
There are more documentation need to be added to these files but
to preserve the changes, I check them in now.
Platforms:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
Misc. update:
Bug fix and minor code enhancement
Description:
Missing methods to read/write C++ String for an attribute and
a dataset.
Solution:
Added overloaded functions read and write to H5::Attribute and
H5::DataSet.
Also, added another constructor StrType so the need to separately
set the length of the string type can be eliminated. It's minor
but convenient.
Made some minor changes to make error messages more readable.
Platforms:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
IRIX 6.5.11 (modi4)
HPUX 11.00 (kelgia)
Adding new platform support
Description:
Added support for the C++ API on hpux11.00 with the compiler aCC.
Because aCC doesn't use "std," a new macro H5_NO_STD is provided
and used where "std" is presented in the library.
In addition, changed several cout's when reporting errors to cerr's.
Platforms tested:
HPUX 11.00 (kelgia)
Linux 2.2x (eirene)
IRIX 6.5.11 (modi4)
SunOS 5.7 (arabica) - by Elena
Misc. update:
New Feature - per library change
Description:
Added new member function DataSet::fillMemBuf for the new
C API H5Dfill. Quincey's description of H5Dfill is as followed:
Added new H5Dfill() routine to fill the elements in a selection for a
memory buffer with a fill value. This is a user API wrapper around some
internal routines which were needed for the fill-value modifications
from Raymond as well as Pedro's code for reducing the size of a chunked
dataset.
Platforms:
SunOS 5.7 (arabica)
Linux 6.2 (eirene)
Purpose:
Small bug fixing
Description:
Replaced NULL by 0 for initializing or passing null "string".
The problem showed up on platinum.
Platforms tested:
SunOS 5.7 (arabica)
Linux 6.2 (eirene)
IA-32 Linux Cluster (platinum)
Purpose: Usability enhancement
Description:
- Added more information about the failure to all the throw's,
i.e, member function name and more detail about the failure, where
appropriate. Also, added exception throws for private functions,
such as p_close to provide more specific details.
- Added two api functions: Exception::getFuncName() and
Exception::getCFuncName() to provide the name of the member
function where failure occurs.
- Fixed some typos, one of which caused segn. fault in some
situations (resetIdComponent was accidentally called twice
in a couple of places :)
Platforms:
arabica (sparc-sun-solaris 2.7)
Purpose:
Small bug fix
Description:
A stub function has returned type hsize_t but returns -1.
Solution:
Changed returned value from -1 to 0
Platforms tested:
Solaris (arabica)
Purpose: bug fix
Description:
I found a couple of places where virtual destructors were missing
and could cause small memory leaks. Also, some destructors were
not virtual when they should be.
Solution:
- added virtual destructors, which also free dynamically allocated
memory
- added virtual to several destructors
- also, fixed several typos
Platforms tested:
Solaris 2.7 (arabica)
Binh-Minh Ribler
Quincey Koziol
Raymond Lu
Albert Cheng