Another Oops
Description:
I accidentally checked in the H5D.c module when I shouldn't have.
Solution:
Rolled back to 1.281 version
Platforms tested:
Linux
Oops
Description:
The H5FPprivate.h file was being #included even if PARALLEL was
turned off.
Solution:
put the #include of the H5FPprivate.h file within the #ifdef block so
that it doesn't get included if H5_HAVE_FPHDF5 isn't defined.
Platforms tested:
Linux...
Bug Fix
Description:
The NBYTE{ENCODE,DECODE} macros were updating the pointer "p" to a
new value instead of one of the "real" pointers passed into the
macro.
Solution:
Changed it so that it updates the destination pointer which gets
passed into these macros.
I'm not sure if this is correct, since neither of these macros are
actually used in our source code...
Platforms tested:
They aren't used, so no testing possible.
Feature Add
Description:
New files for the Flexible Parallel HDF5 stuff.
H5FP.c - Module housing the APIs to FPHDF5
H5FPclient.c - Module housing the internal client APIs
H5FPserver.c - Module housing the internal server APIs
H5FPpublic.h - Header for public APIs
H5FPprivate.h - Header for private APIs
H5Ofphdf5.c - Way of serializing FPHDF5 information to and from the
SAP
H5Oplist.c - Way of serializing a generic property list.
Solution:
[details about the changes, algorithm, etc...]
[Please as detail as you can since your own explanation is
better than others guessing it from the code.]
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}?
[If no, why not?]
Other platforms/configurations tested?
Misc. update:
Update MANIFEST if you add or remove any file.
Update release_docs/RELEASE for bug fixes, new features, etc.
Update applicable document files too.
Feature Add
Description:
Moved some functions from having only module scope to having public
scope, but only available in the HDF5 internals (not public APIs).
Platforms tested:
Eirene, Arabica, Modi4
Bug fix (ID 841)
Description:
h5dumptst (generating h5dump test files) failed with an assertion error
in H5S_select_iterate. H5S_select_iterate did not account for scalar
type that has rank=0, thus no dimension sizes.
Solution:
Put the assertion of valid sizes only after verify rank is larger than
0. (fix is coached by Quincey.)
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}? YES.
Misc. update:
Update release_docs/RELEASE for bug fixes, new features, etc. YES.
New feature.
Description:
Added check for "HDF5_DISABLE_VERSION_CHECK" environment variable to
disable the version checking code between the headers and the library.
Tested:
FreeBSD 4.7 (sleipnir) - no triple check necessary.
Code cleanup/Bug Fix
Description:
Re-do the ID->name code again, taking into account many more weird and
wonderful special cases stumbled across during the last set of test
writing.
Platforms tested:
FreeBSD 4.6 (sleipnir) w and w/o parallel
Linux 2.2.x (eirene) w/FORTRAN & C++
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
New feature.
Description:
Add H5P_DEFAULT_HASH_SIZE macro for users to use as the default size of
hash tables for H5Pcreate_class.
Platforms tested:
FreeBSD 4.6 (sleipnir) w and w/o parallel
Linux 2.2.x (eirene) w/FORTRAN & C++
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
Bug fix
Description:
Generic property classes where incorrectly reference counting their
users, in certain cases, causing a memory leak.
Solution:
Cleanup reference counting code & unify in H5P_access_class()
Platforms tested:
FreeBSD 4.6 (sleipnir) w and w/o parallel
Linux 2.2.x (eirene) w/FORTRAN & C++
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
Code cleanup
Description:
Changed a HRETURN_ERROR to HGOTO_ERROR
Platforms tested:
FreeBSD 4.6 (sleipnir) w and w/o parallel
Linux 2.2.x (eirene) w/FORTRAN & C++
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
Code cleanup
Description:
Shift further toward removing the HRETURN* macros, in favor of the HGOTO*
macros for error reporting.
This change disables them in the header file and is the last change before
removing them entirely after the 1.6 release.
Platforms tested:
FreeBSD 4.6 (sleipnir) w and w/o parallel
Linux 2.2.x (eirene) w/FORTRAN & C++
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
Code cleanup
Description:
Change new H5P_get_class_path and H5P_open_class_path functions to be non-
static and put prototypes in H5Pprivate.h
Platforms tested:
FreeBSD 4.6 (sleipnir) (no triple-check necessary)
Internal feature.
Description:
To complement the "get the class's path" functionality, there needs to be
a way to open a generic property class with a path.
Solution:
Implement the "open a class by path" functionality. Also, add internal
testing routines.
Platforms tested:
FreeBSD 4.6 (sleipnir) (too small for triple testing)
New internal feature.
Description:
Need some way to determine the "full path" for a generic property class,
i.e. where is this class in the class hierarchy, in relation to its parent
class, etc.
Solution:
Added an internal function "H5P_get_class_path" and a testing function
"H5Pget_class_path_test" that builds the full path of a generic property
class back to the top of its class hierarchy.
This implementation uses '/' characters to delimit the components of the
class path, but no special cases are currently supported for having a '/'
character as part of the actual class name. Should this become an issue,
code to support (and test) it will need to be added.
Platforms tested:
FreeBSD 4.6 (sleipnir) (not major enough to justify triple-test)
Bug fix
Description:
H5Pequal's algorithm for comparing property lists wasn't allowing property
lists that are equal but had the properties inserted in a different order
in the list's hash table.
Solution:
Re-did the algorithm a bit to compare the properties better.
Platforms tested:
FreeBSD 4.6 (sleipnir) (minor enough to not need triple testing)
New error code
Description:
Add a new error code for the generic properties to use.
Platforms tested:
FreeBSD 4.6 (sleipnir) (too small to need triple testing)
Purpose:
a bug fix
Description:
modify the condition check for the file close degree.
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
Purpose:
a bug fix
Description:
When a file is opened for a second time, file close degree is supposed to
be either the same as the first open, or default as the first open is also
default.
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
Purpose:
New API functions
Description:
Added API functions to return pointer to low-level file handle
(H5Fget_vfd_handle and H5FDget_vfd_handle) and related property list
setting functions(H5Pset_family_offset and H5Pset_multi_type).
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
Code cleanup
Description:
Clean up ID->name code:
- Reformat to better match library coding standard
- Changed several algorithms to be more efficient
- Integrated into library more smoothly
Platforms tested:
eirene w/FORTRAN & C++
arabica w/FORTRAN
modi4 w/FORTRAN & parallel
sleipnir
Purpose:
bug fix
[ i s this a bug fix? feature? ...]
Description:
the copy of a symbol table entry was done with a shallow copy, in H5T_copy
this was causing an exception on the free call of the ID to name buffer
replaced a shallow copy of a symbo l a edescribe the bug, or describe the new feature, etc]
Solution:
[details about the changes, algorithm, etc...]
[Please as detail as you can since your own explanation is
better than others guessing it from the code.]
Platforms tested:
windows 2000
solaris with cpp, fortran
irix64, with fortran, parallel i r
[machines you have tested the changed version. This is absolute
important. Test it out on at least two or three different platforms
such as Big-endian-32bit (SUN/IRIX), little-endian-32(LINUX) and
64-bit (IRIX64/UNICOS/DEC-ALPHA) would be good.]
Purpose:
__DLL__ is a keyword in some platforms and __DLL__ is also defined as a macro for windows DLL applications.
That causes problems.
Description:
Solution:
Use H5_DLL*** to replace __DLL***__ at all header files.
Change the macro defination at H5api_adpt.h.
Platforms tested:
linux2.2.18smp, irix64, solaris 2.7 and windows 2000
Purpose:
bug fix
Description:
memory leak regarding the ID to name buffer
Solution:
added a new function H5G_free_ent_name that is called on several places of the library
Platforms tested:
windows 2000
linux, with cpp
solaris, with fortran, cpp
irix64, with parallel, fortran
API name change
Description:
Change all "space time" references to "alloc time", including API functions
and macro definitions, etc.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/C++
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
Code cleanup
Description:
Switch order of test on array bounds to avoid reading data outside of array
Located by purify.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/C++
Solaris 2.7 (arabica) w/C++
IRIX64 6.5 (modi4) w/parallel & fortran
Code cleanup
Description:
Two of the parameters to H5S_select_hyperslab are defined as
"const hsize_t foo[]", and then "foo" is assigned another value, which is
technically against the C standard and is now causing problems for a user
with a more strict compiler.
Solution:
Changed "const hsize_t foo[]" to "const hsize_t *foo".
Platforms tested:
FreeBSD 4.6 (sleipnir) - not a significant enough change to worry about
multi-platform testing.
Bug fix.
Description/Solution:
Fix bug in log file driver where the size of the buffer for recording the
log information was being set incorrectly.
Platforms tested:
FreeBSD 4.6 (sleipnir) - no additional testing on other machines neceessary,
due to scope of fix.
Purpose:
bug fix in 'ID to name' function
Description:
the function replace_name was only checking for immutable datatypes
Solution:
added a new function H5T_is_named, that checks for named datatypes
Platforms tested:
windows 2000, linux, solaris with Fortran
Bug Fix
Description:
Some macros had "NULL" instead of "FAIL" as the return value.
Solution:
Change from NULL to FAIL.
Platforms tested:
Eirene (C++), Arabica (Fortran), Modi4 (pp and Fortran).
Purpose:
bug turnaround in test_hdf5_fortran on a h5fmount_c call
Description:
the H5I_nmembers(H5I_GROUP) call that is made inside
h5fmount_c -> H5G_replace_name -> H5I_nmembers(H5I_GROUP)
is not detecteting correctly that the entry belongs to the group list
therefore a call is made to H5I_search(H5I_DATATYPE) (there are always non-named datatypes)
and H5G_replace_ent is called with a search for the datatype group
ent = H5T_entof((H5T_t*)obj_ptr);
which returns a NULL ent
a tweak for this is to add
if( !ent) goto done;
Platforms tested:
windows 2000, Linux, Solaris with fortran
Purpose:
Added 'ID to name' support
Description:
There is a new API function H5Iget_name
Most of the changes are on H5G.c , regarding the symbol table entry struct H5G_entry_t
which has 2 new fields 'name' and 'old_name'
A new private function was introduced H5G_ent_copy, that does a deep copy
between 2 symbol table entries
The test file is getname.c
Platforms tested:
windows 2000, Linux, Solaris
Code cleanup/New Feature
Description:
Improve the space allocation in the file by re-using freed space more
effectively.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/serial & parallel
Bug fix/Code cleanup/New Feature
Description:
Correct problems with writing fill-values to external storage and allocate
the data storage at the correct times.
Also, mostly straighten out the strange code which allocates and fills
raw data storage for datasets. Things are still a bit odd in that the
fill-values for chunked datasets are written when the space is allocated,
instead of in a separate routine, but there are two reasons for this:
it's inefficient (especially in parallel) to iterate through all the chunks
twice, and (more importantly) the space needed to store compressed chunks
isn't known until we've got a buffer of compressed fill-values ready to
write to the chunk.
Additionally, add in the H5D_SPACE_ALLOC_INCR and H5D_SPACE_ALLOC_DEFAULT
setting for the "space time", which incorporate the previous behavior of
the space allocation for chunked datasets.
The default settings for the different types of dataset storage are now
as follows:
Contiguous - Late
Chunked - Incremental
Compact - Early
This checkin also incorporates a change to the behavior of external data
storage in two ways - fill-values are _never_ written to external storage
(under the assumption that writing fill-values is triggered by allocating
space in an HDF5 file, and since space is not allocated in the file, the
fill-values should not be written) and external data files are now created
if they don't exist when data is written to them. The fill-value will
probably need to be revisited at some time in the future, this just seemed
like the safer course currently.
I think I cleaned up some compiler errors also, before getting bogged down
in the fixes for the space allocation and fill-values.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/serial & parallel. Will be testing on IRIX64
6.5 (modi4) in serial & parallel shortly.
Bug fix
Description:
Correctly apply filters (like compression) to fill values in chunks that
are pre-allocated.
This is OK in parallel also, since all the chunks are identical at this
point and any chunk may be written by any process.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/parallel
