| Commit message (Collapse) | Author | Age | Files | Lines |
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Migrate more object header routines to use the H5O_msg_ prefix and put
them into the src/H5Omessage.c code module.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
AIX/32 5.? (copper)
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Finish implementation of H5Literate() [still needs real tests]
Clean up datatype macro warnings a bit more.
Unify iterator callback macros and put up in public header file, with the
iterator directions.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
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This feature is still in progress; Shared Object Header Messages are not
complete as a feature and are not thoroughly tested. There are still
"TODO" comments in the code (comments with the word "JAMES" in them,
so as not to be confused with other TODO comments).
Hopefully this checkin will reduce the liklihood of conflicts as I finish
implementing this feature.
All current tests pass on juniper, copper (parallel), heping, kagiso, and mir.
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Refactor generic property list initialization code to put property list
specific routines in property list modules, instead of scattered to the four
winds. Also, introduce property list class initialization objects, to make
adding new property list classes in the library easier.
Fix daily test failure by using H5Pget_elink_prefix() API routine instead
of looking at the "raw" generic property list information.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/C++ & FORTRAN
Linux/64 2.4 (mir) w/build-all & 1.6 compat
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Finish new version of the I/O pipeline message, which is much smaller than
the previous version. This version is used with the "use the latest version
of the format" flag.
Closed several memory leaks/overruns (found with valgrind).
Also, lots of compiler & formatting cleanups.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Code cleanup to improve formatting & reduce compiler warnings.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Add "use the latest format" support for dataspace object header encode/
decode routines and clean up format a bit for the latest format (new to 1.8.x
releases)
Remove storing 'perm' parameter for array datatypes in memory and the file,
and add test to make certain that if any user applications are attempting to
store them, we get some reports back. (Should be unlikely, since the RefMan
says that the parameter is not implemented and is unsupported).
Carry those changes into the tests, etc.
Clean up a bunch more compiler warnings.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-1.6-compat
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Add the "use the latest version of the format" support to datatype
messages. And a regression test to check that it's working.
Also, found that we have been over-allocating space for compound datatype
messages (when they have array datatypes or can use the latest version of the
format) and trimmed the size back.
Clean up datatype & dataspace encode/decode routines by having them
allocate & release "fake" file structures, which gets them out of needing to
"know" about the internals of file structures.
Other minor whitespace/formatting cleanups, etc.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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File format is not stable, don't keep files produced!
Description:
First stage of checkins modifying the format of groups to support creation
order. Implement "dense" storage for links in groups.
Try to clarify some of the symbols for the H5L API.
Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest
file format options (including "dense" link storage in groups)
Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation
order tracking in groups (although no index on creation order yet).
Remove --enable-group-revision configure flag, as file format issues are
now handled in a backwardly/forwardly compatible way.
Clean up lots of compiler warnings and other minor formatting issues.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-v1.6 compa
Mac OSX/32 10.4.8 (amazon)
AIX 5.3 (copper) w/parallel & FORTRAN
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Users can create external links using H5L_create_external(). These links
point to an object in another HDF5 file. Users can alter the behavior of
external links or create new kinds of links by registering callbacks
using the H5L interface.
Added tests, tools support, etc.
Also a number of other, minor changes have been made (some restructuring of
the H5L interface, for instance).
Additional documentation and examples are forthcoming.
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Feature
Description:
Revised Link APIs.
Solution:
New link APIs use H5L*
H5*create_expand do not create links to the objects created; this must
be done manually with H5Llink.
Added APIs to link an object given its ID (H5Llink), to copy links (H5Lcopy),
and changed creation APIs (H5Lcreate_hard and H5Lcreate_soft) and query
API (H5Lget_linkinfo instead of H5Gget_objinfo).
All old APIs are still supported in H5Gdeprec.c .
Platforms tested:
sol, mir, copper
Misc. update:
Forgot to update MANIFEST and release docs. Will do after checkin.
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Code cleanup
Description:
Trim trailing whitespace in Makefile.am and C/C++ source files to make
diffing changes easier.
Platforms tested:
None necessary, whitespace only change
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Description: Mac OS 10.4 on PowerPC chip has some errors to convert (unsigned)
long long to long double. When the bit sequences are 0x003ff..., 0x007fff...,
0x00ffff..., 0x01ffff..., 0x7fffff..., the converted values are twice as big
as they should be.
Solution: Detect the error in configure and disable the compiler conversion
and test case.
Platforms tested: h5committest, Mac OS 10.4, and fuss.
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New/expanded features
Description:
Check in Peter's changed for the object copy code:
- Allow/fix copying datasets using named variable-length datatypes
- Start adding framework for property list to control how object
copying occurs.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Solution: Support VAX float and double types with new byte order. There're some
details not yet included,
1. the alignment detection for VAX order in H5detect.c.
2. support for special values in library conversion functions.
3. the infinity for VAX in H5T_init_inf.
4. support for VAX types in printing hexadecimal format.
Platforms tested: h5committest and fuss.
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Bug fix
Description:
Retrieving an object's name could fail (in various ways) under certain
circumstances (mostly having to do with mounted files).
Solution:
Re-write & simplify "get object name" code to fix error in a better way
than adding yet another hack to the previous pile of hacks... :-)
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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New feature
Description:
Add in a combination of Peter's & my code to support copying
variable-length data from one file to another, although currently only
supported with contiguous data storage.
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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Configure feature
Description:
Added 'make trace' target.
Solution:
Added tracing to 1.7. This was done automatically in 1.6, but left out
of 1.7 until now (oops!).
Tracing in 1.7 only happens manually, when the user types 'make trace.'
Tracing automatically requires more framework than it's worth.
I also fixed a couple of tracing bugs and ran trace.
Platforms tested:
mir, sleipnir, modi4
Misc. update:
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New feature
Description:
Check in baseline for compact group revisions, which radically revises the
source code for managing groups and object headers.
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
This initiates the "unstable" phase of the 1.7.x branch, leading up
to the 1.8.0 release. Please test this code, but do _NOT_ keep files created
with it - the format will change again before the release and you will not
be able to read your old files!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
Solution:
There's too many changes to really describe them all, but some of them
include:
- Stop abusing the H5G_entry_t structure and split it into two separate
structures for non-symbol table node use within the library: H5O_loc_t
for object locations in a file and H5G_name_t to store the path to
an opened object. H5G_entry_t is now only used for storing symbol
table entries on disk.
- Retire H5G_namei() in favor of a more general mechanism for traversing
group paths and issuing callbacks on objects located. This gets us out
of the business of hacking H5G_namei() for new features, generally.
- Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t
- Lots more...
Platforms tested:
h5committested and maybe another dozen configurations.... :-)
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New feature
Description:
Add in baseline "object copy" code from Peter [in the form of a new API
routine: H5Gcopy()]. There's still some work to do (like handling variable-
length datatypes and possibly support for references) and it hasn't been tested
on mounted files yet, but the core functionality is there and working
correctly.
I've also got a set of patches to update the 1.6 branch with tweaks to
keep the branches mostly in sync, but Elena will kill me if I import them
before the 1.6.5 release is out... :-)
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committested
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Bug fix
Description:
Fix "double root open" bug and apply same fix to datasets & named datatypes.
Also fix bug in symbol table entry lookup code that would "transfer" an
object from one file handle to another file handle when the two file handles
were opened on the same actual file.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Code cleanup/bug fix
Description:
Hoist function call out of inner loop of type conversion by retrieving
source & destination precisions once, outside the loop.
There's still some overhead because this information is stored in
variables set at run-time, when it's really constant for the particular
machine. Further work to set compiler macros would allow this code to be
optimized better by the compiler with dead code removal. We'll continue
to work on this area...
Also, made new internal H5T_compiler_conv routine static instead of of
private, until we need to reference it from another source code module.
Platforms tested:
h5committest
FreeBSD 4.11 (sleipnir)
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Description: H5T_register() replaces any existing data conversion path
with a new path.
Solution: Added a parameter to H5T_register() and H5T_path_find() to
signal the library whether the new conversion path is from API function
H5Tregister() or from private function like H5T_init_interface(). If it
is from H5Tregister(), replace existing path. If it's from H5T_init_interface()
and the library is trying to register default hard conversion functions,
don't replace existing path because the path is registered by the library.
For example, the library registered H5T_conv_int_float() and is trying to
register H5T_conv_long_float(). The size of long is equal to int. There's
no need to replace the path H5T_conv_int_float().
Platforms tested: h5committest and fuss.
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Description: The API function H5Tis_hard() which was recently checked
in has been renamed to H5Tcompiler_conv() to be more descriptive. No
other changes.
Platforms tested: fuss - simple change.
Misc. update: config/lt_vers.am to update libtool version.
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Code cleanup/reorganization
Description:
Merge back some more changes extracted from the "compact group" set.
This bunch cleans up and prepares the H5G_* routines for eventual import of
new features.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Mac OS X.4
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Code cleanup
Description:
Merge back changes from "compact group" work that improve the
infrastructure of the library and may impact others. In this round of
merging, that includes:
- Move datatype allocation into single internal routine, instead of
duplicated code that was spread out in a dozen or so places.
- Clean up guts of object header routines (H5O_*) to allow for some of
the fancieroperations that need to be performed on groups, along with
some general improvements.
- Added a new error code
- Some minor cleanups in other code....
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Mac OS X
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Description: Put in a new API funciton, H5Tis_hard. It checks whether
the conversion function from a native type to another native type is a
compiler (hard) conversion. Also checked a test in test/dt_arith.c.
Platforms tested: h5committest and fuss.
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Description: Changed the names of macros defined in H5Tpkg.h from
H5T_CONV_INTERIM_XXX_XXX to H5T_CONV_INTERNAL_XXX_XXX to be more
descriptive.
Platforms tested: fuss - simple change
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Description: Changed the names of the interim macros for data conversion
checked in yesterday from the SOURCE_DESTINATION style (like FP_FP or
LDOUBLE_LLONG) to the H5T_CONV_INTERIM_SOURCE_DESTINATION style (like
H5T_CONV_INTERIM_FP_FP OR H5T_CONV_INTERIM_LDOUBLE_LLONG), to be more
descriptive. These macros are defined in H5Tpkg.h and used in H5Tconv.c
and H5T.c for interim purpose.
Platforms tested: fuss - simple change.
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Description: Added 2 new configure options, --enable-exception and --enable-accuracy.
--enable-exception lets the library check whether user's exception handling
functions are present during compiler data conversions and use them if they are.
When it's disabled, this step is skipped to improve conversion speed. This
step isn't implemented yet for soft conversions because there would be little
gain in speed.
--enable-accuracy guarantees data accuracy during data conversions. It means
the library will choose compiler conversions only if the accurate data is
secured. Otherwise, the library will go for the library's own conversions. If
this option is disabled, the library uses compiler conversions in favor of
their speed as long as they work even if data can be incorrect.
Platforms tested: h5committest and fuss. Some systems may fail after this
checkin.
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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
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Bug fix
Description:
If a named datatype is copied and the copy is used to create a dataset,
the dataset would inadvertantly refer to the original named datatype instead
of a local (possibly modified) copy of the named datatype.
Solution:
Fixed datatype copying routine.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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New port
Description:
Elena asked me to check in her NEC SX-6 work, so here it is! :-)
Platforms tested:
FreeBSD 4.11 (sleipnir)
NEC SX-6 (by Elena)
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Bug fix
Description:
Correct memory leak when a dataset is attempted to be opened, but turns
out to be a group or named datatype.
Also, clean up code that was leading to the leak and zero out empty
group entries to help prevent similar errors in the future.
Platforms tested:
FreebSD 4.11 (sleipnir)
Too minor to require h5committest
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New feature
Description:
Add group creation & access property lists, dataset access property lists
and named datatype creation & access property lists. Currently have
<foo>_extend() API names, which will need to be changed for the final release.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (heping)
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Description: Data conversion function H5T_conv_i32le_f64le() was unused.
Because we have new conversion functions for integers and floating numbers,
this old function is taken out.
Platforms tested: fuss - simple change.
Misc. update:
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Description: Fix the codes of last checkin(Bug #341). Some failures happened
in daily test from last checkin. Try to fix them in this checkin.
Platforms tested: modi4, mir, and tg-login2.
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Description: The hard conversion functions of "long double" and other floating
point types were left out for registration somehow.
Solution: Added them in.
Platforms tested: h5committest and fuss.
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Bug fix
Description:
Add missing #ifdef's to recent code cleanup that fix daily test failures.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Code cleanup
Description:
Clean up some compiler warnings
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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Bug fix
Description:
Opening a dataset (or named datatype) with "." for the name and using a
group ID for the location ID was not returning an error value.
Solution:
Check the type of the object before attempting to open it (internally,
using a group ID and "." for the name maps to the group object).
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
Too minor to require h5committest
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Optimization
Description:
Speed up I/O on enumerated datatypes (including those nested in compound
datatypes, arrays, etc.) if the destination datatype is a proper superset of
the source datatype.
Solution:
Detect the situation and treat as no-op datatype conversion.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Description: The library didn't handle incorrect hardware conversion for datatype. It simply did
convert to incorrect data if any hardware didn't handle correctly.
Solution: During configuration, incorrect hardware conversion is detected and some macros are
defined. Use these macros to decide whether to register hardware conversion in H5T.c. If no hardware
conversion function is registered for certain pair of datatypes, software conversion function will
be used as the conversion path. Although slower than hardware conversion, we're more confident
software conversion is accurate.
So in one sentence to describe library's behavior, if some hardware conversion doesn't work well,
software conversion will be used instead.
Platforms tested: h5committest and fuss.
Misc. update: some changes to configure's comments.
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Description: Added support of hardware conversion between "long double" and integers(mainly
in H5Tconv.c) and some test cases(mainly in test/dtypes.c).
Platforms tested: h5committest and fuss.
Misc. update: RELEASE.txt
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Description: H5Tget_member_value didn't return correct value if called after
H5Tenum_valueof. It's because there's a sorting on the members of enum type in
H5Tenum_valueof which changed the order of members.
Solution: Made a copy of original type and do sorting on it to protect the
original order.
Platforms tested: fuss; tested v1.6 with h5committest
Misc. update: RELEASE.txt
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Description: For variable-length string, H5Tget_class returned H5T_STRING as
its class. But H5Tdetect_class and H5Tget_member_class considered it as
H5T_VLEN. This is fixed to let all these 3 functions treat it as H5T_STRING.
Some test cases have been added to dtypes.c
Platforms tested: heping - already tested for v1.6 with h5committest
Misc. update: RELEASE.txt
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Description: Removed PABLO from the source
Solution:
Platforms tested: arabica with 64-bit, copper with parallel,
heping with GNU C and C++ and PGI fortran (but
I disabled hl, there is some weird problem only
on heping: F9XMODFLAG is not
propagated to the Makefile files
Misc. update:
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Description: The functions for user-define floating-point type, like
H5Tset_fields, H5Tset_offset, H5Tset_precision, H5Tset_size, have some
minor bugs. For error checking, the library didn't include offset value
somehow.
Solution: Corrected those bugs.
Platforms tested: h5committest and fuss
Misc. update:
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Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
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Code optimization
Description:
Revise mechanism for calling H5open/H5check to better avoid calling them
from internal libray code.
Only copy a datatype's group entry information if it has some.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Solaris 2.7 (arabica)
Too minor to require h5committest
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