| Commit message (Collapse) | Author | Age | Files | Lines |
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Purpose:
Bug fix
Description:
Fix bugs found by daily tests.
Platforms tested:
copper
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Purpose:
Feature
Description:
(Same change to release branch)
Datatypes and groups now use H5FO "file object" code that was previously
only used by datasets. These objects will hold a file open if the file
is closed but they have not yet been closed. If these objects are unlinked
then relinked, they will not be destroyed. If they are opened twice (even
by two different names), both IDs will "see" changes made to the object
using the other ID.
When an object is opened using two different names (e.g., if a dataset was
opened under one name, then mounted and opened under its new name), calling
H5Iget_name() on a given hid_t will return the name used to open that hid_t,
not the current name of the object (this is a feature, and a change from the
previous behavior of datasets).
Solution:
Used H5FO code that was already in place for datasets. Broke H5D_t's, H5T_t's,
and H5G_t's into a "shared" struct and a private struct. The shared structs
(H5D_shared_t, etc.) hold the object's information and are used by all IDs
that point to a given object in the file. The private structs are pointed
to by the hid_t and contain the object's group entry information (including its
name) and a pointer to the shared struct for that object.
This changed the naming of structs throughout the library (e.g., datatype->size
is now datatype->shared->size). I added an updated H5Tinit.c to windows.zip.
Platforms tested:
Visual Studio 7, sleipnir, arabica, verbena
Misc. update:
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Code optimization
Description:
Avoid performing a check on the number of objects in a group (which
currently involves iterating over all entries in the group's B-tree) before
calling H5G_get_obj<foo>_by_idx. Instead, just have H5G_get_obj<foo>_by_idx()
notice when you've walked off the end and return fail then.
Platforms tested:
FreeBSD 4.10 (sleipnir)
h5committest
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Purpose:
Bug Fix
Description:
Trying to create the root group or the working group ("/" or ".") fakes out
HDF5 so that it neither creates a group nor returns an error.
Solution:
H5G_namei now throws an error if it was supposed to insert but didn't.
Platforms tested:
sleipnir, Visual Studio 7 (very minor change)
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Code cleanup
Description:
Clean up a bunch of warnings and bring new code better inline with current
library coding practice.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
Misc. update:
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Bug fix
Description:
The "shared" raw B-tree node can get freed before all the B-tree nodes
had been flushed out to disk and released by the cache.
Solution:
Implement a simple reference counting wrapper for objects in the library
and use it to hold the shared raw B-tree nodes so they aren't freed before all
references to them in memory are released.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir)
IRIX64 6.5 (modei4)
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Refactor bug fix
Description:
Make bug fix for detecting the type of a soft link more general by
registering an "isa" function for soft links.
Platforms tested:
FreeBSD 4.10 (sleipnir)
Too minor to require h5committest
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Bug fix
Description:
Fix small problem with 1.4 backward compatibility
Platforms tested:
FreeBSD 4.9 (sleipnir) w/1.4 backward compatibility
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Code cleanup
Description:
Clean up lots of warnings based on those reported from the SGI compilers
as well as gcc.
Platforms tested:
SGI O3900, IRIX64 6.5 (Cheryl's SGI machine)
FreeBSD 4.9 (sleipnir) w/ & w/o parallel
h5committest
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Code cleanup
Description:
Clean up compiler warnings, especially the 'FUNC' variable not used which
comes out in production mode.
Solution:
Had to add a new FUNC_ENTER_NOAPI_NOINIT_NOFUNC macro for those non-API
functions which don't need the 'FUNC' variable defined. (This will be _so_
much easier when C99 is standard on all our supposed platforms, since it has a
__FUNC__ macro... )
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor for h5committest (although there were lots of files changed, the
change was minor in each one)
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Bug fix
Description:
Make a copy of the index value for H5Giterate and use that instead of
dereferencing the index pointer.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to need h5committest
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Feature add
Description:
Add a few new fields to the H5G_stat_t structure, to allow more information
about the object header to be retrieved.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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Bug fixes and code cleanup
Description:
Lots of changes here:
- Fixed bug #691 - when shared datatypes are used in attributes they
are incorrectly copied into the attribute instead of referring
the the named datatype in the file. This required bumping the
version of the attribute message. The new version of the attribute
message is only written out when a shared datatype is used in
the attribute. [Also, this format change made the size of the
attribute smaller.]
- Added information to attribute debugging routine so that shared
datatypes are displayed correctly with the h5debug tool.
- Refactored the H5O* routines to extract code that was common to
several routines into subroutines to call.
- Added 'link' method for H5O message sub-classes, which increments
the link count on shared objects when a message is created which
shares them.
- Corrected [unreported] bug where the link count was not being
decremented on the shared object when a object header message
with a reference to that object was deleted from the file.
- Reduced size of shared message from 49 bytes (which was incorrect
anyway and should have been 48 bytes) to 10 bytes, which required
bumping the version of "shared" messages.
- Refactored some of the shared datatype routines to allow for easier
queries of "committedness" internally to the library and also
added routine to easily increment/decrement the reference count of
a shared datatype.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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Bug fix
Description:
H5Gget_objname_by_idx should allow NULL for the 'name' parameter, to allow
for querying for the name's length.
Solution:
Allow NULL for the 'name' parameter, the internal functions were already
ready to handle that case.
Clean up RM information about H5Gget_objname_by_idx and
H5Gget_objtype_by_idx also.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Bug fix
Description:
H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx were
only accepting a group ID, instead of a location ID, as our documentation for
them stated.
Solution:
Allow them to accept a location ID.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Bug fix
Description:
Linking and unlinking objects with multiple internal and/or trailing '/'s
was not handled well in the library.
Solution:
"Normalize" strings by removing trailing '/'s and collapsing multiple
internal '/'s down into just one '/' before operating on the name.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committested
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Bug fix (backward compatibility)
Description:
Track changes to allow H5Giterate to pass along iterator callback's return
value
Also, improve range checking on "index" parameter to disallow invalid
starting indices (<0 or > the number of objects in a group).
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Code cleanup
Description:
Tweak internal iterator over IDs to not require constant "operator" data.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Bug fix.
Description:
When a duplicate object was attempted to be created, the library would
leak file memory and object references in the file, potentially causing an
infinite loop when shutting the library down.
Solution:
Clean up after ourselves... :-)
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Code cleanup
Description:
Limit the scope on more function prototypes/macros/typedefs.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest not necessary.
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Code cleanup
Description:
Clean up warnings exposed by compiling on O2K. Also, revert some of Bill
and my changes to the H5S_mpi_opt_types_g, etc. and settle them back into their
original location.
Platforms tested:
h5committested.
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Code cleanup.
Description:
Move many package or internal function prototypes and macro definitions
into tighter scope according to their current use.
Added more comments where appropriate.
Eliminate ancient, unused functions.
Added a couple "accessor" functions to get parts of data structures which
were moved out of scope.
Platforms tested:
h5committested
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New feature/enhancement
Description:
Chunked datasets are handled poorly in several circumstances involving
certain selections and chunks that are too large for the chunk cache and/or
chunks with filters, causing the chunk to be read from disk multiple times.
Solution:
Rearrange raw data I/O infrastructure to handle chunked datasets in a much
more friendly way by creating a selection in memory and on disk for each chunk
in a chunked dataset and performing all of the I/O on that chunk at one time.
There are still some scalability (the current code attempts to
create a selection for all the chunks in the dataset, instead of just the
chunks that are accessed, requiring portions of the istore.c and fillval.c
tests to be commented out) and performance issues, but checking this in will
allow the changes to be tested by a much wider audience while I address the
remaining issues.
Platforms tested:
h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
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Description: 1.4 compatibility for H5G_obj_t type and H5Zregister test.
Solution: use macro H5_WANT_H5_V1_4_COMPAT
Platforms tested: h5committest
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Code cleanup
Description:
Remove some cruft left over from the switch from int->H5G_obj_t
Platforms tested:
FreeBSD 4.8 (sleipnir), triple check not necessary.
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Purpose: A little code rewriting
Description: object types were defined as macros in H5Gpublic.h
Solution: changed them to enumerate type
Platforms tested: h5committtest
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Code cleanup
Description:
Stop using hard-coded constant for the initial size of the root group's
symbol table local heap and use macro.
Also, changed existing (unused) macro for the initial heap size to be the
same as the hard-coded constant.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
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Code/comment cleanup
Description:
Made more information about reference-counted strings private to the
H5RS package by trimming the typedef used in H5RSprivate.h and switching
from using macros for a couple of operations to using functions.
Updated copyright information for a few of these files.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
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Code cleanup
Description:
Clean up miscellaneous warnings which have crept into the code.
Fix "_POSIX_C_SOURCE not defined" warning on FreeBSD.
Adjust gcc compiler flags to be more concise for production mode.
Refactor the H5O code so that there is a stronger boundary between code
in the H5O package and code in the library which just calls H5O routines.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel and gcc 2.95.4 & gcc 3.2.2
Misc. update:
Update MANIFEST if you add or remove any file.
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Update feature
Description:
Relax collective constraint for API functions which only read metadata
from a file.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 w/parallel
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Bug Fix
Description:
Metadata cache in parallel I/O can cause hangs in applications which
perform independent I/O on chunked datasets, because the metadata cache
can attempt to flush out dirty metadata from only a single process, instead
of collectively from all processes.
Solution:
Pass a dataset transfer property list down from every API function which
could possibly trigger metadata I/O.
Then, split the metadata cache into two sets of entries to allow dirty
metadata to be set aside when a hash table collision occurs during
independent I/O.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel
Misc. update:
Updated release_docs/RELEASE
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Code cleanup/new feature.
Description:
Split FUNC_LEAVE into API and non-API specific versions. This allows a
solution to compiling this branch with C++, as well as reducing the size
of the binaries produced.
Platforms tested:
FreeBSD 4.7 (sleipnir) w/serial, parallel (including MPE) & thread-safe
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Code cleanup
Description:
Clean up a few more warnings and update dependencies.
Platforms tested:
Linux 2.2.18smp (eirene) serial & parallel
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Lots of performance improvements & a couple new internal API interfaces.
Description:
Performance Improvements:
- Cached file offset & length sizes in shared file struct, to avoid
constantly looking them up in the FCPL.
- Generic property improvements:
- Added "revision" number to generic property classes to speed
up comparisons.
- Changed method of storing properties from using a hash-table
to the TBBT routines in the library.
- Share the propery names between classes and the lists derived
from them.
- Removed redundant 'def_value' buffer from each property.
- Switching code to use a "copy on write" strategy for
properties in each list, where the properties in each list
are shared with the properties in the class, until a
property's value is changed in a list.
- Fixed error in layout code which was allocating too many buffers.
- Redefined public macros of the form (H5open()/H5check, <variable>)
internally to only be (<variable>), avoiding innumerable useless
calls to H5open() and H5check_version().
- Reuse already zeroed buffers in H5F_contig_fill instead of
constantly re-zeroing them.
- Don't write fill values if writing entire dataset.
- Use gettimeofday() system call instead of time() system when
checking the modification time of a dataset.
- Added reference counted string API and use it for tracking the
names of objects opening in a file (for the ID->name code).
- Removed redundant H5P_get() calls in B-tree routines.
- Redefine H5T datatype macros internally to the library, to avoid
calling H5check redundantly.
- Keep dataspace information for dataset locally instead of reading
from disk each time. Added new module to track open objects
in a file, to allow this (which will be useful eventually for
some FPH5 metadata caching issues).
- Remove H5AC_find macro which was inlining metadata cache lookups,
and call function instead.
- Remove redundant memset() calls from H5G_namei() routine.
- Remove redundant checking of object type when locating objects
in metadata cache and rely on the address only.
- Create default dataset object to use when default dataset creation
property list is used to create datasets, bypassing querying
for all the property list values.
- Use default I/O vector size when performing raw data with the
default dataset transfer property list, instead of querying for
I/O vector size.
- Remove H5P_DEFAULT internally to the library, replacing it with
more specific default property list based on the type of
property list needed.
- Remove redundant memset() calls in object header message (H5O*)
routines.
- Remove redunant memset() calls in data I/O routines.
- Split free-list allocation routines into malloc() and calloc()-
like routines, instead of one combined routine.
- Remove lots of indirection in H5O*() routines.
- Simplify metadata cache entry comparison routine (used when
flushing entire cache out).
- Only enable metadata cache statistics when H5AC_DEBUG is turned
on, instead of always tracking them.
- Simplify address comparison macro (H5F_addr_eq).
- Remove redundant metadata cache entry protections during dataset
creation by protecting the object header once and making all
the modifications necessary for the dataset creation before
unprotecting it.
- Reduce # of "number of element in extent" computations performed
by computing and storing the value during dataspace creation.
- Simplify checking for group location's file information, when file
has not been involving in file-mounting operations.
- Use binary encoding for modification time, instead of ASCII.
- Hoist H5HL_peek calls (to get information in a local heap)
out of loops in many group routine.
- Use static variable for iterators of selections, instead of
dynamically allocation them each time.
- Lookup & insert new entries in one step, avoiding traversing
group's B-tree twice.
- Fixed memory leak in H5Gget_objname_idx() routine (tangential to
performance improvements, but fixed along the way).
- Use free-list for reference counted strings.
- Don't bother copying object names into cached group entries,
since they are re-created when an object is opened.
The benchmark I used to measure these results created several thousand
small (2K) datasets in a file and wrote out the data for them. This is
Elena's "regular.c" benchmark.
These changes resulted in approximately ~4.3x speedup of the
development branch when compared to the previous code in the
development branch and ~1.4x speedup compared to the release
branch.
Additionally, these changes reduce the total memory used (code and
data) by the development branch by ~800KB, bringing the development
branch back into the same ballpark as the release branch.
I'll send out a more detailed description of the benchmark results
as a followup note.
New internal API routines:
Added "reference counted strings" API for tracking strings that get
used by multiple owners without duplicating the strings.
Added "ternary search tree" API for text->object mappings.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Other platforms/configurations tested?
FreeBSD 4.7 (sleipnir) serial & parallel
Solaris 2.6 (baldric) serial
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Code cleanup
Description:
Clean up warnings with gcc 3.2.1
Platforms tested:
FreeBSD 4.7 (sleipnir) w/C++, changes too small for triple check
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Purpose:
new functions
Description:
H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx.
Platforms tested:
modi4, arabica, eirene
Misc. update:
RELEASE.txt updated.
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Purpose:
Bug fix
Description:
#340 - get comment length for H5G;
#435 - H5Aget_storage_size;
#644 - H5Arename
Platforms tested:
eirene, arabica
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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
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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
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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.]
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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
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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
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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
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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
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Code cleanup
Description:
Changed the last HRETURN* statements in the FUNC_ENTER macros into HGOTO*
macros, which reduces the size of the library binary in certain
configurations by another 10%
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel, IRIX64 6.5 (modi4) serial &
parallel
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Code cleanup
Description:
Change most (all?) HRETURN_ERROR macros to HGOTO_ERROR macros, along with
HRETURN macros to HGOTO_DONE macros. This unifies the error return path
from functions and reduces the size of the library by up to 10% on some
platforms.
Additionally, I improved a lot of the error cleanup code in many routines.
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel and IRIX64 6.5 (modi4) serial &
parallel.
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Code cleanup
Description:
Broke the FUNC_ENTER macro into several macros, with more specialized
uses (which followup mail will describe). This was designed to move
most/all of the checks which could be done at compile time to that point,
instead of needlessly performing them (over & over :-) at run-time.
This reduces the library's size (and thus staticly linked binaries) and
has a minor speedup effect also.
Platforms tested:
IRIX64 6.5 (modi4) with parallel & FORTRAN enabled, and additional testing
on FreeBSD and Solaris immediately after the checkin.
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Code cleanup.
Description:
Took Robb's recent ideas for improving the FUNC_ENTER/FUNC_LEAVE macros
equivalents in the SAF library and adapted them to our library. I added
an additional macro which is equivalent to FUNC_ENTER:
FUNC_ENTER_NOINIT - Has the API tracing code, etc. from FUNC_ENTER but
none of the library or interface initialization code. This is to
be used _only_ for static functions and those which explicitly
cannot have the library or interface initialization code enabled
(like the API termination routines, etc.).
This allowed many more of the functions in the library [but not all yet :-(]
to be wrapped with FUNC_ENTER[_NOINIT]/FUNC_LEAVE pairs.
It also reduced the size of the library and executables (by cutting out a
bunch of code which was never executed), I'll e-mail the exact results when
I've finished editing it.
Platforms tested:
IRIX64 6.5 (modi4)
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Migrate from configure macros of XYZ_ABC to H5_XYZ_ABC
Description:
configure generates many macros definitions on the fly and
were stored in src/H5config.h which is included by H5public.h.
But other software that uses hdf5 may also run their own configure.
There can be a clash in macro name space. We decided awhile ago
to prepend all generated macros with "H5_" to avoid conflicts.
The process has started and this commit completes it (at least attempt
to).
Solution:
Many macros symbols (e.g. SIZEOF_xxx and HAVE_xxx were changed to
H5_SIZEOF_xxx and H5_HAVE_xxx). Then H5private.h no longer includes
H5config.h. This cuts H5config.h away from HDF5 source code.
Pending issues:
The module of fortran and pablo are to be resolved in a different
commit.
Platforms tested:
eirene (parallel), arabica (solaris 7 --enable-fortran, --enable-cxx)
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Purpose:
New feature
Description:
Allow H5Glink and H5Gmove to handle links across different locations.
Solution:
Added H5Glink2 and H5Gmove2 functions with new parameter of destination
location.
Platforms tested:
Linux 2.2(eirene)
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