| Commit message (Collapse) | Author | Age | Files | Lines |
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Description:
Versions of the library between 1.3.0 and 1.6.3 have a bug which prevents them
from opening any file that does not have the root group's symbol table
information cached in the root group's entry in the superblock. Prior to 1.8
this was not an issue as this information was always cached. However, 1.8.0
stopped writing this information (which is not required by the file format
specification), and these older versions can therefore not read files created or
last written by versions 1.8.0 to 1.8.2. This fix modifies the library to once
again add this information to the superblock (when using the old file format).
Tested: jam, linew, smirom (h5committest)
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Description:
Changed Skip list package to use a deterministic skip list. This allows the
skip list package to avoid calling rand() and srand(), even on machines without
rand_r(). There is no longer a p-value or maximum level for skip lists.
Tested: jam, smirom, linew (h5committest)
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Description:
Some files apparently exist in the wild which have corrupt symbol table messages
on the root group. These files can be opened by 1.6 (which uses the cached
information in the superblock) but not by 1.8. This patch fixes 1.8 and 1.9 so
they can now open these files, and will correct them if necessary. Also fix
some potential (rare) problems with array datatype versions.
Tested: jam (parallel; h5committest not working on linew or smirom)
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Bring r15800 back from trunk:
- File free space branch changes through r15794
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (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/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
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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...
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Bring back r15510 & r15512 from trunk:
Fix compiler warnings and formatting.
Tested on:
Mac OS X/32 10.5.4 (amazon)
More tests upcoming
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Bring rev. 15488 back from trunk:
Fix bug where library could core dump when an invalid location ID was
passed to H5Giterate() (and add test for this case).
Tested on:
Mac OS X/32 10.5.4 (amazon)
Too minor to require h5committest
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reference count
> 1.
Description: Added a new field 'app_count' to H5I_id_info_t struct, to track
the reference count on an id due to the application. the old 'count' field
tracks the total. Generally any id visible to the application gets placed
in app_count. Added app_ref boolean parameter to H5I_inc_ref, H5I_dec_ref,
H5I_register, H5I_clear_type, and a few other functions, to specify whether
the operation(s) being performed on the id(s) are due to the application
(TRUE) or not (FALSE). Test added for this case.
Tested: kagiso, smirom, linew (h5committest)
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mounted files.
Description:
Moved mount table from top file structure to shared file structure. Moved
parent out of mount table and back into top file structure. mounted files can
now be accessed from any handle of the parent file. Changes to how files are
closed. Stricter cycle checking on mounted files. Removed unused function
H5F_has_mount().
Tested:
kagiso, smirom, linew (h5committest)
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Bring back r15367 from the trunk:
Add check to avoid mounting a file on a group twice, when the mounts
are done on the same HDF5 file, but opened with separate H5Fopen queries.
Also add new 'mounted' flag to the H5G_info_t struct, queried with the
H5Gget_info() API call, to allow applications to detect and avoid this
situation.
Tested on:
Mac OS X/32 10.5.4 (amazon)
Linux/64 10.5.4 (chicago)
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Add H5Ovisit() and H5Ovisit_by_name() API routines.
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Add H5Lvisit() API routine.
Add explicit regression tests for H5Lvisit_by_name().
Correct error with visiting links when links contain loop to group
already encountered.
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Add H5Lvisit_by_name() API routine to library.
Eliminated all (five!) other group traversal routines and changed them
all to use the new API routine.
Cleaned up output of h5ls & h5stat:
- Issue error when requesting recursive traversal of a file
with the "group info" flag, but no group given
- Print info about root group in all(?) appropriate situations
- Don't print "verbose" information about root group until the
root group is in the list of objects to display
(mostly because h5ls & h5stat had a different twist on traversing the
groups in a file that the other utilities)
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Change H5Llink to H5Olink, which makes more sense.
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
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Change existing H5Gget_info -> H5Gget_info_by_name and add new version
of H5Gget_info, with simpler parameters, to better match new API routines.
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
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Finish deprecating last H5G symbol (H5G_obj_t) - yay!
Lots of misc. library fixes to remove confusion between links and
objects. The tools could still use another pass, to remove h5trav_type_t type
and make the correct distinction between links & objects.
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 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
AIX/32 5.3 (copper) w/FORTRAN, w/parallel, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Correct another typo in return value on error FAIL -> NULL
Tested on:
FreeBSD/32 6.2 (duty)
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Remove all plain calls to H5Gopen() from source, replacing them with
either H5Gopen2().
Add test for H5Gopen1().
Reformatted several pieces of code, to clean them up.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
Mac OS X/32 10.4.10 (amazon)
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Pursue calls to H5Gcreate() relentlessly and ruthlessly exterminate
them, leaving only a few tame specimens in text files and comments. ;-)
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
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Run bin/reconfigure to update infrastructure files/information.
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Change H5[D|G|T]<foo>_expand() "temporary" API routines to
H5[D|G|T]<foo>2() "versioned" routines. Also added
H5[D|G|T](create|commit)_anon() routines to continue to allow "anonymous"
objects to be created in a file.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Eliminate storing # of links in "link info" message, regenerate it
when the object is opened instead.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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running on kagiso.
The static szip libraries are working as intended, but when shared szip
libraries are present and intended for use they cannot be opened. A check
has been implemented to test if shared szip libraries are functional on
current platform. If they are not, and the user is trying to use them,
szip is now disbaled and the user is informed.
This issue occurs on kagiso, and the resolution was tested on kagiso.
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Straighten out some of the code for handling superblocks, in preparation
for revising the format of the latest version of the superblock before the
beta release.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 6.2 (duty)
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Checkpoint progress on H5Aiterate2().
Mark H5Aiterate() as deprecated.
Various code cleanups.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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copyright notice.
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.
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object header
information, rather than storing it directly in the superblock.
This should make future updates to the superblock much less painful.
Tested on Windows, kagiso, and smirom.
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More cleanups on the object header message handling code, to make it
easier to work with and move forward on the creation order coding.
Various other minor cleanups & warning fixes.
Tested on:
FreeBSD/32 6.2 (duty)
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haven't
been run in a while, so many of the source files were updated with
tracing macros, etc. No code changes by me.
Tested on kagiso and smirom.
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Switch from using H5L_index_t/H5L_INDEX_<foo> to H5_index_t/H5_INDEX_<foo>
in order to accommodate indices on aspects of attributes as well as links.
Add basic support for deleting attributes in dense storage (needs more
support/tests for shared attributes in dense storage still).
Misc. cleanups, etc.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Finish moving object header message routines into their own source code
module, along with renaming them to have "H5O_msg_" prefix...
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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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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Propagate object creation properties up into group, dataset and named
datatype property lists, when those property lists are retrieved for
existing objects in a file.
Also, add H5Tget_create_plist() API routine, to allow named datatype
property lists to be retrieved for named datatypes.
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
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Added H5Gget_info[_by_idx] routines and deprecated H5Gget_num_objs routine.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Finish removing library's internal code that uses H5G_get_objinfo() and
retarget it at either getting the link information or the object information,
as appropriate. (Still need to add user-level tests for H5Oget_info(), but
since several internal components of the library depend on the internal version,
it appears to be working correctly).
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/322.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
Mac OS X/32 10.4.8 (amazon)
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Refactor internal code that retrieves the object's type to use the new
H5O_type_t (which only definitions for object types, instead of links as well)
instead of the older H5G_obj_t (which included links, etc.)
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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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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Basic support for H5Literate() routine. Still needs to be fleshed out and
refactored to simplify. Also, needs tests. :-)
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
Mac OS X/32 10.4.8 (amazon)
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Add H5Lget_name_by_idx routine & tests
Move more H5G routines to deprecated API file
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) C++ & FORTRAN
Linux/64 2.4 (mir) w/build-all & enable_compat1.6
AIX/32 5.? (copper) w/parallel & FORTRAN
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Rename new H5Gcopy() routine to H5Ocopy() as discussed in last Friday's
design discussion.
Tested on:
Linux/32 2.6 (chicago)
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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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Change H5Lget_linkinfo() to H5Lget_info() to better align with coming API
changes.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Clean up formatting and re-organize a bit...
Tested on:
Max OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
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Rudimentary support for creating creation order index (but not inserting
links in it yet).
Testedon:
Mac OS X/32 10.4.8 (amazon)
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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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Review, revise & checkin in Peter's latest round of object copy changes,
which add basic support for datasets & attributes with reference datatypes.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Object header locations (H5O_loc_t's) can now "hold open" a file and
decrement its open object count when they close. This means that
locations (H5O_loc_t's and H5G_loc_t's) should always be freed.
Added more thorough tests to ensure that external files are closed.
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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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Clean up some compiler warnings.
Tested on:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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comments,
fixed a few tests that used incorrect names for H5L APIs (formerly hidden behind
H5_GROUP_REVISION ifdefs
Mostly cosmetic changes, tested on mir.
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