| Commit message (Collapse) | Author | Age | Files | Lines |
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Bring revisions 15210:15289 from the trunk into the metadata journaling branch.
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Switch v1 B-tree nodes from using previous cache to use the new journaling
cache code. This is a major switch for the cache callbacks.
Switched the metadata caching code from having a pointer to the file it's
in to receiving a pointer to the file, when needed. This was necessary in
order to avoid crashing when two files IDs were open on the same underlying
file and one of those files was closed with cache entries using the file
pointers. Also took out the check in the caching code for reading off the
end of the file, which didn't play nicely with the multi-file VFD.
Switching the cache from having a pointer internally to requiring one
externally meant tweaking almost all the test code. :-/
Added correct exit codes to cache2 tests that didn't have them already,
so the 'make check' will stop when they fail.
Use the path to the h5diff in this build in the tools/h5recover testing
script, since we can't guarantee a user has HDF5 already installed.
Assorted minor tweaks to get everything to compile more cleanly and pass
all the tests (on my Mac :-).
Tested on:
Mac OS X (10.5.2) w/C++
(more testing coming up shortly, I just didn't have my "rsync testbed" set
up for this branch when I started making changes to the code)
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Rename new error handling API routines from H5E<foo>_stack() to
H5E<foo>2().
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
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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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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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Make API routines that don't initialize the library more consistent, to
help with future internal library changes.
Tested on:
Linux/64 2.6 (chicago2)
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Clean up initialization of H5F & H5L APIs.
Tested on:
Linux/64 2.6 (chicago2)
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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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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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Break out a bunch of the misc. routines that were in src/H5.c into more
specific modules.
Add optimized fletcher32 checksum routine, for checksumming metadata as
well as raw data.
Tested On:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Will test further after checkin...
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Clean up code a bit by reformatting and using portable macros for direct
C library calls.
Tested On:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
Solaris/64 2.9 (shanti)
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Call the H5L API's termination routine when the library is terminating.
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/64 2.4 (mir)
Solaris/64 2.9 (shanti)
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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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Refactored free space manager to use metadata cache for serialized free
space sections. This speeds up the fractal heap test considerably...
Tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4/32 (chicago)
Linux 2.4/64 (mir)
Mac OS X (amazon)
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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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New feature
Description:
Add '%t' format for HDfprintf() to print htri_t (and hbool_t) values.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (chicago)
h5committest
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Code checkpoint
Description:
Checkpoint fractal heap improvements, as well as move the free space
manager code that it's using into a separate package.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4/64 (mir) w/C++ & FORTRAN
Linux 2.4/32 (heping)
Solaris 2.9 (shanti)
AIX 5.? (copper) w/FORTRAN & parallel
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Description: Function prototype H5E_walk_t and structure H5E_error_t wasn't backward
compatible.
Solution: Make them compatible with v1.6 and provide new definitions of H5E_walk_stack_t
and H5E_error_stack_t.
Platforms tested: fuss and h5committest.
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Improvement
Description:
Modified the warning messages from the Version mismatch checking to suggest
the users to try recompiling or checking the shared lib setting.
Platforms tested:
Tested in heping only since it was just a simple text string changes.
(I did moved the strings around a bit.)
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Code cleanup
Description:
Remove remnents of references to unimplemented H5S_COMPLEX dataspace.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 32-bit (heping)
Linux 2.4 64-bit (mir)
Solaris 2.9 (shanti)
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Description: Unix remove function removes only the latest version of a file
on VMS. Some of our tests create multiple versions of the testfiles
and as a result, test programs may be confused, give false negative result,
etc.
Solution: Created HDremove_all function for VMS that removes all versions of the files.
HDremove on VMS is an alias to HDremove_all.
Platforms tested: VMS server and heping (to check that nothing is borken on UNIX side)
Misc. update:
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Optimization
Description:
Get rid of unnecessary function call for systems that don't have rand_r.
Solution:
If rand_r isn't present on a system, then macros can be used to simply call
the underlying random function instead of calling the HDrand/HDsrand functions
that keep track of the random seed within the library.
Platforms tested:
heping (minor change)
Misc. update:
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Bug fix.
Description:
Fix typo. srand/srandom don't return anything, so don't attempt to return
their value.
Solution:
Platforms tested:
heping
Misc. update:
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Bug fix/Feature
Description:
Modify the library to use rand_r, when available, instead of srand. If
rand_r is not available, it will try to use srandom/random, and then finally
fall back to srand/rand.
Solution:
A couple places in the library use the srand() function to seed the random
number generator. This can cause problems on certain platforms and could theoretically
cause problems for users who expect a certain sequence of random numbers following their
own call to srand().
Most platforms have an implementation of rand_r, which is identical to rand, except that
it allows for explicit storage of the seed value. The configure script will now check
for the existence of rand_r to facilitate its use in the library.
Two new functions are added, to replace the macros HDsrand/HDrand. These functions are HDrand and
HDsrand. HDrand will call rand_r, if available, or random(), if available, and fall back to rand() if neither
of those is available. HDsrand will store the seed value locally, if rand_r is available. Otherwise, it will call
srandom if available, and fall back to srand otherwise.
Platforms tested:
heping, mir. Really need to test on Red Storm, since that platform motivated this fix, but the machine
is currently not available.
Misc. update:
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Porting.
Description:
Red Storm's lustre used srand and rand to initialize their user mode
of lustre. HDF5 also uses srand and that messes up Lustre.
Solution:
Use -DRED_STORM to block out the HDF5 code that calls srand.
This is a temporary fix since Lustre has fixed its code from
calling srand and rand but the fix is not deployed at Red_storm
yet.
Platforms tested:
Tested at Red-Storm.
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Patch for red-storm.
Description:
A temporary patch for redstorm, must open a file in the same parallel
data filesystem before H5_init_library. Otherwise, it hangs with error:
(client.c:568:ptlrpc_check_status()) @@@ type == PTL_RPC_MSG_ERR, err == -114 req@0x57a9660 x1/t0 o38->mds_l2@MDS_PEER_UUID:12 lens 240/272 ref 1 fl Rpc:R/100000/0 rc 0/-114
Platforms tested:
Red-storm.
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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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Cleanup.
Description:
Removed the home-made version of snprintf and vsnprintf since they
do not actually enforce the size parameter correctly and could corrupt
memory or as a security hole.
This block of code has been turned off since Aug 11, 2005 for all platforms
except Tflops. No one has reported any problem since--sort of empirical
evidence that all platforms except Tflops support both functions.
Tflops has retired in September. So, no need to keep this block of code.
Also, fixed the HDxxx macro to call the corresponding xxx function.
Platforms tested:
Tested in heping, both serial and parallel.
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Code cleanup
Description:
Added some comments about the thread-specific memory for the error and
function stacks.
Changed H5close() to not use the function stack (since it causes it to
be re-enabled after shutting it down)
Changed thread-safe semaphore code to not use dynamicly allocated memory.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Too minor to require h5committest
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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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Code cleanup
Description:
Take out odd definition of HDalarm() and replace with standard macro
like the rest of the library.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Maintenance on Windows
Description:
No alarm function on Windows, opt out
Solution:
Platforms tested:
MSVS 6.0 on Windows XP
Misc. update:
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Bug fix.
Description:
Reactivated the code for snprintf and vsnprintf for Tflops but added
the SN_SIZ_MIN as an attempt to require the minimum amount of space needed,
hoping vsnprintf/snprintf do not print larger than it per request.
Also added code to detect overflow and return error (IF overflow has
not crashed the application yet.) These are all short term patches.
Platforms tested:
Tested at Tflops.
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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:
The code for functions snprintf and vsnprintf ignored the size parameter.
It could overflow the buffer. The two functions are supported by many
platforms now. Disable the code and see what platform(s) still need
it.
Platforms tested:
h5committested
Misc. update:
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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:
Rewrite code for mounting files to clean up layers of kludges and implement
a much cleaner and more maintainable design.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
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Feature
Description:
Added "support" for UTF-8 character encoding.
Solution:
Wrote tests to check that UTF-8 can be used in a number of places in
HDF5 (object names, data, etc.). These tests live in test/tunicode.c.
Added a new UTF-8 character encoding for datatypes.
Platforms tested:
mir, modi4, heping
Misc. update:
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Code cleanup
Description:
Clean up some compiler warnings
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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Code cleanup
Description:
Clean up a few warnings flagged by the Intel C compiler.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/Intel C
Too minor to require h5committest
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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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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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Bug fix
Description:
Correct typedef for dataset region references to avoid struct alignment
issues on Crays.
Solution:
Change the typedef for hdset_reg_ref_t from a struct to an array of
unsigned char's of the correct size and propagate the appropriate adjustments
around the code.
Platforms tested:
FreeBSD 4.10 (sleipnir)
Linux 2.4 (verbena) w/fortran
Cray T90 (subzero) w/fortran
Cray SV1 (wind) w/fortran & parallel
Cray T3E (cyclone) w/fortran & parallel
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Code cleanup
Description:
Tweak recent "forward compatibility" changes to the H5E* API (which allowed
for the old H5E API functions to remain unchanged) by allowing for the error
stack callback function (H5E_auto_t) to also remain unchanged from the 1.6
branch. This required changing the H5E{get|set}_auto routines to have the
old style H5E_auto_t type (which didn't have a stack ID parameter) and the new
H5E{get|set}_auto_stack routines to have a newer "H5E_auto_stack_t" type (which
has a stack ID parameter). This should make the H5E API changes as forwardly
compatible as possible.
One side-affect of this change was that it was impossible to determine if
the current auto error callback was the old style (H5E_auto_t) or the new style
(H5E_auto_stack_t) of callback, so a new API function (H5Eauto_is_stack) was
adde to query this.
Platforms tested:
FreeBSD 4.10 (sleipnir)
IRIX64 6.5 (modi4)
h5committest
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Description: Restore 6 old error API functions back to the library to be backward
compatible with v1.6. They are H5Epush, H5Eprint, H5Ewalk, H5Eclear, H5Eset_auto,
H5Eget_auto. These functions do not have error stack as parameter.
Solution: Internally, these functions use default error stack.
Platforms tested: h5committest and fuss.
Misc. update: RELEASE.txt
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performance.
Description:
Replaced the old metadata cache with a cache with a modified LRU
replacement policy. This should improve the hit rate.
Solution:
Since we want to flush cache entries in increasing address order, I
used the threaded binary B-tree code to store the cache entries.
There is a fair bit of overhead here, so we may want to consider
other options.
While the code is designed to allow the support of other replacement
algorithms, at present, only a modified version of LRU is supported.
The modified LRU algorithm requires that a user selectable portion
of the cache entries be clean. The clean entries are evicted first
when writes are not permitted. If the pool of clean entries is used
up, the cache grows beyond its user specified maximum size. The
cache can also exceed its maximum size if the combined size of the
protected (or locked) entries exceeds the maximum size of the cache.
Platforms tested:
eirene (serial, parallel, fp), h5committested
Misc. update:
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Code cleanup & small bug fix
Description:
Regenerate dependency files
Add htri_t as separate type from hbool_t for code tracing purposes.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
too minor to require h5committest
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Code cleanup
Description:
Reduce compiler warnings on SGI IRIX
Platforms tested:
FreeBSD 4.10 (sleipnir)
SGI IRIX6 (Cheryl's machine)
Too minor to require full h5committest
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