| Commit message (Collapse) | Author | Age | Files | Lines |
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Fix serial build
Description:
I accidentally put the "use_par_opt_io" variable in an #ifdef PARALLEL
section.
Solution:
Hoist it out of parallel section
Platforms tested:
Eyeballed it - very trivial
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Code cleanup
Description:
Straighten out more goofiness in the MPI code dealing with collective I/O
transfers - mostly make certain that a view is set if-and-only-if collective
I/O is occurring on raw data (and vice versa for views and independent I/O)
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel & FPHDF5
too minor to repquire h5committest
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Code cleanup
Description:
Remove collective parallel I/O checking code, now that it's impossible to
get into this code with collective access enabled.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Code cleanup
Description:
More refactoring on setup of MPI-IO parameters: hoisted the code to change
the transfer mode from collective to independent up into the H5D_read and
H5D_write routines, instead of duplicating it inside each of the chunk/contig
read/write routines.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Code cleanup
Description:
Clean up setup code for collective I/O transfers to make the logic more
obvious.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor for h5committest
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Bug fix
Description:
Single hyperslab selections (which were set with only one call to
H5Sselect_hyperslab) that had dimensions that could be "flattened" but were
interspersed with dimensions that could not be flattened were not correctly
handled, causing core dumps.
Solution:
Re-work "flattening" code to handle this case properly.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
h5committest
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Code cleanup
Description:
Refactored handlier of VFL drivers in file access and data transfer property
lists in order to simplify and unify the code dealing with them.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Bug fix
Description:
Change "H5_HAVE_PARALLEL" to "H5_HAVE_FPHDF5" around VFL ID, to prevent
daily builds from failing.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
too specialized to require h5committest
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Bug Fix
Description:
The owners and reference counts of locks weren't being handled
correctly.
Solution:
Allocate an array the size of the COMM FPHDF5 is invoked with for
each lock. Then reference count within this array. Keep an extra
"counter" to see how many different processes have this particular
lock. Free the lock when that counter reaches zero.
Platforms tested:
Linux & Copper (FPHDF5 specific).
Misc. update:
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Bug Fix
Description:
Was using HGOTO_ERROR within a "done:" block.
Solution:
Changed HGOTO_ERROR macro to HDONE_ERROR inside of a done: block.
Platforms tested:
Linux (Small change).
Misc. update:
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Message Correction
Description:
Uncapitalized the beginning of the error messages.
Solution:
Platforms tested:
Linux (Very small change).
Misc. update:
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Bug fix
Description:
Remove the [duplicated] native C9x datatype initializatin code from H5T.c
and let the automatically generated code in H5Tinit.c handle initializing them,
if they are allowed by the compiler.
Platforms tested:
FreeBSD 4.9 (sleipnir)
Linux 2.4 (verbena, eirene)
probably should be h5committested, but it's late and I'm fairly certain
this will fix the problem... :-/
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Bug fix
Description:
Avoid "OPAQUE" symbol in template macro invocation, since it's already
defined as a macro on Windows.
Solution:
OPAQUE -> OPAQ
Platforms tested:
FreeBSD 4.9 (sleipnir)
Windows ? (Pedro's machine :-)
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Tweak comments.
Testing:
Not necessary..
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Refactor code
Description:
Use "template macro" technique to eliminate a huge amount of repeated code
in type initialization code (almost 1000 lines, between this change and the
changes to the H5Tconv.c file earlier).
This centralizes the common parts of the code and makes the different parts
of the code more obvious.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Optimize code
Description:
Eliminate some computations from inner loop, giving about a 5% speedup.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to h5committest
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Code cleanup
Description:
Remove duplicated "core" conversion macros.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor for h5committest
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Refactored code
Description:
Switched float->double and double->int conversions to use new, more generic
conversion looping macros.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too small to require h5committest
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More refactoring
Description:
Re-wrote inner loop of integer conversion routines with "psuedo-template"
macros, to hoist 'if-else's out of inner loop in an easy to understand way.
This speeds up the integer type conversions by 15-20%.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Code cleanup
Description:
Re-wrote duff's device with some macro substitution to make algorithm more
obvious.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too small to require h5committest
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Refactor integer conversion macros
Description:
Turned integer conversion macros "inside" out, using an interlocking
macro technique similar to templates in C++. The macro which actually performs
the conversion is now invoked "genericly" from inside another macro, which
will allow the inner conversion loop to be optimized in a much easier way.
This "psuedo-template" technique could be useful for other semi-repetitious
patterns in the library - possibly the datatype initialization code...
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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Code cleanup
Description:
Clean up compiler warnings
Platforms tested:
h5committest
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Update dependencies and tracing information
Platforms tested:
Linux 2.4 (verbena) w/FORTRAN
too minor for h5committest
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Code cleanup
Description:
Change field member count and indices for compound and enumerated types from
'int' to 'unsigned' to better reflect actual use.
Cleaned up a few other minor compiler warnings, etc.
Platforms tested:
FreeBSD 4.9 (sleipnir)
Linux 2.4 (verbena)
too minor to require h5committest
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Code cleanup
Description:
More linting of the library.
Platforms tested:
FreeBSD 4.9 (sleipnir)
Linux 2.4 (verbena)
too minor to require h5committest
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Bug fix
Description:
Add MPE "color" for new H5Fget_freespace() API function.
Platforms tested:
None - just eyeballed - too minor to require testing.
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Bug fix
Description:
The 'char *' type is one of the "strongly" aligned types on Crays, but
a 'void *' is "weakly" aligned. So, assigning a 'void *' (pointing to a
location to place a 'char *') to a 'char **' can change the pointer value
during the assignment.
Solution:
Don't alias the 'void *' where the variable-length information ('char *'
or 'hvl_t') will go. Use a temporary variable on the stack to build up the
information about the VL string or sequence and then memcpy() the temporary
variable directly to the location pointed to with the 'void *'
Platforms tested:
FreeBSD 4.9 (sleipnir)
Cray SV1 (wind)
specific to Cray problems, h5committest not necessary.
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Bug fix
Description:
Correct the size of the buffer needed for the destination value to use
the actual destination type size.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Bug fix
Description:
The VL type conversion routine attempt to align it's destination buffer to
an offer that will work for both hvl_t and char * types, but the algorithm used
fails to work correctly on Cray machines.
Solution:
Give up on attempting to align the buffer when it's allocated on the stack.
Just dynamically allocate it instead.
Platforms tested:
FreeBSD 4.9 (sleipnir)
Cray SV1 (wind)
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Bug fix
Description:
When too many messages were inserted into an object header, the library
had an internal pointer to the "new message" that was pointing to the incorrect
location when the array of messages was re-allocated.
In the worst case, this could cause a file to be corrupted.
Solution:
Update the internal pointer when the array is re-allocated.
Platforms tested:
FreeBSD 4.9 (sleipnir)
Too small to require 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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Add feature
Description:
Add H5Fget_freespace() routine, to check the amount of free space in a
file. This information is only valid until the file is closed currently,
however (until we start recording the free space information in the file
itself).
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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Improved algorithm (bug fix, sorta)
Description:
The internal algorithm for adding new IDs in the ID manager code (H5I) was
adding new IDs to the front of the linked list and never adjusting the order
of the items on the list (unless an ID was deleted). If many new objects were
created, they would push earlier ones _way_ down the list (especially if the
objects were being leaked in the application, as they appear to be in the
current HDF-EOS5 library) and would cause O(n) search time for items on the
list.
The ID caching code in the ID manager was avoiding this behavior sometimes,
but it was adding IDs that were looked up to the very tail of the cache and
they would frequently leave the cache before helping.
Solution:
Implemented a "move to front" scheme for the linked list of IDs, which
improves the lookup situation for frequently accessed objects.
Removed ID caching code now, as the "move to front" algorithm actually
works better.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Bug/feature fix.
Description:
Relax restriction on parallel writing to compact datasets to allow partial
I/O.
Updates to reference manual mentioning the issues involved are delayed until
reference manual 'lock' is removed later this week.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require 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:
The FPHDF5 code couldn't create a dataset then access it. Turns out
that the "O_find_in_ohdr" code was protecting the object header which
pulls it into the cache then unprotecting it. However, this caused
the cache entry to be blown away and THEN we'd try to reread the
entry (via AC_protect) but it didn't have all of the data that the
find_in_ohdr function decodes for us decoded. It was also kind of
unnecessary since we can just protect then call O_find_in_ohdr.
Solution:
Removed the AC_protect and AC_unprotect from O_find_in_ohdr. Called
AC_protect before calling the O_find_in_ohdr function.
Platforms tested:
Linux (Fortran, C++)
IRIX (parallel, Fortran)
Sun (Fortran)
Misc. update:
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Code cleanup
Description:
Clean up a few loose ends and warnings for the 1.6 compatibility changes
to the error API.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Fix typo in comment.
Description:
Looks like a cut & paste error.
Platforms tested:
None - just comment fixup
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Description: add backward compatibility for thread safety.
Platforms tested: RH 8(fuss)
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Code cleanup
Description:
Clean up various warnings and parameter mis-matches, etc.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to need h5committest
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Removed Dead Code
Description:
Some of the FPHDF5 code was dead (I thought it'd be useful at one
point, but was wrong).
Solution:
Removed
Platforms tested:
Linux (FPHDF5 specific. No need for h5committest)
Misc. update:
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Bug fix
Description:
Buffer for decoding superblock's driver information was too small when
using some VFDs (like the multi-file VFD).
Also made FPH5 code more portable and obvious when it's broadcasting the
superblock from the captain process to the other clients.
Solution:
Allocate the buffer for the driver information dynamicly
Platforms tested:
Copper
No h5committest because it's already working on other platforms.
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FPHDF5 Update
Description:
Added locking/unlocking to the AC_protect/AC_unprotect calls. The SAP
does all of the caching so nothing should be saved on the client
side. So, when the client unlocks the metadata, it can destroy it.
The metadata is always read from the SAP during a lock.
Platforms tested:
Linux (FPHDF5 specific change. No need for h5committest)
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Update
Description:
A lot of modifications for the FPHDF5 stuff:
H5AC.c
H5ACprivate.h - Removed AC_find (it's replaced with AC_protect
and AC_unprotect). Added flushing if it's an FPHDF5 driver and
we're doing an AC_set or AC_unprotect with the dirty flag set.
H5B.c - Split up the B_flush function into different functions
since the one function was doing serialization which is better
left as a separate entity.
H5D.c - Removed some FPHDF5 code that was incorrect
H5F.c - Split up the F_flush function so that it no longer
allocates file space. Created new functions (F_init_superblock,
F_read_superblock, and F_write_superblock) for greater modularity
and so that the FPHDF5 non-captain processes can read the
superblock after the captain process writes it.
H5FD.c - Error message correction.
H5FDfphdf5.c - Removed MPI barrier call that wasn't needed.
H5FPclient.c
H5FPserver.c - Modified so that if a process requests data that
isn't exactly aligned, we can return it if we have the block that
contains the requested address.
H5G.c
H5Gent.c
H5Gnode.c
H5HL.c
H5HLpkg.h
H5HLprivate.h
H5Oefl.c - Removed the H5HL_peek function since it was doing a
(now unsafe) holding of the information in the cache. Replaced
with protect and unprotect calls.
H5TB.c - Error fix. The TB_dless function wasn't working
properly.
H5Gstab.c - Format change.
H5err.txt
H5Edefin.h
H5Einit.h
H5Epubgen.h
H5Eterm.h - Added new error code.
Platforms tested:
Modi4 (paralle, Fortran)
Sol (Fortran)
Linux (C++, Fortran)
Copper (Parallel, Fortran)
Misc. update:
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