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)
Move ref. count of # of links to an object out of the object header's
prefix and make it a header message instead (since it's a "rare" occurence),
eliminating some more space for each object in the file.
Inserting this "ref. count" message exposed a flaw in the library's
mechanism for locating a message to promote to another chunk and replace
with a continuation message, which required some additional work to fix.
It's still not completely robust, but it's working for more cases now and
detects failures robustly.
Reduced the minimum size of an object header chunk to just enough to
contain a header message prefix and continuation message.
Tested on:
FreeBSD/32 6.2 (duty)
The main purpose of this checkin was to eliminate the
space used for tracking creation time indices when there is no way they
can be used (i.e. attributes can't be shared in the file and the user hasn't
turned on attribute creation tracking), however there were some other minor
changes which crept in:
- Fix a cache locking deadlock when a shared attribute and one of its
components end up in the same fractal heap direct block.
(This is fixed the "slow" way for right now, until John has time
to add support for readers/writer locking to the cache.
- Optimize attribute copying when a copy will be kept during a v2 B-tree
search.
- When freeing a block on disk, attempt to merge it with the metadata
and "small data" aggregators.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 6.2 (duty)
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.
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.
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)
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
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
"Hide" file format changes (for now)
Description:
Add ifdef's (controlled by the --enable-group-revision configure flag)
to disable group revision changes to the file format, in order to allow alpha
release to go ahead without releasing an unsupported version into the wild.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 32-bit (heping)
Linux 2.4 64-bit (mir)
Solaris 2.9 (shanti)
Description: By default on VMS system file cannot be opened twice; also
VMS has file versioning. This brakes some of our tests.
Solution:
Tests are commented out with H5_CANNOT_OPEN_TWICE and H5_HAVE_FILE_VERSIONS
that are defined in the vms/h5pubconf.h file only. This change cannot affect
any other platform.
Platforms tested: heping, VMS server
Misc. update:
Extra test
Description:
Add test to make certain that trying to call H5Fopen() on a non-existant
file fails.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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.... :-)
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
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
Bug fix & code cleanup
Description:
Fix another bug in the file mounting code and refactor the unmount
code that it is simpler.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Too minor to require h5committest
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
Bug fix/new feature
Description:
Setting "SEMI" or "STRONG" file close degrees causes problems when multiple
file IDs exist for the same file on disk.
Solution:
Make the "SEMI" and "STRONG" settings only apply to the file ID that is
being closed.
Also, add an "H5F_OBJ_LOCAL" flag for the H5Fget_obj_count() &
H5Fget_obj_ids() calls, so that applications can query about objects opened
with a particular file ID instead of all the objects opened in the file on
disk.
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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
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:
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
Code cleanup for VS.NET
Description:
Clean up several issues that VS.NET was having problems with.
Platforms tested:
Eyeballed against Kent's bug reports.
Bug fix
Description:
Make --disable-hsizet work properly again by fixing a couple of tests and
correcting the definition of SSIZET_MAX.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest not used, as it doesn't test this configuration.
Code cleanup & add a feature
Description:
Added support for querying the file ID of named datatypes to new
H5Iget_file_id function.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
Bug fix
Description:
The tests recently added for checking a file's freespace and verifying the
new fields added to the H5G_stat_t structure use H5T_NATIVE_INT as the type for
the datasets and attributes they create. Because the tests check explicit file
sizes, this causes problems on Crays, where a native int is 64-bit instead of
32-bit.
Solution:
Change the tests to use H5T_STD_U32LE instead of H5T_NATIVE_INT.
Platforms tested:
FreeBSD 4.9 (sleipnir)
Cray SV1 (wind)
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
Bug fix.
Description:
Correct bug where a file opened twice, once with read-write permission
and once with read-only permission would cause closing the file with the
read-only file ID to fail because it was trying to flush information out
of the file.
Solution:
Check the permissions on file IDs that are being closed and only flush
when the particular file ID was opened with write permission.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too small to need h5committest
Misc. update:
Code cleanup
Description:
Finish converting the B-tree 'K' values to use unsigned integers, rather
than signed ones, since negative amounts of entries in a B-tree node aren't
meaningful.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
code warrior fix
Description:
eliminate the CW failure on getname.c
restrict the H5_NO_FILE_SHARING just to the test file_close of testhdf5 test
Solution:
the CW failure on getname.c can be eliminated if a unmount of the file is made before closing it
on tfile.c the failure is due to the file sharing flag of CW, and the test is maintained as before
Platforms tested:
Windows 2000 (octopus)
Linux 2.4 (rockaway)
SunOS 5.7 (arabica)
IRIX 6.5 (modi4)
Misc. update:
Revert last change (at least temporarily)
Description:
Revert last "NO_SHARED_WRITING" ifdefs after reviewing the tests that were
ifdef'ed out. I don't think that these tests should cause a problem, so I
would like them reviewed again to see if there is a file handle leak in the
library (or test).
Platforms tested:
FreeBSD 4.8 (sleipnir)
Triple check not needed.
code warrior port
Description:
added a flag H5_NO_SHARED_WRITING, it is defined only for CW in the H5pubconf.h
this avoids doing some tests for CW that fail on shared writing
Solution:
Platforms tested:
windows (cw and ms)
Linux 2.4 (rockaway)
SunOS 5.7 (arabica)
IRIX 6.5 (modi4)
Misc. update:
Purpose: Verify library behavior
Description: A file is first opened as read only. Then it's closed with
an object left open. A second open of the same file for read and
write should fail.
Platforms tested: arabica - simply test to verify correct library behavior.
Update
Description:
Updated the Copyright statement
Platforms tested:
Linux (This change is only in the comments, so I just check that the
modules still compile)
Misc. update:
Purpose:
a bug fix
Description:
modify the condition check for the file close degree.
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
Purpose:
a bug fix
Description:
When a file is opened for a second time, file close degree is supposed to
be either the same as the first open, or default as the first open is also
default.
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
Bug Fix
Description:
When file space was returned to the file space free-list for reuse,
occasionally raw data allocations which used space from the free-list
would overlap with the metadata accumulator and get over-written with
the cached information in the accumulator, corrupting the data.
Solution:
Check if the space about to be recycled on the free-list is going to be
used for raw data and also overlaps with the metadata accumulator cache,
avoiding using space that fits those criteria.
This fixes bug #701
Platforms tested:
FreeBSD 4.5 (sleipnir)
Code cleanup
Description:
Tweaked internal error handling macros to reduce the size of the library's
object code by about 10-20%.
Also cleaned up some compiler warnings...
Platforms tested:
FreeBSD 4.4 (sleipnir)
Purpose:
Modify H5Fclose behavior
Description:
The HDF5 actual file close behaves in several ways in terms of if there
are still objects(dataset, group, datatype) opened in file.
Solution:
Added a new file access property, file close degree. It has four values,
H5F_CLOSE_DEFAULT
H5F_CLOSE_WEAK
H5F_CLOSE_SEMI
H5F_CLOSE_STRONG
The way a file is closed is decided by these values.
Platforms tested:
IRIX64 6.5, SunOS 5.6, FreeBSD 4.4
Backward Compatibility Fix
Description:
One of H5P[gs]et_sym_k's parameters changed between v1.4 and the development
branch.
Solution:
Added v1.4 compat stuff around H5P[gs]et_sym_k implementation and testing
to allow v1.4.x users to continue to use their source code without
modification.
These changes are for everything except the FORTRAN wrappers - I spoke with
Elena and she will make the FORTRAN wrapper changes.
Platforms tested:
FreeBSD 4.4 (hawkwind)
Update
Description:
Changed includes of the form:
#include <hdf5_file.h>
to
#include "hdf5_file.h"
so that gcc can pick them up easier without including the system
header files since we don't care about them.
Platforms tested:
Linux
