Modified the current h5dump test script to use h5import/h5diff calls to validate the binary output. At this moment it can only be used with the native test, since h5import does not deal with input endianess.
tested: linux, sunos 5.10
Add "fail if unknown" and "mark if unknown" flags to object header messages.
This gives the library a clean way to tell older libraries that a message should
not be just ignored if it's unknown, but that other actions should occur.
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)
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)
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)
bug fixes
substituted hize_t array index variables for int
stack corruption in the h52gif reading routine, wrote a new routine
shell script for gif tests, added check of program return value
enabled the gif test script
tested: linux pgcc, solaris, linux 64
Bug fixes
Reset external file list slots name_offset to a state when created (0) in H5P_dcrt_copy
so that it conforms to an assertion in H5D_update_entry_info that assumes the name_offset is 0 at this point
this fixes the problem of h5repack and external files, add a new test and files for an external file
h5diff, check for an error return in H5D_get_storage_size
tested linux 32, 64
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)
Revise latest form of superblock format pretty drastically, to
eliminate unused fields and move rarely used fields into superblock extension.
Finished removing last vestiges of references to (never used) i"shared"
object header message ID.
Added object header messages for non-default v1 B-tree 'K' values
and for driver info.
Updated testfiles to reflect size changes, etc.
Various minor cleanups, etc.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
Bug fix: the macro used for percentage in the unsigned types needed a cast to signed (the difference can be negative)
Unlike the 1.6 branch the unsigned long long conversion to float is supported by H5Tconvert , so the test commented for 1.6 is run (tools/testfiles/h5diff_16_2.txt)
Add '-p' flag to h5copy tool, to create intermediate "parent" groups
that don't exist in destination file yet.
Add more tests to h5copy script.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Add small 'h5mkgrp' tool to create groups in an HDF5 file from the command
line, allowing the group structure for a file to be created in a script. This
tool closely follows the 'mkdir' command line tool in UNIX/Linux.
Allow tool library applications to pass a FAPL to the h5tool_fopen() call,
giving some additional flexibility to tools which are adding objects to an
existing HDF5 file (like h5copy & h5mkgrp).
Fix missing files in MANIFEST from previous checkin(s).
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Add support for deleting all the attributes on an object, when they
are dense and possibly shared.
Also, add some testing routines, for better error detection.
Should fix daily test failures also...
Tested on:
FreeBSD/32 6.1 (duty)
Add more tests for checking that writing to shared attributes works
correctly. (Looks like it still has a bug when dense storage is used, which
I'll correct shortly).
Add testing routine to shared message code, to retrieve reference count for
a shared message.
Add fractal heap 'op' callback for efficiently computing the hash value of
an existing encoded message in the shared message fractal heap.
Various minor cleanups and warning placations.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Add support for opening attributes in dense and/or shared storage by
index.
Move routines for building and operating on tables of attributes into
separate source module.
Fix bug where reverting from "dense" to "compact" storage would 'unshare'
attributes.
Minor code cleanups, etc.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Fix several bugs
1) the parsing of subsetting was using atoi to convert the parameter to an int, which caused problems for numbers greater that int. Substitute with atof
2) the printing of indices in the subsetting case was not being done. Solution: calculate the element position at the start of the subsetting using the algorythm
Given an index I(z,y,x) its position from the beginning of an array of sizes A(size_z, size_y,size_x) is given by
Position of I(z,y,x) = index_z * size_y * size_x
+ index_y * size_x
+ index_x
And pass that position to the function that dumps data, h5tools_dump_simple_data.
3) several index counters were declared as int, use hsize_t instead
4) modified the test generation program so that it includes test cases for subsetting of 1d, 2d, 3d, and 4d arrays and add these tests to the shell script
Migrate "internalish" attribute operations into new source code file.
Add test & basic support for opening attributes in dense storage (shared
attributes not tested or supported yet).
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Add first pass of "dense" attribute storage to objects. Lots of parts of
this are stubbed out, but all the tests are passing and I'll work on the corner
cases soon.
Eliminated several unused parameters from object header message callback
routines.
Other, miscellaneous code cleanups, etc. (and probably some things I've
forgotten about... :-)
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
AIX/32 5.? (copper)
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)
Added a relative error formula to deal with floating point uncertainty
in the comparison of floats and double types.
Added new tests for this feature to the file generator program and to
the shell script
Add # of attributes to the object info struct and deprecate
H5Aget_num_attrs().
Tested on:
FreeBSd/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
Add src/H5Oalloc.c file forgotten in previous object header checkin
Break out more object header routines into separate file (debugging routines
this time).
Fix "//" style comment in recent ISOHM source changes.
Fix 'size_t' vs. 'unsigned' problem (visible in 64-bit testing) in recent
ISOHM test changes.
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
Added new refreg_name.c file to test H5Rget_name and H5Iget_name for region references.
H5Rget_name tests are skipped for now since they do not work (at least for me :-)
Platforms tested:
heping and copper
h5repack revision:
1. added a new test due to the introduction of H5Ocopy in the copy of objects (compressed dataset with references, that still must go a second sweep of the file to be regenerated).
2. Moved all the source files from the h5repack test program to a new file h5repacktst.c and removed the old ones (testh5repack*.c).
3. Renamed the binary files from test*.h5 to h5repack*.h5 for easy reference.
4. Modified the shell script to use variables for file names instead of hard coded names
Move compact storage routines into separate file, to make room for internal
routines that operate on links within group operations.
Tested on:
Linux/32 2.6 (chicago)
Introduced the second sweep of the file for a case a reference is present and H5Ocopy was not used.
Moved the code from file h5repack_refs.c to h5repack_copy.c and removed the first file
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
1) added a new parameter to the h5diff function diff_array that contains
the beginning position of the hyperslab, so that the total position in
the array is printed correctly when reading by hyperslabs.
2) added a new test to h5diff that reads and diffs by hyperslabs. The
test reads a 1GB dataset, from which a 1KB hyperslab was written with
differences .
3) added the generation of 2 files to the generator program to test the
h5diff hyperslab read.
4) changed the h5diff binary pre-generated file names to be more
descriptive (e.g, instead of file1.h5, made it h5diff_basic1.h5)
5) changed the name of the h5repack options text file to info.h5repack
Fixes for bugs 676, 228
676: both h5repack and h5diff use H5Dread. In the case of a "big"
dataset, use read/write by hyperslabs the same way h5dump uses. An
arbitrary value of 1GB was defined for "big", i.e, if the dataset is
greater than 1GB, then read/write by hyperslabs
228: use the file type in read/write by default. A new switch -n was
introduced if the user wants to use a native type, which was the
previous use by default.
Added a new test for h5repack that repacks a 1GB dataset
Tested: heping (serial, parallel), sol, copper
option --enable-direct-vfd/--disable-direct-vfd to enable/disable Direct I/O support. The default
is enabled. There's a small test in test/vfd.c. Another way to test it is to set environment
variable HDF5_DRIVER to "direct" and run "make check" in the test/ directory. There'll be some
further improvement in the following checkin including allowing user to provide memory boundary
value, file block size, and copying buffer size.
Add the "use the latest version of the format" support to datatype
messages. And a regression test to check that it's working.
Also, found that we have been over-allocating space for compound datatype
messages (when they have array datatypes or can use the latest version of the
format) and trimmed the size back.
Clean up datatype & dataspace encode/decode routines by having them
allocate & release "fake" file structures, which gets them out of needing to
"know" about the internals of file structures.
Other minor whitespace/formatting cleanups, etc.
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
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...
Several changes, all mooshed together:
- Add support for "tiny" objects - which can be stored in the heap
ID itself, instead of in the heap data blocks.
- Flesh out support for compressed direct blocks, but comment it
out until John's got some metadata cache changes in place to
support it.
- Add support for applying I/O pipeline filters to 'huge' objects
- Refactor 'huge' object code to store information for 'huge' objects
directly in the heap ID, when there are I/O pipeline filters
applied to the heap (and the heap ID is large enough to hold the
information)
- Update h5debug tool to correctly handle 'huge' & 'tiny' objects.
- Misc. other code cleanups, etc.
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/64 2.4 (mir)
Solaris/64 2.9 (shanti)
Initial revision to add support for "huge" objects in the heap (which are
actually stored directly in the file, but are tracked with v2 B-tree that is
accessed through heap header).
Testing:
FreeBSD 4.11 (sleipnir)
Linux/64 2.4 (mir)
Linux/32 2.4 (heping)
Mac OS X.4 (amazon)
Added files created by James for user-define links to the command files
Added new script check_h5jam.com to test h5jam/h5unjam; test script
needs more work.
Platforms tested:
VMS server and test script only.
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.
Added test script to test h5import tool; added new source file
to the make.com file in the src directory.
Platforms tested:
Only h5import was tested on the VMS server
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)
1. changed the -F flag option names to "BE and "LE" for big and little endian
2. added a more verbose usage message for these options
3. add a new test
4. add a make clean instruction to *.bin
the last one
h5ls -w80 -v -S tattr2.h5
h5ls prints "native" for all types instead of the complete datatype definition.
I will look into the problem next.
it uses the API function H5Gcopy to copy groups and datasets from file
to file, read from a command line
note: the test script is not finished yet
tested on heping, copper, shanti
new feature
Description:
added support for h5dump to dump binary data using the file type format
added one test to the test script that tests this
Solution:
Platforms tested:
mir
shanti
copper
Misc. update:
new feature. h5dump output of binary data
Description:
a new switch -b FILE_NAME that dumps the contents of memory data to file FILE_NAME in binary form
new program binread.c that reads the contents of this file and outputs it to stdout
added a test for the h5dump shell script that does a run of -b
the binread.c program reads the data used in this run, usage is ./binread FILE_NAME
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Description: Added support for HPUX11.23
Solution: Added configuration file for the system.
Both C, C++, F90, HL 32-bit and 64-bit are supported. Known problems:
C++ library will not build in 64-bit mode if shared is enabled.
Platforms tested: HPUX 11.23 at UMKC
Misc. update:
Description: Added a command file for testing tools; it has a framework
to do exactly (almost) what UNIX tools test scripts do:
- run test tool and save output
- compare output with expected result
- figure out the difference and
- print PASSED /*FAILED* in a manner similar to the UNIX output
It needs to be populated with more tests and reused for other tools.
Solution:
Platforms tested: VMS server
Misc. update:
Description: Added test script and two test files in the tools/misc/testfiles
directory for testing h5stat tool; modified Makefile.am in tools/misc
and configure.in files to run the new test script; reran bin/recofigure
to update relevant configuration files; updated MANIFEST
Solution:
Platforms tested: heping with in place and srcdir builds; will do more testing
after the checkin.
Misc. update:
Bug fix - bugzilla #552
Description:
On Cray X1, trying to use : as an argument confused the system.
Solution:
Added a test in configure to see if : as an argument is bad.
If so, skipped the test.
Platforms tested:
mir, Cray X1 (change to configure only)
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
Code checkpoint
Description:
More progress on fractal heap, can now re-open an existing heap, although
the free space algorithm still needs work.
Also, use the new "pinned entry" metadata cache code.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (heping)
Solaris 9 (shanti)
Linux 2.4/64 (mir)
Code cleanup
Description:
Big clean up on high-level library code, including:
- Removing include of HDF5 private header file(!)
- Reduce number of compiler warnings
- Untangle header files, etc.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/C++
Linux 2.4/64 (mir) w/C++ & FORTRAN
Add pinned entry capability to cache.
Description:
For frequently accessed cache entries, the protect/unprotect overhead
is sometimes a bottleneck.
Solution:
Allow entries to be pinned in the cache. Pinned entries can't be
evicted, but can be flushed or modified.
Platforms tested:
h5committested -- minus one small typo in test/cache.c whose fix was
tested on copper and heping only.
Misc. update:
new feature
Description:
added support for the printout of dataset region references differences
added a new test for this
merged the h5diff generator of test files into a single file
Solution:
Platforms tested:
linux 32, 64
solaris
Misc. update:
Several bug fixes
Description:
Added config file for Cray X1 (previous file was misnamed)
Simplified some code in hyperslab.c test that seemed to have been
confusing compiler on Cray X1.
Fixed typo in config/commence.am
Cleaned up hl/src/Makefile.am
Solution:
All four fixes should be straightforward. The failure on Cray was
very difficult to debug, but involved arithmetic errors.
This change seems to fix it.
Platforms tested:
heping, copper, sol, some Cray X1 (more testing when system comes back up)
Bug fix.
Description:
./hl/src/H5LTparse.h was marked as DO_NOT_DISTRIBUTE by mistake.
It should not be installed but must be present for building.
Solution:
Fixed.
Platforms tested:
Should work.
Description: Here is what I did:
modified MANIFEST according Quincey's instructions to fix
the problem exposed by bin/release (compilation fails
because some header files were not included in the distribution)
fixed small typo and modified include_HEADERS line in
src/Makefile.am to address the problem exposed by bin/release
ran bin/h5vers to change version number to 1.8.0-alpha0
ran bin/release to release tar ball to the ftp server
Solution:
Platforms tested: mir MANY,MANY,MANY times
Misc. update:
Code checkpoint
Description:
Add in more fractal heap support for odd allocation patterns (entries that
are too large for various block sizes, etc.)
Broke out fractal heap code into more source code modules.
Refactored fractal heap test to make it more understandable and
maintainable for the long term.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (heping)
Linux 2.4/64 (mir)
Solaris 2.9 (shanti)
new feature
Description:
1) separated the HL library into "public" and "private" header files, with the same caracteristics as the basic library
2) added the public headers to hdf5.h (with a conditional include macro, defined in configure.in)
3) added the path to HL in all Makefile.am 's , because of the inclusion in hdf5.h
Solution:
Platforms tested:
linux 32, 64
AIX
solaris
with fortran and c++
(one packet table example fails)
Misc. update:
bug fixes
Description:
h5dump/h5ls were not displaying long doubles correctly
Solution:
1) the print datatype functions were incorrectly testing for the valid return value from H5Tequal,
(TRUE), causing the display of an incorrect name of a dataype in error cases from H5Tequal
2) h5tools_print_str did not have a case for native long double
3) added a file generator for a long double dataset
4) added one script test for the long double data (commented , some sytems don't have a native long double match, and the output differs)
5) added a vms file and h5dump script test
Platforms tested:
linux 32, 64
solaris
AIX
Misc. update:
Description: cross_read.c is a new program to test reading data created
on an OpenVMS, a little-endian, and a big-endian machine. The three
data files are vms_data.h5, be_data.h5, and le_data.h5. To generate
these data files, run gen_cross.c on these machines and change the file
names.
Platforms tested: fuss and h5committest
Misc. update: MANIFEST
bug fix
Description:
percent relative error was done using integer arythmetic; use floating point instead
added the case for unsigned long long integer to float conversion
Solution:
Platforms tested:
linux (32,64)
AIX
solaris
Misc. update:
bug fix
Description:
1) added a more explainative usage message
2) the percent relative error for the integer type (division) was being done using integer arythmetic; use floating point arythmetic instead
3) added a new test for integer percent
Solution:
Platforms tested:
linux (32,64)
AIX
solaris
Misc. update:
bug fix, new features
Description:
when comparing links , the output for the number of differences found was not being done
Solution:
print it
add 3 more tests that test the output of differences for 1) groups 2) datatypes 3) links
Platforms tested:
linux
Misc. update:
Code checkpoint
Description:
The fractal heap code is reasonably stable and is passing all its
current tests, so checkpoint everything with CVS.
Also, add "statistics" module for v2 B-trees code, which is only a
stub right now.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Mac OSX (amazon)
Linux 2.4 (chicago)
Description: I ran bin/chkmanifest BEFORE adding files to CVS. Therefore
script ignored all new files and reported success.
Solution: Added missing files and told myself to remember this next time.
Platforms tested: heping with bin/chkmanifest
Misc. update:
New feature & code cleanup
Description:
Update fractal heap to be able to insert objects into a direct block
hanging off the header.
Extract "octal dump" code into separate routine so that both the local
heaps & fractal heaps can use it.
Other code cleanups & support to get this far.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Moved gif2h5 tool to hl directory
Description:
Added a tools directory under the hl directory and moved the gif2h5 tool
to that directory.
Solution:
The gif2h5 tool was originally built in the tools directory, but this
introduced dependency issues that required special checks in the
Makefiles.am and required the top-level build order to be changed
because it depended on the HL library.
For simplicity in the Makefiles now and in the future, the gif2h5 tool
was moved to be underneath the hl library.
Platforms tested:
mir, copper, modi4, shanti
Added HL examples
Description:
Examples existed for the HL lite, image, and table interfaces, but
were never included in the distro... until now!
Solution:
Added source files to CVS, updated Makefile and MANIFEST.
Platforms tested:
mir, heping, shanti
Incrementtal checkin
Description:
Revise & update v2 B-tree code to separate the internal package-specific
routines from the library-callable "private" routines.
Similar updates for the fractal heap code.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Mac OSX (amazon)
New feature
Description:
Check in initial "fractal heap" code, for supporting the group redesign.
Also, remove some remnants of the segmented heap/block tracker/B+tree code
which I didn't find during the last pass.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Mac OSX (amazon)
Linux 2.4
Maintenance
Description:
Remove half-built (half-baked? :-) implementation of B+tree, block tracker
and segmented heaps. (In preparation for starting the new heap coding)
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (heping)
1) Add parallel test for metadata cache
2) Split serial test for metadata cache into two parts
3) Fix bug in which cache was flushed needlessly when the
cache wasn't full.
4) Performance improvements
Description:
See above.
Solution:
See above.
Platforms tested:
h5committest
Misc. update:
Code cleanup
Description:
Check in some of the code cleanups from working on the external link
support. (This doesn't include any of the external link features)
Platforms tested:
FreeBSD 4.11 (sleipnir)
Mac OSX.4 (amazon)
Linux 2.4
Description: Renamed lex.yy.c to H5LTanalyze.c, y.tab.c to H5LTparse.c, and
y.tab.h to H5LTparse.h in hl/src. Changed definition of opaque type to ommit the tag.
Changed the test for opaque type in hl/test, too.
Platforms tested: h5committest, fuss, and sleipnir.
Misc. update: MANIFEST
Bug fix
Description:
Fogot to commit file config/examples.am in previous checkin.
Solution:
The examples.am file contains common Makefile rules for the example
directories.
Added high-level example directories
Description:
Refactored common code out of examples Makefiles.am, added high-level
example directories, added packet table examples.
Solution:
Examples now draw from a common config/examples.am file, which
contains rules for installing, uninstalling, and cleaning examples.
High-level example directories are mostly empty, except for the
C and C++ packet table tests.
Platforms tested:
mir, sleipnir, copper, shanti
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
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.... :-)
New feature
Description:
Add in baseline "object copy" code from Peter [in the form of a new API
routine: H5Gcopy()]. There's still some work to do (like handling variable-
length datatypes and possibly support for references) and it hasn't been tested
on mounted files yet, but the core functionality is there and working
correctly.
I've also got a set of patches to update the 1.6 branch with tweaks to
keep the branches mostly in sync, but Elena will kill me if I import them
before the 1.6.5 release is out... :-)
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committested
Bug fix.
Description:
The previous way of detecting the MPICH version fails if the suspected
$CC does not give the expected MPICH version information. Though no
consequence, it generates error messages that alarm users.
Also, mpich2 gives the version information as if it were mpich v1.0.2
which was incorrectly included as an earlier version of the origianl
mpich.
Solution:
Implemented a more robust code to detect the version and narrow the
recognition down to v1.2.0-v1.2.5. Also, the code were duplicated in
two files (linux-gnulibc1 and ia64-linux-gnu). Combined them into a
new file called mpich.
Platforms tested:
Tested in heping using mpicc and mpich2/mpicc and also in tg-ncsa.
Misc. update:
Updated MANIFEST.
new h5diff test
Description:
added a test to the test h5diff script that compares a file to itself.
this test is done to test some features of the library that
open the same file and the root group twice
Solution:
Platforms tested:
linux
solaris
Misc. update:
Bug fix
Description:
Changed the name of a file from the last fix.
createnoenc.c is not gen_noencoder.c
Solution:
This is just a more standard name for the file.
Platforms tested:
tested in previous check-in; forgot to commit to cvs.
Code cleanup/reorganization
Description:
Merge back some more changes extracted from the "compact group" set.
This bunch cleans up and prepares the H5G_* routines for eventual import of
new features.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Mac OS X.4
Code cleanup/bug fix
Description:
Add missing files to manifest
Remove C++ style single-line comment from recent checkin and also re-indent
in a few places.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/thread-safe
Not configured w/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
new test hor h5repack, to syncronize tests between unix and windows
it requires a new file added
Description:
Solution:
Platforms tested:
linux
Misc. update:
bug fix.
Description:
-nt is not a universal option for the test command in all platforms.
The use of it in conclude.am cause some platforms to bark at the
Makefile generated.
Solution:
Created a command script bin/newer which tests if file1 is newer
than file2. Replace the "test file1 -nt file2" by
"newer file1 file2".
Platforms tested:
Tested in sol.
Description:
1.7 daily tests failed in HL library when Fortran was not
enabled; also long long instead of long_long declarations
were used and caused failures on Windows
Solution:
Removed Fortran related functions (except H5IM_find_palette) from
H5IM.c file and put it into fortran/src/H5IMcc.c
Modified appropriate Makefile.am files, regenerated Makefile.in files, updated header files, MANIFEST, etc.
Note: H5IM_find_palette should be also in H5IMcc.c, but
for some unknown to me reason, linking fails if the function is
included in H5IMcc.c. I will really appreciate if some C guru
will look into the code and figure out what is wrong :-) Thanks!
Platforms tested: mir with g95, heping with and without Fortran enabled
Misc. update:
New feature
Description:
Add group creation & access property lists, dataset access property lists
and named datatype creation & access property lists. Currently have
<foo>_extend() API names, which will need to be changed for the final release.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (heping)
Add new html document files for windows users
Add new project file dt_arith.dsp and dt_arithdll.dsp
Remove dt_atomic.dsp and dt_atomicdll.dsp
Description:
Solution:
Platforms tested:
Misc. update:
Description: Renamed test/dt_atomic.c to test/dt_arith.c(an abbreviation
of "arithmetic data types") to better describe the program. This checkin
broke down into three sections when the floating-point numbers are the
source, normalized, denormalized, and special values. If there's any
difference of destination values, only normalized value test reports
failure. The other 2 report only as warning.
Platforms tested: h5commitest and fuss
Misc. update: MANIFEST
Several files added into windows directory
Description:
Added:
Batch files for intel and .net
Documents for windows
Removed:
Short instruction for windows
Solution:
Platforms tested:
Misc. update:
Two new project files added.
Description:
Two new test tools h5repart project files added into windows/tools/testfiles
Solution:
Platforms tested:
Misc. update:
Bug fix/improvement
Description:
Added another step to fortran type detection. This should help on some
bizarre platforms.
Solution:
Formerly, H5fortran_detect.f90 was included in the distribution. Now
it is generated by H5test_kind.f90 (written by Elena).
Platforms tested:
verbena, modi4, copper
Description:See details from Bug #213. Family member file size wasn't saved
anywhere in file. When family file is opened, the first member size determine
the member size.
Misc. update: Added a family file as the source file for backward
compatibility test.
Description: See details from Bug #213. Family member file size wasn't saved
anywhere in file. When family file is opened, the first member size determine
the member size.
Solution: This is the fourth step of checkin. A test suit is added for h5repart,
including a program to generate the test files, a script file to run h5repart,
and a program to verify repartitioned files can be opened by the library.
There's a change from the first step of checkin. Family name template is no
longer saved in the superblock because different pathname can make the name
different.
In the third step of checkin, h5repart has been modified. If h5repart is used
to change the size of family member file, the new size(actual member size) is saved
in the superblock.
In the second step of checkin, multi driver is checked against the driver
name saved in superblock. Wrong driver will result in a failure with an error message indicating
multi driver should be used. This change includes split driver because it's a special case for multi
driver.
In the first step of checkin. Family member size and name template(unused at this stage) are saved
in file superblock. When file is reopened,the size passed in thrin superblock. A different size
will trigger a failure with an error message indicating the right size. Wrong driver to open family
file will cause a failure, too.
Platforms tested: h5committest and fuss.
Misc. update: MANIFEST
Added documentation
Description:
Added "Automake Use Cases" document to Tech Notes.
This is intended as a reference or an introductory document; more
in-depth documentation is in progress.
Platforms tested:
Change only to documentation. Documentation is viewable on Windows.
new fortran parallel test
Description:
added a test that writes and reads several datasets
Solution:
Platforms tested:
linux (intel compiler, tungsten)
AIX (copper)
Misc. update:
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:
Three project files and three workspaces added into hdf5/windows/misc
Description:
Add the following files
/windows/misc/H5fortran_detect_gen/H5fortran_detect_gen.dsp
./windows/misc/H5fortran_detect_gen/H5fortran_detect_gen.dsw
./windows/misc/fortrantypegen/H5fortran_detect.dsp
./windows/misc/fortrantypegen/fortrantypegen.dsw
./windows/misc/matchtypegen/H5match_types.dsp
./windows/misc/matchtypegen/matchtypegen.dsw
Solution:
Platforms tested:
Misc. update:
New feature.
Description:
Add "memory pool" internal data structure. This set of routines is
designed to add a way to allocate small pieces of information for a particular
purpose and then free all the pieces at once (i.e. without having to free each
piece individually). Memory pools are also good for localizing lots of small
allocations that logically belong together.
For example, if you were constructing a temporary linked list, you could
create a new memory pool, allocate all the nodes for the list from the memory
pool and when you were done with the list, just destroy the pool instead of
tracking through the list and freeing each block independently.
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
Cray X1 Port
Description:
Porting 1.7 branch to Cray X1. With these changes, HDF5 builds, but
there are some errors in the tests. Working on the errors.
Solution:
Added nv1-cray file to config directory.
Cleaned up some code in hl/c++ that was causing compiler to complain.
Platforms tested:
Cray X1, mir, sleipnir
Misc. update:
Configuration feature
Description:
Fortran integer types (not reals) are now automatically detected at
build-time.
Solution:
Two helper programs are used, one to detect what types the Fortran compiler
has access to, and one to generate header files for C and Fortran matching
up types.
Platforms tested:
mir, copper, modi4, pommier (last week)
Misc. update:
MANIFEST updated, H5f90fortran_types.f90 removed from configure.in, since
it is not longer generated by configure.
Bug fix/code cleanup
Description:
Add tests to determine that very long (64K+) object names are working.
Fixed a couple of bugs in h5dump where they weren't...
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
Feature - libtool shared library versioning
Description:
Libtool provides a mechanism for different versions of the same shared
library to be distinguished. Now this is applied to HDF5 when it is
built as a shared library.
Solution:
The version number is stored in config/lt_vers.am, and included in
src/Makefile.am.
This number will be automatically updated by bin/h5vers; developers
only need to update it when they change the API.
*** IMPORTANT ***
Any time the API changes, the version number in config/lt_vers.am must
be updated!
Platforms tested:
mir, eirene, verbena, modi4
Misc. update:
Description: Removed support for SRB driver
Solution: Removed or modified appropriate files; ran reconfigure
to regenerate Makefile.in and configure files.
Platforms tested: heping and shanti
Misc. update: ran bin/chkmanifest on heping
Description: Split test/dtypes.c because it's so big. Moved all integer-integer,
floating-floating, integer-floating, floating-integer, derived integer, derived
floating conversion tests to a new test program, dt_atomic.c. The test remains
the same basically.
Platforms tested: fuss and h5committest
Misc. update: MANIFEST
add a new feature for the test image API, read a palette from an ASCII file and attach several
palettes to an image
Description:
Solution:
Platforms tested:
linux
solaris
AIX
IRIX
Misc. update:
New feature
Description:
Add first iteration of "segmented heap" code, which will be used to store
links in groups in a more flexible way than the previous "local heap" mechanism.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/parallel
Solaris 2.9 (shanti)
add 1 test that reads realistic dimension scales data from an ASCII file and generates an hdf5 file with DSs
Description:
Solution:
Platforms tested:
linux
solaris
IRIX
Misc. update:
Update MANIFEST for windows project files.
Description:
Many windows project files are added into CVS. MANIFEST needs to be updated.
Solution:
Platforms tested:
Misc. update:
Purpose:
Added C++ wrapper for Packet Table API.
Description:
Added macro for high-level C++ library (LIBH5CPP_HL), which changes every
Makefile.in.
Added directories for high-level C++ library (though currently only Packet
Table API is supported).
Added both C++ source and tests.
Platforms tested:
sleipnir, mir, modi4
Misc. update:
Added Packet Table to high-level APIs
Description:
The Packet Table is an API that allows the user to append records
("packets") to a table, and read the back again. It supports
fixed-length records with a defined datatype and variable-length
records. It also supports a "current record" index to track the
user's position in the table.
Solution:
The Packet Table code lives in hl/src, and its tests in hl/test.
Some code is shared between the H5TB table and the H5PT Packet Table
in the form of functions in H5HL_private.c.
Some documentation exists for a previous version of the API. Updated
documentation and C++ wrapper API coming soon.
Platforms tested:
sleipnir, eirene, copper, modi4
Description: Somehow, the hardware conversions between "long double" and other native floating-point
types were left out.
Solution: Added the hardware conversion functions in H5Tconv.c and test cases in dtypes.c.
Platforms tested: h5committest and fuss.
Misc. update: updated MANIFEST to replace bin/reconfigure.sh with bin/reconfigure
feature
Description:
h5repack support for scaleoffset compression
Checking in early to help debug the filter.
Solution:
Added messages and command line to handle new scale offset filter.
Note: TESTS ARE DISABLED FOR NOW. The filter is not
complete, repack tests may fail due to know problems.
PLEASE DO NOT MESS WITH THE SCALEOFFSET TESTS AT THIS TIME.
They will be enabled when the filter is ready.
Platforms tested:
verbena,copper,shanti
Misc. update:
MANIFEST
