h5diff: print a message of "not comparable" in a case where the relative error
compare is not possible, due to the denominator being zero. Modified
the test file generator program to include a example for this and a new
test on the shell script
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
1. bug fix. the h5_cleanup file names were not build properly on the h5repacktest call
2. added only a call to test_bigout.h5 to be clean, because the other files are generated anyway by the shell script. test_bigout.h5 is only made on the C program part (h5repacktst)
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
Overhaul usage of object header chunks to reduce I/O operations and
memory allocations. The object header prefix is now stored in the first
object header chunk's "image" in memory.
Also, lots of formatting cleanups.
Taught h5debug tool about new object header format (which isn't enabled
just yet).
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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 "use the latest format" support for dataspace object header encode/
decode routines and clean up format a bit for the latest format (new to 1.8.x
releases)
Remove storing 'perm' parameter for array datatypes in memory and the file,
and add test to make certain that if any user applications are attempting to
store them, we get some reports back. (Should be unlikely, since the RefMan
says that the parameter is not implemented and is unsupported).
Carry those changes into the tests, etc.
Clean up a bunch more compiler warnings.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-1.6-compat
and quote its arguments. Also checks for the 'socket' library on
Solaris.
If this patch passes the Daily Tests and makes the user happy, I'll
port it back to the 1.6 branch.
Tested on mir and sol.
Further minor modifications to the file format for tracking links in groups.
This is tentatively the "final" file format for groups.
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
revised binary flags, added a new file to the test generator program to
be used in the binary tests
usage is now
-o F, --output=F Output raw data into file F
-b F, --binary=F Binary output, of form F (into file -o F).
Recommended usage is with --dataset=P
Form F of binary output is: MEMORY for memory type,
FILE for the disk file type, LE or BE for pre-existing
little or big endian types
example
./h5dump -d integer -b MEMORY -o out.bin tbinary.h5
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)
Improve density of the B-tree further. For greater depths of B-trees,
the gains are over 100%...
Also, don't split internal nodes with 3->4 splits, use a 1->2 split
instead, so that the density of the nodes around a split is maximized.
Tested:
Mac OS X/PPC 10.4 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Code cleanup.
Description:
Removed argc and argv from the function arguments of h5tools_get_fapl() and
h5tools_fopen(). They were used to call MPI_Init() which was no longer
needed.
Tested:
heping (serial and parallel).
Refactor the file storage of "twig" nodes in the B-tree to allow them to
store more records, increasing the average density of the B-tree 30-40%.
Increase # of records in "insert lots" regression test to still create
B-tree of depth 4
Update h5debug to interpret difference of 'branch' and 'twig' internal
nodes in B-tree correctly.
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
Solaris/64 2.9 (shanti)
Since these examples need to follow filesystem paths, the Makefiles need
to create directories in the examples directory; added this to the
Makefile.am.
Tested on Windows, mir, juniper
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)
Clean up compiler warnings/failures in test/links.c, especially when
--disable-production flag used with --enable-group-revision
Modify binary dumping in h5dump to clean up files created [a band-aid
solution to not actually creating the files in the srcdir, but better than
just leaving the files around... :-/ ]
Tested:
FreeBSD 4.11 (sleipnir) (w/ configure flags above)
Too minor to require h5committest
Bug fixes.
Description:
There were MPI_init and MPI_finalize calls in the code of h5tools_fopen in
parallel mode. But if a non-MPI tool is invoke to open a non-existing
file, it tries to open the non-existing file with different VFD and
eventaully came to try with the MPIO or the MPIPOSIX vfd, then it would
try to do MPI_Init which would fail in the MPI environment if the a.out
was not launched by MPI properly.
Solution:
MPI_Init and MPI_Finalize in general should be called by the MPI application,
not called by a library subroutine as in the manner that was done here.
Removed the MPI_init and MPI_Finalize calls. Used MPI_Initialized to
verify if this has been launched as an MPI application in the proper
manner before attempting to use the MPIO or the MPIPOSIX VFD to open
the file.
Tested:
In tg-ncsa parallel, where it had failed explicitly and also in Heping,
using both serial and parallel mode.
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.
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)
the $srcdir properly. It is not right to chdir into testfiles and write
files there because in real srcdir mode, one should not changes things
in the srcdir area which could be shared by multiple builds simultanteously.
Solution: added the proper $srcdir components to the source file name.
Also clean up the indentation by cb.
Tested: only by hand in heping.
"make check-vfd" will now run all tests in the test directory with different
file drivers (at least, all of those tests that use the testing framework's
FAPL). Tests that fail will be skipped.
This is not a perfect fix, but is better than nothing.
Along with this change, check-vfd should be added to the Daily Tests.
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
bug fix
calling h5tools_get_fapl running the mpio driver caused H5FD_pl_copy to
fail silently in some conditions. a MPI call was made before MPI_Init.
solution: corrected the MPI call to be made after MPI_Init and added error return
conditions to H5FD_pl_copy and h5tools_get_fapl
tested on copper parallel, mir, shanti
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
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.
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:
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
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:
Configuration feature
Description:
'make install' now tests both static and shared libraries if both are installed.
Solution:
Previously, shared libraries were only tested when static libraries were not installed.
Also cleaned up line in commence.am that was including HL library in all Makefiles.
Platforms tested:
mir (Makefile change only)
Description: Added new tests for the h5stat tool; added --version flag
to display library version information and updated expected
output files.
Solution:
Platforms tested: heping, shanti
Misc. update:
Description: Added new tests for the h5stat tool; added --version flag
to the h5stat tool to display library version information
Solution:
Platforms tested: heping, shanti
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)
Description: I am checking in changes for the h5stat tool:
- updated Makefile.am to use tools library
- regenerated Makefile.in
- added command flags to display selected information
- added support for external files and filters
- small output formatting changes
For more information about current features and output see
updated h5stat RFC http://hdf.ncsa.uiuc.edu/RFC/h5stat/h5stat-spec.pdf
Solution:
Platforms tested: mir, heping, shanti, copper 64-bit, copper 32-bit parallel
using files from tools/testfiles directory and some NASA files
from our Web site.
Misc. update:
Bug fix.
Description:
The ${TR}, though avoid the error, is inconvenient. It is needed
because configure.in use the char range in the style of 'a-z'.
The other style of '[a-z]' is more commonly accepted by all tr
but autoconf tends to strip away [], making the syntax rather
clumsy.
Solution:
Learned from autoconf that it avoids the use of character range
by just spell all the letters out. Changed our tr commands to
use those variables defined by autoconf. Also removed the
definition of ${TR} since it will cause inconsistancy when
autoconf also use plain 'tr' in its generated code.
The Makefile.in are changed because the elimination of ${TR} from
configure triggered its removal from all Makefil.in. That is okay
because ${TR} is not used at all in Makefile.
Platforms tested:
h5committested. (sol failed to connected). also tested in shanti
using both /usr/ucb/tr and /bin/tr (the bad one before.)
Misc. update:
Updated both INSTALL and RELEASE files.
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
new feature
Description:
modified the test case for region points, so that there is not an ordered sequence of points that differ, but one with gaps
Solution:
Platforms tested:
linux
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)
Anti-feature
Description:
Revert changes to H5G_stat_t struct, to make it compatible with the 1.6.x
branch again. The information that was added to the H5G_stat_t struct will
be reported through other API routines.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/C++
Linux 2.4/64 (mir) w/C++ & Fortran
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:
"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)
new feature
Description
some more check in related to the print of compression ratios: print warning messages after the print of the dataset name and compression:
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
new feature
Description:
some more formatting of the output for the new compression ratio printout
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
new feature
Description:
added some alignment for the printout of attributes, so that is formatted with the new printout of datasets compression
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
new feature
Description:
added the printout of the compression ratio for filters in h5repack, after the filter name, obtained with H5Dget_storage_size, before and after applying the filter
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
bug fix
Description:
the percent error calculation in h5diff using double precision floating point were causing different results
on the release and debug versions of Visual Studio version 6, due to a compiler bug
Solution:
used single precision (float)
Platforms tested:
windows
linux
solaris
AIX
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:
bug fix
Description:
h5repack was not dealing with family files
Solution:
use the toolslib function h5tools_open to open the file instead of H5Fopen in h5repack
Platforms tested:
linux
solaris
AIX
Misc. update:
bug fix
Description:
regenerate a binary file. the previous one was not being open on the scale offeset filter dataset, probably due to a solved bug with the corresponding binary file not being updated
Solution:
Platforms tested:
linux
Misc. update:
Bug fix
Description:
Previous checkin did a bad thing; 'make clean' failed in example directories.
Solution:
Fixed commence.am so that examples no longer break, and fixed a mistake
in conclude.am.
Platforms tested:
heping (minor makefile change)
Misc. update:
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:
make check-clean didn't clean results of example tests
Solution:
Fixed Makefiles so that check-clean recurses into example directories.
Also a little Makefile cleanup.
Platforms tested:
mir, modi4, heping, copper
portable issue on windows
Description:
setvbuf on visual studio 2005 needs the size to be greater or equal to 2.
<description of setvbuf from msdn library>
Buffer size in bytes. Allowable range: 2 <= size <=
INT_MAX (2147483647). Internally, the value supplied
for size is rounded down to the nearest multiple of 2.
h5import used linebuffer option of setvbuf for stderr and stdout and the size is
0 by default. This causes core dump with visual 2005 on windows 64-bit.
Solution:
1. Use HDsetvbuf inside h5import.c,
2. Define HDsetvbuf inside windows H5pubconf.h for windows to work around
the core dump of h5import test. This is probably a bug inside visual studio 2005.
Platforms tested:
h5committest( shanti refuses to be connected)
windows 6.0 at XP
visual 2005 at XP-64bit
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:
Code cleanup
Description:
Clean up some compiler warnings (esp. those flagged on Windows builds)
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
bug fix
Description:
the compare check for the datatype sign was not done in the correct place, causing invalid
comparisons to be made
Solution:
put it on the correct place
Platforms tested:
linux 32, 64
AIX
Misc. update:
bug fix
Description:
1) the compare flag test was not being put in a correct place, making comparisons attempts that were not supposed to be done
2) some duplicate warnings were being made
Solution:
eliminate the duplicate warnings, put the if compare flag on the correct place
Platforms tested:
linux 32, 64
solaris
Misc. update:
bug fixes
Description:
1) the option logic for the print of long types was done incorrectly (extra lines of code that were not supposed to be there)
2) the print of loong long types was incorrect
Solution:
1) removed the incorrect code
2) made a long long cast on the printf call
Platforms tested:
linux (32 and 64)
solaris
Misc. update:
bug fix
Description:
long long type was being incorrectly printed
Solution:
added a long_long cast to print function
Platforms tested:
linux
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:
Solution: Support VAX float and double types with new byte order. There're some
details not yet included,
1. the alignment detection for VAX order in H5detect.c.
2. support for special values in library conversion functions.
3. the infinity for VAX in H5T_init_inf.
4. support for VAX types in printing hexadecimal format.
Platforms tested: h5committest and fuss.
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: Return value from H5Pget_layout is 0 for the compact datasets;
It was assumed in the code that it was always greater than 0; therefore
assertion failed when h5stat walked a compact dataset.
Solution: Fixed assertion statement
Platforms tested: h5stat doesn't have testscript yet; tested manually
with tfilters.h5 file on heping.
Fix is too minor to test it on multiple platforms.
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
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)
Change to release script
Description:
Silenced doxygen's output when bin/release doc is run. Now if doxygen
has an error the release script will exit.
Someone forgot to run reconfigure after a Makefile.am, so testing the
release script seems to have had the side effect of regenerating a
Makefile.in.
Platforms tested:
mir
bug fix
Description:
the --disable-hl switch was causing linking errors on gif2h5 that uses image api (bugzilla #1)
Solution:
used the condional macro for hl to build gif2h5
Platforms tested:
linux
Misc. update:
bug fix
Description:
the linking order in Makefile.am of the gif2h5 tool was causing linking errors on some configurations (pgcc, --disable-shared)
Solution:
changed the order of the linking (hl before hdf5)
Platforms tested:
linux, several configurations
solaris
Misc. update:
bug fix , bugzilla bug #1
Description:
the gif2h5 was not writing HDF5 images correctly
Solution:
use the Image API to write the image, rewrote the writing functionY
Platforms tested:
linux
solaris
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
bug fix
a call to sprintf was giving incorrect output in the system Fedora Core 4 with gcc 4.0
(not supported by us, but user reported)
Solution:
the call was using the same buffer for source and destination variables, used different ones
Platforms tested:
linux (mir)
solaris (sol)
Misc. update:
Purpose:
Bug fix
Description:
Libraries were listed in the wrong order in tools/gifconv Makefile.am, confusing
the linker.
Solution:
Put HDF5 library after tools library in Makefile.am and ran reconfigure.
Platforms tested:
mir, sleipnir
h52gif bug fix (494)
Description:
the reading routines were using file datatype sizes for memory allocation
Changed the HDF5 read routines to use memory types and sizes,
for both the image and pallete datasets
Solution:
Platforms tested:
linux
solaris
Misc. update:
Makefile fix
Description:
The h5diff parallel test script depends on the serial test script.
Added this dependency.
Solution:
Used SCRIPT_DEPEND variable. Also added ph5diff (when it is compiled).
Platforms tested:
mir
Improvement
Description:
Some parallel system would dump some system messages in the stdout
stream of an MPI application. That caused the output matching script
to fail unnecessarily.
Solution:
Added the STDOUT_FILTER feature to filter out those system messages
out of stdout result.
Platforms tested:
Tested in LANL Lambda.
Bug fix
Description:
Remove several macros that are already defined in H5private.h and are
causing failures on copper.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Bug fix
Description:
Include more header files with prototypes to make CC=g++ builds work.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/CC=g++
Too minor to require h5committest
Code cleanup
Description:
Fix a bunch of warnings flagged by Windows compilers.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Bug fix
Description:
Fortran type generation was broken in two ways. Fixed both.
Solution:
Firstly, there were a couple of path problems. Fixed a typo and
specified the full path of a file.
Secondly, the dependencies weren't right when building with HDF5-specific
commands (make lib, make check-s, etc.). Tweaked dependencies
to fix the problem.
Platforms tested:
mir, modi4, sleipnir
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:
Bug fix
Description:
Before this checkin, 'gmake check-s' would fail if there was a file in
the current directory named 'check-s'.
This is fixed under gmake (not sure how to fix for other makes).
Solution:
check, progs, install, etc. are what gmake calls "phony" targets,
which means that no file should be created. These targets can be
specified by a line of the form
.PHONY: check progs install ...
Automake adds this line for targets it knows about, but HDF5 has a
lot of custom rules. This checkin adds a .PHONY line for those rules.
I believe that only gmake recognizes the .PHONY line (at least, pmake
doesn't seem to), but a partial solution is better than none.
This error should occur very rarely anyway (the user has to manually
create files with names like 'build-check-s' or '_test').
Platforms tested:
mir, sleipnir, modi4
Cleanup.
Description:
Removed reference to H5_HAVE_VSNPRINTF and the corresponding abort
since we do not use the home-grown potentially memory wacking version
any more.
Platforms tested:
heping.
Misc. update:
Bug fix
Description:
Correct use of H5Gget_objinfo() which recent compact group checkins
exposed: we were attempting to follow dangling soft links.
Solution:
Don't follow links for H5Gget_objinfo() when initializing object tables
for h5dump.
Platforms tested:
Solaris 2.8 w/64-bit enabled
Linux 2.4
FreeBSD 4.11 (sleipnir)
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.... :-)
Copyright fix
Description:
Added a blank line so that Automake would put the copyright at the top of
the file.
Platforms tested:
Trivial change
Misc. update:
Bug fix/feature
Description:
Added support for -shlib in h5fc and h5c++.
Made check-install use -shlib when only shared libraries have been installed.
Solution:
h5fc and h5c++ didn't recognize -shlib. Stole code from h5cc to link against
shared libraries.
When static libraries are disabled, the examples Makefiles will automatically
use the -shlib option to link against shared libraries. Thus,
--disable-static and make check-install should work together.
Platforms tested:
heping(disable-static, enable-static, fortran, c++), modi4 (disable-static, fortran, c++, parallel, enable-static)
Update copyrights.
Description:
Solution:
This should address almost all of the "simple" cases in the repository.
There's still work to do, but it's going to require actually thinking about
the files in question instead of just copying & pasting.
Bug fix
Description:
Failed parallel tests now cause make to exit with an error.
Solution:
Edited config/conclude.am to throw an error if parallel test programs fail.
Platforms tested:
heping, modi4
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:
Added additional targets to build-all
Description:
Surveyed files to find out which ones are not built.
Added test/space_overflow and perform/benchpar to programs built with
--enable-build-all.
Discovered that tools/misc/pdb2hdf5 and tools/misc/h5import were
obsolete and deleted them.
Platforms tested:
mir, modi4, sol
Misc. update:
Update of release file and removal of --enable-pdb2hdf5 to follow.
bug fix
Description:
an assertion after the search for objects was saying that the number of
objects in file should be > 0
removed it, since there can be a case where the number of objects is 0.
in this case this was found by a case where zlib was not present and the output file
was not written any objects to
note: this was only detected on the windows batch files, that do not have a conditional
condition to not run tests when a filter is not present
Solution:
Platforms tested:
linux
Misc. update:
Description: VMS doesn't like file names with more than one "."
Some h5repacktst output file names were of the form
<name>.out.h5 causing h5repacktst to choke.
Solution: Renamed output files to be of the form <name>out.h5
Platforms tested: heping, unnamed VMS machine
Misc. update:
Bug fix
Description:
Changed configure.in to use an environment variable TR to set the path
to the tr utility.
Solution:
There are two kind of tr on Solaris with slightly different syntax.
HDF5's configure relies on the "standard" tr. Traditionally, HDF5ers
have needed to make sure that the "right" tr was found before the
wrong one in their path; now they can use an environment variable.
Platforms tested:
mir, shanti, sol
Misc. update:
Forgot to update release notes. Off to do that now.
Makefile bug fix
Description:
Previously, automake didn't output rules to build perform/mpi-perf or
the test/gen_* programs.
Now these can be built by typing 'make mpi-perf' (or 'make foo') or by
configuring with --enable-build-all.
Solution:
Automake doesn't like having rules for programs it doesn't build. Tricked
it by having these programs built "sometimes"--whenever the user enables
--build-all. This should be used mostly for testing and to ensure that
these helper programs compile.
***IMPORTANT***
These programs do *not* currently compile. When --enable-build-all is used
(not the default), gen_new_fill fails because it uses an old API. This is
an existing "bug" that has simply been exposed by this checkin.
Platforms tested:
sleipnir, modi4, sol
Misc. update:
SETUP Was using "cp" command which means file $2 will inherit the permission
setting of file $1. If $1 is read-only, so will $2. That will cause
failure when the test attempts to write it later on. Changed to use
the "cat" command.
Tested in LANL QSC and Flash.
bug fix.
Description:
When a parallel test script test fails, make would continue because the
way it was setup inside a for loop. Fixed it by issuing an exit 1 inside
the loop.
There was also a typo error in the newer command comparision that it
must be $${chkname} in order to be valid. Also, the test script itself
was not checked in the newer lists. All fixed.
Platforms tested:
h5committested and also hand tested in heping pp mode.
h5diff new feature
Description:
a user asked for the message
"Some objects are not comparable"
to be more noticeable
Solution:
--------------------------------
Some objects are not comparable
--------------------------------
Platforms tested:
linux
Misc. update:
new features
Description:
added support for the scale/offset filter
there is a new filter symbol 'SOFF'
-f SOFF=<scale_factor,scale_type>
scale_factor = integer
scale_type = 'IN' or 'DS'
Solution:
Platforms tested:
Linux
SunOS
Misc. update:
New feature.
Description:
Added the time command to the make check target to report time usage
of the execute of each test and test scripts. This gives us some idea
how long each test takes and some vague idea it is compute bound or
not.
powerpc-ibm-aix5.x:
Change $RUNPARALLEL default setting to allow it being invoked by the
time command.
Platforms tested:
h5committested.
Feature
Description:
Added H5_CFLAGS, etc. to 1.7 branch.
Now compilation flags can be put in H5_*FLAGS and they'll be used when
building hdf5 but not in h5cc.
Platforms tested:
mir, sleipnir, modi4
Misc. update:
Bug fix
Description:
Disabled C++ shared libraries for Sun Workshop compiler.
Solution:
This bug only seems to happen when using the -xarch=v9 flag to compile in
64-bit mode, but disabling shared libraries entirely for this compiler is
an easier fix (I don't know how to detect 64 bit mode from the command line).
The framework for disabling shared libraries for other C++ compilers is
in place.
Platforms tested:
sol, mir, sleipnir, modi4
Bug fix/feature
Description:
Disabled shared libraries for a number of Fortran compilers that don't
support them.
This allows other compilers to support shared Fortran libraries.
Solution:
Added a conditional, SHARED_FORTRAN_CONDITIONAL, which is true if
Fortran supports shared libraries. It is set in configure.in.
Platforms tested:
mir, sleipnir, colonelk, heping
Bug fix
Description:
Building with --disable-static seems to have been broken on several platforms.
Fixed this.
Configure will now disable shared libraries automatically when using pgf90
or when building on Cygwin.
Solution:
To avoid errors when using shared libraries with pgf90 (which I had not
realized were compiler-specific), I had manually set convenience libraries
to use the -static linking flag. Apparently, this is not necessary, and
caused these libraries to be created as empty archives when --disable-static
was used.
Also, some libraries were including other libraries, which was not
necessary.
I also fixed code in configure.in to correctly detect whether shared
or static libraries are enabled, and moved code that disables shared libraries
to before libtool is created (rather than editing libtool after the fact).
Despite repeated warnings that only one shared library can be linked at a
time, I have yet to have shared libraries break the linking of tests on
any system. We'll see if the Daily Tests turn up anything.
Platforms tested:
mir (fortran, C++), sleipnir (C++), modi4 (fortran, C++, parallel),
sol (fortran, C++), cygwin
Description: Brought back changes from SX-6.
Solution: Program will not compile. Fixed.
Platforms tested: SX-6, heping and mir with new g95
Misc. update:
bug fix
Description:
during the generation of some test files, H5Fclose was not called
during the #ifdef detection of the scale ofsset filter, a wrong macro symbol was used
Solution:
Platforms tested:
linux
Misc. update:
Code cleanup
Description:
Changed some scale+offset filter symbols from H5_SO_... -> H5Z_SO_...
to indicate that they are in the H5Z package.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Updating the filter based on H5Pset_scaleoffset API change.
Description:
Still more changes are needed for the filter for floating-point.
Solution:
Platforms tested:
Misc. update:
tidy up.
Description:
MPE option created *.clog file whenever it is executed in MPI.
The cleanup of *.clog files were done in individual Makefile.in.
Often, it is forgotten.
Solution:
Moved the cleaning of *.clog files to CHECK_CLEANFILES in commence.am
so that it is applied whenever check-clean is called.
Platforms tested:
heping pp using MPE.
Bug fixes
Description:
This checkin fixes an occasional error on kelgia on sol during distclean.
It also causes test scripts to depend properly on the programs they're
supposed to be testing.
Solution:
The kelgia bug was due to some files being cleaned by automake and manually.
Removed the manual cleaning in src/Makefile.am.
Test script dependencies now need to be specified manually, since the
makefile can't guess what they test from their name. Currently all test
scripts in a given directory have a single list of dependencies--this was
easy and seems to be sufficient.
These dependencies are listed in the SCRIPT_DEPEND variable in the Makefile.am.
Platforms tested:
heping, mir, modi4, sol
Misc. update:
Code cleanup (sorta)
Description:
Adjust H5G_stat_t to prepare for eventual "external link" information.
This also puts the information for regular objects and soft links into more
obviously separate places.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
minor tidy up.
Description:
Changed both test programs and test scripts to use the same suffixes
(.chkexe and .chklog). Changed from .log to .chklog to avoid running
into potential conflicts by other "things" (e.g., config.log).
Tested:
Heping.
Code cleanup & speedup
Description:
Refactor h5dump & related code to be considerably cleaner & faster for
files with large #'s of objects.
Platforms tested:
FreeBS 4.11 (sleipnir)
Linux 2.4
bug fix
Description:
The set of h5diffdebugN macros that printed nothing did not have
the proper number of parameters. Some compilers (gcc) did not
like it.
Solution:
Fixed them to have the matching number of parameters.
Platforms tested:
heping pp (using both mpich-icc and mpich-gcc), modi4 pp.
Code cleanup
Description:
Clean up code somewhat:
- Move from HDmemset() -> H5G_ent_reset() to clear out group entry info
- Simplify H5G_unlink() call
- Use portability macros instead of direct system calls in more places
- Improve readbility by neatening whitespace, etc.
- Move some macros into source code module instead of header files
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Feature and bug patch
Description:
Added the SKIP feature which skips a test.
The latest code will hang the very last test. Skip that test for now.
Platforms tested:
heping pp.
Description: repart_test.c was mistakenly treated as a tool, instead of a test program.
Solution: Took it out of the tool list.
Platforms tested: fuss - simple change.
Bug fix
Description:
ph5diff had been hanging in Tflops. Found out that vsnprintf ph5diff
uses was a local coded that did not limit printing according to the size
argument. That resulted in buffer overflow and other problems.
Solution:
Added some sort of size checking in the home-grown vsnprintf and
had ph5diff checked for error return of vsnprintf. Leon also
revamped the ph5diff manager's way of handling communications with
the workers. That eliminated all but the last case of hanging.
Platforms tested:
Tflops.
Misc. update:
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
Description: The change made yesterday regarding repart_test.c wasn't right.
Solution: Roll back to v1.6 until a solution is figured out.
Platforms tested: fuss - simple change.
Description: repart_test.c was mistakenly treated as a tool, instead of a test program.
Solution: Took it out of the list of tools.
Platforms tested: fuss - simpl change.
Description: repart_test.c was mistakenly treated as a tool, instead of a test program.
Solution: Took it out of the list of tools.
Platforms tested: fuss - simple change.
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 and improvement.
Description:
The test output were not displayed for parallel tests.
The serial tests output were always displayed whether the test was
actually ran this time or not.
Solution:
Moved the display of test output inside the target where the actual
tests are run.
Platforms tested:
Tested in heping using pp and fortran.
Bug fix and code minor cleanup.
Description:
The attempt to redirect stderr together to the log files were
done in the wrong order such that stderr output goes to where
stdout WAS. Fixed that.
Code minor cleanup--use shell variables to hold the name of the
log file and the test instead of generating them repeatedly. This
makes easier code reading, less crowded and avoid typos.
Only conclude.in is changed. The Makefile.in changes are all
derived from automake.
Platforms tested:
h5committested.
Makefile feature
Description:
'make check-clean' now cleans *.h5 files created by tests as well as
.log and .chkexe files.
Solution:
check-clean is now a separate target in its own right, which cleans less
than mostlyclean (check-clean < mostlyclean < clean < distclean).
Platforms tested:
mir, heping, modi4 (serial and parallel)
Feature: check-clean target
Description:
'make check-clean' cleans up output files from tests.
Solution:
Tests create foo.chkexe and foo.log files. Scripts create foo.chksh and
foo.logsh files. 'make check-clean' will clean these files up so that
the tests can be re-run.
Also suppressed some not-very-useful output of Makefiles when it would
echo commands.
Platforms tested:
mir, sleipnir, modi4
Misc. update:
Configuration feature
Description:
Serial test output is now stored in log files and printed when all tests
in a directory complete, or when a test fails. This should make test output
more readable and useful.
Also made changes to clean up ii_files directories that are created by some
C++ compilers/linkers.
Also fixed a few minor Makefile bugs.
Solution:
When serial tests run, their output is saved in *.log or *.logsh. While
running, tests only print when they begin and when they complete; their
more specific output (from the log file) is printed if the test fails or
when all tests have completed.
Comments welcome.
Platforms tested:
mir, modi4 (parallel and serial), copper, shanti
Bug fixes
Description:
A number of minor changes to Makefiles. Some files will now be cleaned
properly, some comments are more informative, etc.
Platforms tested:
heping, mir, modi4
Bug fix
Description:
The testh5diff.sh script fails on mcr because of random srun messages
thrown into the output
Solution:
Added some code to filter out the srun messages before the output is compared.
Platforms tested:
LLNL mcr
Misc. update:
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:
The ".chksh" file for a test script was being created in the "source"
location rather than the build location. This can cause problems when
multiple builds are running because "slower" machines will see the ".cshsh"
file from faster machines and will not run the test script as they should.
Solution:
Use 'basename' command to strip off the path of the script and create
the ".chksh" file in the build location.
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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.
bug fix
Description:
a string buffer did not had space for the trailing null
Solution:
add one more element to the buffer
Platforms tested:
linux
Misc. update:
Bug fix
Description:
Fixed bugs that caused tests to be unable to find testhdf5.sh during
daily tests, and another that broke sol and shanti.
Solution:
When tests are run, their path is ./$testname .
When scripts are run, their path has no leading "./". Fixed.
Sol and shanti don't recognize the -e option for test, but they do know
-f. Fixed.
Also modified release notes.
Platforms tested:
mir, shanti, heping
Feature: tests now use parallel make and only run once
Description:
When make is invoked in parallel (using the -j option), several tests will
now be run simultaneously. This should speed up testing on a number of
systems.
When a test passes, it creates a foo.chkexe or foo.chksh file, which prevents
the test from running again unless the test or library changes.
Solution:
Most of the changes live in config/conclude.am. Added *.chkexe and *.chksh
files to the list of files to be cleaned at "make mostlyclean" time.
Parallel tests still run one at a time, but use the same make instructions
as serial tests.
Platforms tested:
mir, eirene, sleipnir, pommier, copper, modi4 (some errors occurred, probably
due to the test being run before updating hdf5. Will re-run tests after
checkin.)
bug fix
Description:
when diffing a string type string , a cycle is made using the hdf5 get_size function, which returns
the type size
some strings might have a NULL terminator character before the type size position
this was noticed on a HDF-EOS file on the HDFEOSVersion attribute which was defined as a type with a 32 size,
but contained a string with 12 characters, making h5diff to compare the extra garbage characters
Solution:
detect the NULL terminator character and end the diff at that position
Platforms tested:
linux
Misc. update:
Bug fix for parallel case for new "Some objects were not comparable" patch to h5diff.
Description:
The parallel h5diff wouldn't print out "Some objects were not comparable" because the worker
tasks were not communicating the not_cmp flag of the diff_opt_t struct back to the manager, who ultimately
prints everything.
Also, some miscellaneous fixes for error printing. Some errors were printed out with printf instead of fprintf(stderr,...).
In parallel environments, this can result in output getting lost.
Solution:
Had the worker tasks pass along the not_cmp flag to the manager when they sent along
the number of differences they found.
Platforms tested:
heping (pp), sol (pp)
Misc. update:
modified the script test so that when the test files do not exist , they are created
Description:
Solution:
Platforms tested:
linux
solaris
Misc. update:
bug fix
Description:
when 2 objects were not comparable, the final print information for the non verbose mode printed "0 differences found"
Solution:
replaced instead with a Summary message that says
"Some objects were not comparable"
Platforms tested:
linux
solaris
Misc. update:
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: Hopefully, this is the last step of checkin for this stage. This step
mainly enables h5repart tool to be able to convert file driver from family to
sec2. Because the library saves family information in file, in trying to convert
to sec2 driver, the library simply change the address of driver information to
undefined so that the driver information block can be ignored. This step also
updates the reference manual of H5Pset_fapl_family() and h5repart.
In the fifth step of checkin, backward compatibility with v1.6
is tested. A family file created was created with the v1.6 library and opened
with this version of the library.
In 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: doc/html/RM_H5P.html and doc/html/Tools.html
Description:
while compiling in mir with pgcc -O2 a condition
if (name ) {
do_something(name);
}
is executed when name is NULL
Solution:
avoid the error by checking the NULL pointer inside do_something(name);
Platforms tested:
linux (mir with pgcc 6.0)
Misc. update:
Description: Let this short script file check whether the tests pass
and report pass or fail.
Platforms tested: fuss only - a simple change to the script file.
Description: After recent fix of family driver bug(#213), some failure
was discovered on sol and kelgia in daily test. Family files can't be
opened by hdf5/tools/misc/repart_test.c. It turned out to be the
destination size of "off_t" type wasn't passed in through H5Pset()
correctly.
Solution: In tools/misc/h5repart.c, copy the destination size to a
variable of "hsize_t" type and pass in to H5Pset().
Platforms tested: sol and kelgia where the failure was discovered.
Improvement
Description:
The actual stderr output was modified by the FILTER and was not
available for display if errors detected later.
Solution:
Copy the actual stderr to a temporary file and do filtering on that.
Platforms tested:
LANL Flash.
Misc. update:
Improvement.
Description:
assign testph5diff.sh to the Parallel test scripts so that
it will be tested for the check-p target.
Platforms tested:
heping pp.
Misc. update:
bug fix
Description:
check-s and check-p were set as pre-requistics of test. They
would get executed in parallel if parallel make is used. This
could cause problems since serial tests are used to be executed
before parallel tests. It is not known if it is always okay to
run serial and parallel tests in simultantously.
Solution:
Change check-s and check-p as actions of the target test so
that they get executed sequnentially.
Platforms tested:
heping PP.
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 check-s and check-p targets.
Description:
Added check-s and check-p targets to 1.7 branch to match changes to 1.6
branch. Now parallel and serial tests can be run separately.
Platforms tested:
mir, modi4, copper
Bug fix
Description:
Various system or software (e.g. MPE) will print some diagnosis
messages to stderr that cannot be suppressed. They messed up
the output matching. Installed the STDERR_FILTER() to remove
all these messages.
Platforms tested:
LANL flash.
Misc. update:
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 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: RELEASE.txt
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:
bug fix 366
Description:
the printing of the array indices was done relatively to the stripmine data (data read
by hyperslabs when its memory requiremnts are too large)
this was causing an incorrect numbering of the array indices (the next read would initialize
the indices to zero)
Solution:
added a field to the print context that keeps track of the stripmine position
and pass to the rendering function the total element position
Platforms tested:
Linux
Misc. update:
H5Pset_scaleoffset API is changed due to addition of the floating-point filter
Description:
Only add a parameter, nothing should change for the tool.
Solution:
Platforms tested:
Linux 2.4
Misc. update:
H5Pset_scaleoffset API is changed due to addition of the floating-point filter.
Description:
Only add a parameter, nothing should change for the tool.
Solution:
Platforms tested:
Linux 2.4
Misc. update:
Update usage of H5Pset_scaleoffset.
Description:
H5Pset_scaleoffset API is changed due to addition of the floating-point filter.
Solution:
Only add a parameter, nothing should change for the tool.
Platforms tested:
Linux 2.4
Misc. update:
Bug fix
Description:
Remove declaration of 'prefix' variable that was moved into the h5tools
library.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/CC=g++
Too minor to require h5committest
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)
Code cleanup
Description:
Clean up various warnings reported by the Windows team.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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
Configuration feature
Description:
Different Fortran compilers mangle function names in different ways
(upper case, lower case, adding underscores). To link between
Fortran and C functions, we need to know what a given function's
name is under a given compiler.
Solution:
Use autoconf's FC_WRAPPERS check to determine the Fortran
naming scheme and define the FC_FUNC_ macro to name our
functions (in H5f90proto.h). Removed references to
our old FNAME macro, as well as flags that indicated whether
function names were upper or lower case.
Platforms tested:
mir, pommier, modi4, copper, more
Bug fix
Description:
On some machines, $RUNSERIAL variable needs to be used to run
tests. Set $RUNTESTS (which is used for non-parallel tests) to
be $RUNSERIAL in configure.am.
Also, since I was updating all Makefiles.in anyway, I updated
commence.am to point to autotools installs in AFS instead of
those on heping.
Platforms tested:
mir, sleipnir, modi4, copper
Purpose:
"Bug fix"
Description:
Hardcoded Makefiles to use /bin/sh instead of letting configure
detect shell automatically. This is what v1.6 does, and avoids
problems on janus.
Platforms tested:
sleipnir, copper, modi4, mir
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)
Feature - conditional compilation
Description:
SRB file driver and tests are now compiled only when SRB is enabled
(using --with-srb during configure).
Solution:
Added an automake conditional in configure.in, altered Makefiles.am in
src and test directories to depend on that conditional.
This should make a nice example for posterity to add conditionally
compiled sources.
Platforms tested:
heping (only configure change)
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:
Bug fix
Description:
Typo in #ifdef to check for snprintf functionality.
Solution:
That should have been H5_VSNPRINTF_WORKS.
Platforms tested:
heping, modi4
Misc. update:
Purpose:
Bug fix.
Description:
ph5diff fails on modi4 due to the way snprintf works on IRIX.
Solution:
The C99 standard says that, if there isn't enough room in the string,
snprintf should return the number of characters that
would have been written to the output string if there were enough room.
The snprintf on modi4 would return the number of characters that is was able to write
succesfully to the string if space ran out. The ph5diff logic that checks if
the output buffer was full did not handle this sort of return value correctly.
Used VSNPRINTF_WORKS from configure test to check how snprintf works and do
the logic accordingly.
Platforms tested:
modi4
Misc. update:
New feature
Description:
Add new "block tracker" data structure to library, for tracking blocks of
bytes in a file. Block trackers will be used to keep track of the blocks
belonging to the soon-to-be-implemented "segmented heap" which is designed to
replace the current local & global heaps (starting with the local heap).
Block trackers will also keep track of the free space in the segmented heap
and someday could be used to track the free space in the entire HDF5 file.
They are implemented as a small header of information to cache the state
of the blocks (max & min sizes of blocks tracked, etc.) and the records of
the blocks themselves are stored in a v2 B-tree.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
h5committest
Bug Fixes
Description:
Fixes for several bugs, including dumping of excess output to a temporary file, fix for printing
hsize_t datatype, and the long awaited fix for intermixed output.
Solution:
Fix 1: Overflow file
Previously, any output that a worker task made was buffered locally in memory, up to a point. Any
output beyond the size of the buffer (used to be 10k) was discarded. Now, the memory buffer size has been
changed to 1k and any output beyond this amount is sent a temporary file. This way, no output is lost
and memory usage is kept under control. The temporary file is deleted as soon as a worker task finishes
sending its contents to the manager.
Fix 2: hsize_t printing
Printing of the hsize_t datatype used to be handled by %Hu passed to HDfprintf. However, there is no corresponding HDvsnprintf that
is able to print hsize_t types. These are now printed with the aid of H5_PRINTF_LL_WIDTH.
Fix 3: Intermixed output fix
Intermixed output would occur on some machines (although I haven't seen it happen for a while) due to the unpredictability of the underlying network
and the speed at which various message would travel. This has been fixed by having all output send to the manager
for printing. The worker tasks no longer print the output themselves upon receipt of a token, but instead
send that data to the manager.
Platforms tested:
heping, eirene, tg-login (the only place that seems to still experience intermixed output every now and then)
Misc. update:
Automake version upgrade
Description:
Upgraded automake version from 1.6.2 to 1.9.5.
Changed bin/reconfigure script to use automake 1.9.5.
Changed configure.in and Makefiles to use new FCFLAGS and FC variables
instead of FFLAGS and F9X.
Automake and configure should now do the lion's share of the work
supporting Fortran 9X; macros in acsite.m4 are now mostly unused (will
be cleaned later).
Altered how configure handles pmake; now root-level Makefile.in is
processed by bin/reconfigure to have a .MAKEFLAGS target, since
automake no longer allows us to define unused variables.
Configure now always checks for C++ compiler even if it is not
used, since automake thinks this is the Right Thing To Do and
will break otherwise.
Platforms tested:
Sol, copper, heping, mir, sleipnir, eirene, pommier, kelgia, modi4.
Bug fix
Description:
The GASS VFL driver header file was bringing in the <string.h> header file,
which several other source code modules needed also, but weren't including
explicitly themselves.
Solution:
Add includes for <string.h> to files which actually need them.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/C++ as CC
Configuration not tested by h5committest...
Bug fix.
Description:
MPI_LONG_LONG, which is not standard yet, was used to pass the
nubmer of differences found. This was needed because number of
differences is defined as type hsize_t which can be arbitary large
such that there is no MPI type that matches it. The value is passed
between processes as an array of bytes in order to be portable. But this
may not work in non-homogeneous MPI environments.
This fix was actually Leon's idea.
Platforms tested:
Tested in QSC in which this failed.
Removed GASS configuration and software packages associated with
it. The following software are no longer configurable.
checking for main in -lcrypto... yes
checking for SSL_get_version in -lssl... yes
checking globus_common.h usability... yes
checking globus_common.h presence... yes
checking for globus_common.h... yes
checking for globus_module_activate in -lglobus_common... yes
checking for main in -lglobus_gass_cache... yes
checking for main in -lglobus_gaa... yes
checking for main in -lglobus_gss... yes
checking for main in -lglobus_gss_assist... yes
checking for main in -lglobus_io... yes
checking for main in -lglobus_gass_transfer_assist... yes
checking for main in -lglobus_gass_transfer... yes
checking for globus_gass_open in -lglobus_gass_file... yes
Platforms tested:
h5committested (but copper was down.) tested in modi4 too.
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
Description: On SGI Altix(cobalt) Linux, wrong values were printed out for enum data type
members. No apparent reason was discovered.
Solution: use another pointer to the buffer containing the member value. It seems fix the
problem.
Platforms tested: cobalt - simple change, where the bug was discovered.
bug fix.
Description:
When MPE library is used, it prints two extra message lines that
interfere with the expected output.
Solution:
Filter out those two lines of text from stderr.
Also added a provision to print the whole generated output when failure
is detected.
Platforms tested:
Tested in copper, serial, parallel and parallel with MPE.
Misc. update:
bug fix/new feature.
Description:
(committing changes made by Leon.)
ph5diff now is a real program by itself. It has its
own main (ph5diff_main.c).
Codes common to h5diff and ph5diff are in h5diff_common.c.
Removed the hack that hide failures from testh5diff.sh.
Platforms tested:
heping(serial, pp), sol (pp), copper(pp).
Misc. update:
Purpose:
Bug fix
Description:
modi4 dies during build with strange errors.
The root cause of these is a two-year-old hack in HDF5's libtool
script that only takes effect on IRIX.
Solution:
Edited the libtool hack (by editing ltmain.sh) to correct a bug in
the hack.
Also made sure that compiler-specific DEFAULT_LIBS are used
when linking.
Platforms tested:
sleipnir, copper, modi4, sol
Bug fix.
Description:
ph5diff is still being fixed.
Changed this to report all failures but will not flag them as
errors so that daily tests can continue. Will be fixed soon.
Platforms tested:
Tested in sol (pp) where it has most failures.
Misc. update:
bug fix
Description:
in 1 case when there was not a requested layout, the original chunk was not preserved
Solution:
Platforms tested:
linux (small change)
Misc. update:
Purpose:
Bug fix
Description:
Fixed the error on copper where output would match, except the worker tasks are forcefuly terminated at the end.
Solution:
If an exit code other than 0 was returned, the
parallel environment would assume that there
was an error and would terminate all other
tasks. Because h5repack relies on the return
value of h5diff, it was necessary to return
values other than 0. Fixed by having parallel
runs of h5diff always return 0, whereas the
return value of serial runs is unchanged.
Platforms tested:
copper
Misc. update:
Bug fix
Description:
Arabica exhibited strange errors when linker found wrong versions of
header files. This happened because include directories were
given to linker in the wrong order.
Solution:
Move include directories from AM_CFLAGS variable to INCLUDES
variable to put them before CPPFLAGS variable. Trust me, it works.
This bug may also have contributed to strange errors on other platforms
(kelgia?).
Platforms tested:
copper, sleipnir, arabica.
(h5dump broke while building on arabica, but this happened in
a clean checkout, too).
Bug fix
Description:
pmake (on modi4, for instance) complains about undefined variables
if it is run without the -V flag, which turns those errors to warnings.
Solution:
Added test to configure.in to see if $MAKE will allow Makefiles
with undefined variables. If not, sets -V flag in AM_MAKEFLAGS.
Ensured that all custom make targets use AM_MAKEFLAGS.
Also defined all variables that caused errors in top-level Makefile.am.
This means that pmake can be used to build hdf5 *from the top level
only*. To run make from a subdirectory, still need to use -V flag
(or use make or gmake).
Platforms tested:
modi4, heping, copper, sleipnir
bug fix.
Description:
Need eval before the RUNCMD command because some machines like
AIX, has RUNPARALLEL in the style as
MP_PROCS=3 MP_TASKS_PER_NODE=3 poe ./a.out
that throws the shell script off.
Platforms tested:
Tested in copper (pp) where it failed before.
Tested in heping pp too.
Misc. update:
Bug fixed.
Description:
Heping used to have a network limit that if too many rsh connections
occurred in a second, it stopped accepting connections for 30 seconds.
That caused testph5diff to fail when too many mpi jobs are executed
repidly. A sleep 2 was in to go around this problem. Heping's limit
has been raised, thus no more need for this hack. Sleep 2 is removed.
Platforms tested:
Tested in heping (pp).
Misc. update:
Correction to previous print_manager_output bugfix
Description:
Although the previous bugfix did fix all the errors, it was not the correct way
to fix the problem. Since the manager will only buffer output when run in
parallel mode, in serial mode this function should not even be called.
Solution:
Wrapped print_manager_output in #define's to prevent it from being included in
serial builds.
Platforms tested:
heping (serial + parallel)
Misc. update:
Purpose:
bug fix
Description:
a string with 2 characters was declared as having size 2. changed to size 3 (+ null character)
this was causing compiler warnings with g++
Solution:
Platforms tested:
linux
free bsd (g++)
Misc. update:
bug fix
Description:
g++ was not happy with missing protocols of external functions.
Added print_manager_output(void) and phdiff_dismiss_workers(void)
to the public declarations.
Platforms tested:
Tested in sleipnir (g++) and heping (serial, pp)
Misc. update:
Purpose:
bug fix, new test file
Description:
h5dump was not properly displaying array indices > 3D
Solution:
added the same algorythm and data structure that h5diff uses to calculate the array index
from a element number position
Platforms tested:
linux
solaris
Misc. update:
Bug fix.
Description:
print_manager_output was missing because it was compiled in
only parallel mode.
Solution:
Made it available all the times.
Platforms tested:
h5committested. (testph5diff.sh failed in copper but that
is a different error.)
Also tested in heping, serial and pp.
Misc. update:
Fixed numerous ph5diff bugs.
Description:
Fixed manager output printing
Fixed out of order output printing
Fixed test script execution problem
Temporary fix for large amounts of output overflowing buffer.
Solution:
The manager task buffers its output. However, since the manager task
never gets a print token, this output was lost. Solution: new function called
print_manager_output that prints buffered output is called in places where the
manager buffers its output.
printf was apparently buffering output. This means that a task would sometimes
print even after it had given up its print token. Added fflush() call after
printf() calls, which seems to have fixed the problem.
calling rsh multiple times in succession seems to overwhelm something in Linux,
as it begins to refuse new connections until the old ones reset. Since each
call to mpirun in the test script starts up 4 rsh sessions, the test script
eventually is unable to run any further tests. Solution: Added a short delay in the
testscript between successive calls to mpirun to allow old connections to reset.
The 10k output buffer was of insufficient size to hold the large amounts of
output generated by some of the tests. Since code to buffer to a file has not
been implemented yet, a temporary fix was to increase the size of the output
buffer to 50k.
Platforms tested:
heping
Misc. update:
Description: The byte order for all 1-byte integer types was fixed as little-endian
even on a big-endian machine. This's corrected in h5detect.c. When types are only
1 byte long, a native int is used substitute the type to detect byte order. Some tools
like h5dump and h5repack are also corrected in this case.
Platforms tested: fuss, copper, sol.(There're some failures from the recent configure
change).
Misc. update: Information in the RELEASE.txt.
Bug fix
Description:
h5diff sometimes will 'exit(status)' but if it is in parallel mode,
it needs to close up the workers and the MPI environment before exit(..).
Solution:
Created h5diff_exit() that will just exit in serial mode but does all
the shutdown properly if in parallel mode.
Platforms tested:
tested in heping, serial and parallel.
Misc. update:
Feature
Description:
Added a new function, phdiff_dismiss_workers, which tells the phdiff
worker processes to end.
Platforms tested:
Tested in heping, serial and parallel.
Misc. update:
Bug fix
Description:
h5diff_main.c contained some debug printf statment that produced
unexpected output. Commented them out.
testh5diff.sh: implemented code to test ph5diff tests but
ph5diff has some errors that generated unexpected output.
Temporary hacked to skip tests if run by daily test account.
Platforms tested:
Tested in heping, serial and parallel.
new features
Description:
Added a parallel option to testh5diff.sh to do parallel h5diff tests.
Added testph5diff.sh to invoke testh5diff.sh with parallel mode.
Platforms tested:
Tested in heping (serial and pp).
Purpose:
Bug fix
Description:
Parallel builds were breaking in tools/lib
Solution:
talign didn't realize it depended on libh5tools.la because its
dependencies listed the full path (../../tools/lib/libh5tools.la).
Changed this, and made similar changes in a couple of other
directories.
This checkin should also add the --foreign flag to every Makefile.in
Platforms tested:
sleipnir (minor change)
Features
Description:
Added the option to build ph5diff and run testphdf5.sh when
parallel mode is enabled.
Platforms tested:
tested in heping, both serial and parallel.
Misc. update:
New feature
Description:
Add basic code for new B-tree implementation. They don't do much yet,
aren't hooked up to anything yet and the format may change, but I'd like to
start getting them into the daily tests.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/parallel
Too minor to require h5committest
Bug Fix
Description:
Permanent fix for the incompatibilities between h5diff and h5repack.
Solution:
h5diff now contains the code to run both parallel and serial diffs.
Depending on how the binary is called, it will run either the serial or
the parallel versions respectively.
Platforms tested:
heping(serial + parallel), copper.
Misc. update:
Bug fix (#56)
Description:
h52gif creash for data > 1 byt
Solution:
check datatype and return with error message if not 1 byte int
Platforms tested:
shanti,verbena
Misc. update:
Bug fix
Description:
Found the permanant fix to automake/CVS dependency problem
Solution:
Added AM_MAINTAINER_MODE macro to configure.in.
Now automake will never try to regenerate Makefiles, Makefiles.in,
configure, H5config.h, etc. when they are out of date, nor will it
print any warnings.
Developers should be very very careful to use reconfigure script,
and can add --enable-maintainer-mode flag to configure on heping
to regenerate these files correctly.
Platforms tested:
heping sleipnir copper
Bug 181
Description:
Attributes written incorrectly.
Solution:
Do them right, as in H5IM.c
Platforms tested:
verbena, output checked on windows.
Misc. update:
Bug fix
Description:
Configuration files' timestamps were incorrect.
Solution:
Update Makefiles.in. Also added correct paths to autotools on heping,
so heping build should be able to re-generate configuration files even
if they are still broken.
Platforms tested:
sleipnir
Bug fix
Description:
Dependencies between configure files (aclocal, configure.in, configure,
Makefiles.am and .in) are still causing Makefiles to try to run autotools
during build.
Solution:
Committed all Makefiles.in to update their timestamps.
As a temporary measure, forcibly prevented automake from running
autotools during build by redefining the variables it uses.
Platforms tested:
sleipnir (No changes to Makefile content)
Bug fix
Description:
Different compilers use different flags to include Fortran module files
Solution:
Changed boilerplate to use configure variable rather than hardcoded -M flag.
Platforms tested:
sleipnir, sol, copper
fix bugs.
Description:
The three variables, g_nTasks, outBuff, and outBuffOffset, were
declared in ph5diff.h. That means they are declared in various
*.c files that include it, thus having the appearance of multiple
defined. Most C compilers are forgiving of this error but
the g++ rejects this practice.
Solution:
Make it only an extern declaration in ph5diff.h but really
defined them in h5diff_util.c
Platforms tested:
sleipnir using g++ since this only failed in Daily test.
Also testes in heping, serial and parallel modes.
Configuration feature
Description:
HDF5 now uses automake to generate Makefiles
Solution:
Makefile.in files are now generated from Makefile.am files.
To reconfigure (after chaning a Makefile.am or configure.in):
/bin/sh bin/reconfigure.sh
Platforms tested:
Many
Temporary daily tests fix.
Description:
The newly added ph5diff is not quite compatible with the h5repack tool.
Disabled the ph5diff build (reverted back to building serial h5diff)
to allow daily tests to work while ph5diff is fixed.
Platforms tested:
Tested in heping both serial and parallel modes.
Misc. update:
bug fix
Description:
calling h5diff from the h5repack test script running mpicc , the path of one of the files was not found
Solution:
inserted the full path in the script
Platforms tested:
linux (with mpicc and gcc)
Misc. update:
Description:
the print_paralell h5diff function had a call to vsnprintf.
this causes a linking error on Windows
Solution:
replaced with HDvsnprintf
Platforms tested:
windows (vs6)
linux
Misc. update:
Bug fix: Temporary fix for h5repack failures in all parallel builds.
Description:
The parallel additions to h5diff interfered with h5repack.
Solution:
Added a second set of "parallel" functions to h5diff.c. h5repack uses the serial versions, whereas h5diff will use the parallel versions.
Also, h5diff will now be smart about when to enter parallel mode. If is run with mpirun with more than 1 task, it will enter parallel mode. Otherwise, it will stay in serial mode as before.
Platforms tested:
heping (serial and parallel)
Misc. update:
New feature.
Description:
Added new tool ph5diff. (Code done by Leon Arber.)
Code is changed but test is not working yet. For now,
it skipped all tests.
Platforms tested:
Tested in heping, serial and parallel modes.
Bug fix
Description:
In an earlier bug-fix, I inadvertently inverted the meaning of the
"% utilization" in h5ls.
Solution:
De-invert it. :-)
Platforms tested:
FreeBSD 4.10 (sleipnir)
Too minor to require h5committest
Remove feature
Description:
Retire threaded, balanced binary tree code from HDF5 use. Requiescat in
pace...
Also, regenerate dependencies files.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require full h5committesting (the code is already
disconnected from everything except its tests)
Bug fix.
Description:
When building h5dumpgentest.c with Visual C++ 6.0, I got the following warning message:
h5dumpgentest.c(4528) : warning C4013: 'h5tools_can_encode' undefined; assuming extern returning int
Solution:
Add the header file h5tools.h into h5dumpgentest.c.
Platforms tested:
Heping (Linux)
Visual C++ 6.0 on Windows XP/2000.
.NET on Windows XP.
(Tested with SZIP-with-encoder and SZIP-without-encoder).
Misc. update:
Bug fix.
Description:
creat(name, (mode_t)0777) is used to create a new file. However, creat() is not available in Visual Studio.
Solution:
Use a Win32 macro so _creat() will be used on Windows and creat() will be used on Unix.
#ifdef WIN32
fd = _creat(name, _S_IREAD | _S_IWRITE);
#else /* WIN32 */
fd = creat(name,(mode_t)0777);
#endif /* WIN32 */
(Note: At first, I tried to define HDcreat() as _creat() for WIN32 and creat() for other platforms in H5private.h. But _creat() and creat() use different parameters for file permission settings. So, I added the WIN32 macro in h5jamgentest.c.)
Platforms tested:
Heping (Linux)
Visual C++ 6.0 on Windows XP/2000.
.NET on Windows XP.
(Tested with SZIP-with-encoder and SZIP-without-encoder).
Misc. update:
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:
bug fix
Description:
added a condition that checks if the hl library is enabled to add it to the list of linking libraries
Solution:
Platforms tested:
linux
Misc. update:
modified h5cc to link with the high level library (libhdf5_hl)
Description:
added libhdf5_hl.a to the list of libarries to link with
Solution:
Platforms tested:
linux
Misc. update:
new feature
Description:
when requesting a filter for all datasets and the filter cannot be applied for one dataset
use the original dcpl withou filter and print a warning
this check was done previously with buit in functions for szip that are now in the library
Solution:
Platforms tested:
linux
solaris
aix
Misc. update:
bug fix
Description:
the routine for applying the layout for the new file of h5repack was not
handling the logic correctly in cases where an input layout was not set
Solution:
changed the logic so that the original layout is preserved
(this bug was introduced in the last change, October 19 04)
Platforms tested:
linux (small change)
Misc. update:
Bug fix (#264)
Description:
h5dump did not print attribute data in ASCII format when
-r is used.
Solution:
Added the ability to print in ASCII for Attributes Data also.
Added a test for printing Attributes with -r option.
tall-2B.ddl is the standard output for printing attributes with -r option.
Platforms tested:
H5committested.
Also in heping.
Misc. update:
Update MANIFEST.
Bug fix (#264)
Description:
h5dump did not print attribute data in ASCII format when
-r is used.
Solution:
Added the ability to print in ASCII for Attributes Data also.
Added a test for printing Attributes with -r option.
Platforms tested:
H5committested.
Also in heping.
Misc. update:
Update MANIFEST.
enhanced performance for h5diff
Description:
the comparison cycle for the 2 buffers read from file was using a compare function
where the type must be checked for each datum (e.g due to recursive calls in compound types)
for atomic types this checking can be avoided
Solution:
introduced cycles for each one of the atomic integer and float class types
Platforms tested:
linux
aix
solaris
Misc. update:
Description: H5Pset_fapl_family sets family member size only for creating
new file. The file doesn't keep this size information. When the file is
re-opened, the size of first member file is used as the member size.
Solution: Assume user knows the original member size and sets it through
H5Pset_fapl_family. That will be the member size. User can pass in value 0
as member size if he doesn't know the original member size. Library will
choose the size of current first member size as the member file size.
Platforms tested: h5committest and fuss.
Fix SZIP filter to dynmically detect encoder.
Description:
Solution:
See:
http://hdf.ncsa.uiuc.edu/RFC/SZIP/Szip_dynamic_12_Oct.pdf
Changes to h5repack tests, contingent on detecting SZIP encoder.
Note new program:
testh5repack_detect_szip
Checks fo rencoder, prints out "yes" or "no". Used by hrepack.sh
to detect encoder. Can also be used for windows tests. This is
only used as part of the tests.
Had to modify Makefile to build and clean this program.
Make talign work on windows.
Description:
msvc++ uses _unlink instead of unlink.
Solution:
change the code to use HDunlink and include H5private.h(Not good?).
Platforms tested:
windows, Linux 2.4
Misc. update:
Bug fix
Description:
Correct values used in "space utilization" equation: the 'used' and
'total' values were backwards.
Platforms tested:
FreeBSD 4.10 (sleipnir)
Too minor to require h5committest
bug fix
Description:
Description:
one case was not handled in the combination of input options (layout and filters)
Solution:
redo the algorythm that handles all cases
Solution:
Platforms tested:
linux
Misc. update:
bug fix
Description:
when specifying both an input object e.g -f mydset:GZIP=1 and a defined chunk -l CHUNK=20x20
the filter used a defined default chunk instead
Solution:
add a check for the input chunk
Platforms tested:
linux (small change)
Misc. update:
The script does not use $RUNSERIAL to execute programs.
This failed badly in parallel systems like Tflops.
Patched $RUNSERIAL in to make it work.
Tested in tflops only.
Bug fix
Description:
Correct a couple of array bounds issues exposed by the PGI compiler
Platforms tested:
Linux 2.4 (verbena) w/PGI compilers
Too minor too requie h5committest
Refactor code
Description:
Refactor common code for determining the native type for using in the
tools into separate routine.
Also, reduce diffs between the two branches and bring back some fixes from
the development branch to the release branch.
Platforms tested:
FreeBSD 4.10 (sleipnir)
too minor to require h5committest
Purpose: change feature
Description: Back up support bitfield and time datatypes in H5Tget_native_type.Leave it to future support. Let it return "not supported" error message for
now.
Platforms tested: h5committest and fuss.
Misc. update: RELEASE.txt
Purpose:
Feature
Description:
Datatypes and groups now use H5FO "file object" code that was previously
only used by datasets. These objects will hold a file open if the file
is closed but they have not yet been closed. If these objects are unlinked
then relinked, they will not be destroyed. If they are opened twice (even
by two different names), both IDs will "see" changes made to the object
using the other ID.
When an object is opened using two different names (e.g., if a dataset was
opened under one name, then mounted and opened under its new name), calling
H5Iget_name() on a given hid_t will return the name used to open that hid_t,
not the current name of the object (this is a feature, and a change from the
previous behavior of datasets).
Solution:
Used H5FO code that was already in place for datasets. Broke H5D_t's, H5T_t's,
and H5G_t's into a "shared" struct and a private struct. The shared structs
(H5D_shared_t, etc.) hold the object's information and are used by all IDs
that point to a given object in the file. The private structs are pointed
to by the hid_t and contain the object's group entry information (including its
name) and a pointer to the shared struct for that object.
This changed the naming of structs throughout the library (e.g., datatype->size
is now datatype->shared->size). I added an updated H5Tinit.c to windows.zip.
Platforms tested:
Visual Studio 7, sleipnir, arabica, verbena
Misc. update:
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
bug fix
changed some datset names for h5repack etsts
Description:
Description:
the dataset region reference data was not portable between the Cray T3E and other machines
Solution:
this was due to the fact that the buffer to store the heap ID and index was using a sizeof(int) for its
size
4 is used instead of sizeof(int) to permit portability between
the Crays and other machines (the heap ID is always encoded as an int32 anyway)
Solution:
Platforms tested:
linux
aix
solaris
Misc. update:
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
h5repack test
Description:
modified a test file generation contents, for more easy debugging
(generated just one reference dataset and one region reference )
Solution:
Platforms tested:
linux
aix
solaris
Misc. update:
new test
Description:
added a test that generates and copies a file with a dataset with fill value
(this is to test the property list function H5Pequal)
Solution:
Platforms tested:
linux
solaris
aix
Misc. update:
new feature
Description:
added a check that the chunk size must be smaller than pixels per block in SZIP request
prints a message and exits, if not met
Solution:
Platforms tested:
linux
aix
solaris
Misc. update:
Update.
Description:
Make some minor change so that h5jamgentest.c is compatible with Windows.
Solution:
Change open() and write() functions to HDopen(), and HDwrite().
Platforms tested:
Windows 2000
Windows XP
eirene
(Note: I talked with Bob and Kent about these changes before check-in)
Misc. update:
Update.
Description:
Make some minor change so that tellub.c is compatible with Windows.
Solution:
1. unistd.h is not available in windows system. Add a macro for this header file as:
#ifdef H5_HAVE_UNISTD_H
#include <unistd.h>
#endif
2. Change open, read, write, lseek functions to HDopen, HDread, HDwrite, and HDlseek,
as these HD functions are more comtatible with Windows system.
3. add #include H5private.h
4. remove #include <stdlib.h>
Platforms tested:
Windows 2000
Windows XP
eirene
(Note: I talked with Bob and Kent about these changes before check-in)
Misc. update:
Update.
Description:
Make some minor change so that h5jam.c is compatible with Windows.
Solution:
1. unistd.h is not available in windows system. Add a macro for this header file as:
#ifdef H5_HAVE_UNISTD_H
#include <unistd.h>
#endif
2. Change open, read, write, lseek functions to HDopen, HDread, HDwrite, and HDlseek,
as these HD functions are more comtatible with Windows system.
3. add #include H5private.h
4. remove #include <stdlib.h>
Platforms tested:
Windows 2000
Windows XP
eirene
(Note: I talked with Bob and Kent about these changes before check-in)
Misc. update:
Update.
Description:
Make some minor change so that h5jam.c is compatible with Windows.
Solution:
1. unistd.h is not available in windows system. Add a macro for this header file as:
#ifdef H5_HAVE_UNISTD_H
#include <unistd.h>
#endif
2. Change open, read, write, lseek functions to HDopen, HDread, HDwrite, and HDlseek,
as these HD functions are more comtatible with Windows system.
3. add #include H5private.h
4. remove #include <stdlib.h>
Platforms tested:
Windows 2000
Windows XP
eirene
(Note: I talked with Bob and Kent about these changes before check-in)
Misc. update:
bug fix
Description:
the option CHUNK:NONE (remove chunking ) was not setting the layout to contiguous
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Bug fix
Description:
Correct compilation errors w/--enable-hdf5_v1_6 and using the C++ compiler
as a C compiler
Platforms tested:
FreeBSD 4.10 (sleipnir) w/above flags
Not tested with h5committest
Adding new 'jam' utility
Description:
New utility, plus changes to makefiles
Solution:
See http://hdf.ncsa.uiuc.edu/RFC/Jam
Platforms tested:
verbena (fortran,C++), arabica, hirdls (SGI Irix64)
Misc. update:
Manifest will be done in next checkin.
Purpose: Small bug fix
Description: When SZIP filter is present but encoding is not enabled
test_misc21 and h5repack tests failed.
Solution: Those tests should not run in this situation at all.
Used conditonal compilation to disable the tests.
Platforms tested: sol (today I will enable the daily tests with the szip library
that doesn't have encoder for few other platforms)
Misc. update:
bug fixes
Description:
the return error code for a function was not initialized.
in HP-UX it happened that this variable was initialized to -1
causing the function to return with an error condtion
solution : initialized the variable to 0
the name of the dataset was printed after the differences in verbose mode
and report when differences were found
solution : check first if differences were found and then
print the name of dataset and differences
in verbose mode always print the name first
Solution:
Platforms tested:
linux
aix
solaris
Misc. update:
update documentation and usage message
Description:
updated the html documentation for the new h5diff modes
added a section for h5repack
Solution:
Platforms tested:
linux
Misc. update:
h5diff and h5repack changes
Description:
h5diff
introduced the following four modes of output:
Normal mode: print the number of differences found and where they occured
Report mode: print the above plus the differences
Verbose mode: print the above plus a list of objects and warnings
Quiet mode: do not print output (h5diff always returns an exit code of 1 when differences are found)
h5repack
added an extra parameter for SZIP filter (coding method)
the new syntax is
-f SZIP=<pixels per block,coding>
(pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN')
Example of use:
./h5repack -i file1 -o file2 -f SZIP=8,NN -v
updated usage messages, test scripts and files accordingly
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
bug fix, new feature
Description:
fixed bug in the parse function:
cases where we have an already inserted name but there is a new name also
example:
-f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20
dset1 is already inserted, but dset2 must also be (it was not)
added a CHECK_SZIP symbol to enable/disable checking of library related szip parameters
added the print of the filter name in verbose mode (confirms visually that the filter was applied )
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
h5repack changes
Description:
there were some requests to change some minor h5repack features
h5repack only made a warning about a non available filter in verbose mode ( -v )
without -v it kept silent, and users sometimes missed this warning
the request was that it should print this warning always. so, the new format, is e.g
./h5repack -i test_szip.h5 -o out.h5
Warning: dataset </dset_szip> cannot be read, SZIP filter is not available
due to this, and to avoid a lot of these messages in the shell test script, I modified
the script h5repack.sh so that it detects the presence of all filters in the environment
(previously it only detected SZIP)
the test files were also divided in more files , to make the script code easier to
follow
Solution:
Platforms tested:
linux
AIX (no szip)
solaris (no szip, no gzip )
Misc. update:
h5dump new tests
Description:
added new tests for the print of array indices (nested objects, several ranks)
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
bug fix
Description:
when printing array indices , the calculation of the current column was not done correctly
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
h5dump new tests
Description:
added more tests for the escape/not escape feature for string data (with vlen, with
compound, with char data)
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
h5dump new tests
Description:
added new tests for the -p option, superblock, file contents, fill values, array indices.
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
change features
Description:
for the file contents dump and for hardlinks, one arrow "->" is printed, followed
by the first found name for that object
options for not printing specific types of objects were postponed
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Description:
the original code that showed a name for HARDLINK was reassigning that name to a name
made in the dump traversal (made by concatenation by nested objects)
Solution:
removed this reassigmnet
now the name showed after HARDLINK is always the first name found for that object
(this object is printed once interely; subsequent printings show the word HARDLINK
and the first name )
Platforms tested:
linux
AIX
solaris
Misc. update:
Code cleanup
Description:
Clean up almost all warnings from Windows builds.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
Purpose:
HDF5 now supports SZIP with no encoder.
Description:
SZIP can be configured to have both encoder and decoder or just to have the decoder. HDF5 can now query the configuration of any filter, and will throw errors if users try to write using a filter with encoding disabled.
Solution:
Added H5Zget_filter_info function, changed API for H5Pget_filter and H5P_get_filter_by_id. See SZIP RFC.
Platforms tested:
Copper (fortran, C++, parallel), Sleipnir (C++), Arabica (fortran, C++), Verbena (fortran, C++)
Misc. update:
bug fix
Description:
the indentation was not made properly for nested objects when printing array indices
Solution:
added the indentation to h5tools_simple_prefix function
Platforms tested:
linux
AIX
solaris
Misc. update:
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
h5dump new feature, bug fix
Description:
added the dump of unmamed types to the file contents
fixed a bug in the type array, it was printing invalid characters with the array indices option on
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
dumper new features
Description:
1) added options for not printing : datasets, groups, datatypes, links
2) added a section for the user block
3) in the traversal routine, added the printing of an arrow for soft links and t
he word HARDLINK for hardlinks
the print of the file contents is made during traversal , instead of at the e
nd of it (this is helpful
for very large files, where the wait time can be very long)
4) changed the description of the fill value properties
5) added a colon after the printing of the array indices
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
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
h5dump output change, new tests
Description:
the storage layout output format the storage layout output format had some changes
same for the user defined filter
add an option (-y) for not printing the array indices (default is print indices )
the option for escaping non printable characters covers all characters (default is not escape)
(this might be not very portable, the test files are tstring.ddl and tstringe.ddl )
add tests for the new options
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Description: After I added H5S_NULL dataspace to dumper test, the output violate
XML schema for attribute data.
Solution: changed.
Platforms tested: RH8(fuss), minor change, only dumper is involved.
h5dump new feature
Description:
add processing of tab characters (in the context of the new option process CR/LF)
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
bug fix
Description:
a prototype for a new function used by h5tools_str.c was accidently left in that file
the c++ treats this as an error
Solution:
removed the prototype, and pointed to the correct one (in h5tools_ref.h )
Platforms tested:
Free BSD (c++)
linux
Misc. update:
Code cleanup
Description:
Add more files that should be removed to the clean & distclean targets.
Platforms tested:
FreeBSD 4.10 (sleipnir)
Too minor to require h5committest
bug fix
Description:
the file tfilters.h5 was missing the szip dataset, due to a absent szip configuration when
it was generated
Solution:
generated it it again with szip on
Platforms tested:
linux (smalll change )
Misc. update:
h5dump update
Description:
updated the h5dump test files generator , so that it coincides with the 1.6 branch
Solution:
Platforms tested:
linux (small)
Misc. update:
Description:
added the code for print strings with new line and display the path of references (new source files h5tools_ref.c and .h )
added a test suite in testh5dump.sh.in for
( note : to create testh5dump.sh , one must redo ./configure; this detects the availability of filters
and generates testh5dump.sh accordingly)
1) storage layout
2) fill value
3) print reference with path
4) print strings with new lines
5) filters
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Bug fix
Description:
Correct path to new testh5dump.sh, now that it's generated.
Platforms tested:
FreeBSD 4.10 (sleipnir) w & w/o srcdir
Too minor to require h5committest
Update shell scripts
Description:
Switch to generating the testh5dump.sh script at configure time, so we can
determine which filters are available to test.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too small to require h5committest
h5dump new version
Description:
added the changes already made for 1.6
support for dumping of
1) filters
2) storage layout
3) fill value
4) comments
5) superblock
6) file contents
7) array indices
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Refactor code
Description:
Move chunk and contiguous cached raw data from file information to dataset
information. This simplifies a number of internal interfaces, aligns the
code with it's purpose better and should allow more optimizations to the
chunked data I/O performance.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir)
h5committest
bug fix
Description:
Currently h5dump test on windows won't separate error form standard output; which shows at function error_message.
A #ifdef WIN32 macro at this file make stderr to be the same as stdout on windows.
Solution:
Separate standard error from standard output.
Platforms tested:
windows xp VS 6.0(by xuan bai), no needs to test on other platforms
Misc. update:
Bug fixes
Description:
Updated dependencies
Fixed error with C++ compiler builds of main library
Added H5Pset_data_transform to MPE info
Platforms tested:
FreeBSD 4.9 (sleipnir)
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
Description:
Regenerated with older version of dataspace information, since these files
don't contain null dataspaces.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
