Bug fix
Description:
I/O on chunked datasets with point selections was not working correctly.
Solution:
Re-wrote some parts of raw data I/O routines that build the selections for
each chunk to correctly handle point selections.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Bug fix
Description:
When a non-default indexed storage B-tree internal 'K' value is set by the
user, the chunked datasets created in that file (until it is closed) use the
user's 'K' value and the data can be accessed correctly, but the 'K' value is
not stored in the file.
However, once the file is closed and re-opened, the non-default 'K' value
is lost and the data in the chunked datasets will not be able to be accessed
correctly.
Solution:
Store the indexed storage B-tree internal 'K' value in the superblock.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Code cleanup
Description:
Finish converting the B-tree 'K' values to use unsigned integers, rather
than signed ones, since negative amounts of entries in a B-tree node aren't
meaningful.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Code cleanup
Description:
Add in rest of szip "options mask" macros that were missing. Also made
"raw" options mask set by the library, instead of requiring users to always set
it.
Platforms tested:
FreeBSD 4.8 (sleipnir)
Minor tweaks too small fo h5committest
Improve test a bit
Description:
Add a small bit of testing for the array field in a compound datatype.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Cray SV1 (wind)
Cray T3E (hubble)
Cray T90 (gypsy)
Code cleanup
Description:
Include roughed-in, but commented out code for performing I/O on time
datatypes.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Cray SV1 (wind)
Cray T3E (hubble)
Cray T90 (gypsy)
Bug fix (backward compatibility)
Description:
Changes we've made during development of the 1.5.x branch had broken the
feature of allowing user's callbacks to H5Giterate to return a value
through the library back to the application which called H5Giterate.
Solution:
Better testing for this feature.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Expand test
Description:
Expanded # of dangling objects from 2 to 1000, to stress ID cleanup code
in library more.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
More tests
Description:
Added tests to make certain that failed dataset, group, named datatype and
attribute creations clean up the file space they allocated before failing.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Refactored code
Description:
Moved duplicated "get_file_size()" function from a couple of tests into a
central location.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Improved tests
Description:
Added test for dangling attributes.
Also added code to test with weak, semi & strong file close degrees for
all tests.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Test bug fix
Description:
The fill time in a dataset with no fill value information created with an
older version of the library was getting set to H5D_FILL_TIME_ALLOC instead of
the new default H5D_FILL_TIME_IFSET and was causing H5Dcreate() calls with that
dataset creation property list to fail now.
Solution:
Set the new default in the fill time initialization for missing fill value
information.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Driver error
Description:
The tmtimeo.h5 file was supposed to have been generated from gen_old_mtime.c
which was compiled with a pre-1.5.x version of the library, however it appears
to have been created with a newer version of the library and did not contain
the older form of the mtime object header information that was being tested for.
Solution:
Run a version of gen_old_mtime that was compiled & linked against an older
version of the library to generate the tmtimeo.h5 file.
Had to update the modification time used for testing in the mtime.c file
also.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
New feature/Bug fix
Description:
Add new fill time value - H5D_FILL_TIME_IFSET which writes the fill value
to a dataset if the user has defined one, otherwise not writing the fill value
to the dataset.
Platforms tested:
FreeBSD 4.8 (sleipnir) serial & parallel
h5committest
Description: H5Tget_native_type fails for multiple kinds of datatype on Cray; it fails
fix-length string type, too.
Platforms tested: Cray, h5committest
Test bug fix
Description:
Chunked datasets with early space allocation and unlimited dimensions were
running into problems where the dataset's "layout" message was marked as
constant too early, preventing the dataset's dimensions from being extended.
Solution:
Change logic for marking the layout message constant to wait a bit longer.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/parallel
h5committest
Bug fix
Description:
An earlier checkin changed some of the assumptions about single block
hyperslabs, causing them to fail in odd ways.
Solution:
Fix errors with single block hyperslabs by keying off of count==1 instead
of stride==1.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/parallel
h5committested
Code cleanup & performance improvements
Description:
Optimize hyperslabs that are built to detect situations where "regular"
hyperslabs can be recovered from span tree descriptions.
Also, improve "same shape" routine to correctly work with all the different
combinations of selections.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
FreeBSD 4.8 (sleipnir) w/parallel
h5committested
API tweak.
Description:
The H5Sget_select_bounds() API call was using hsize_t arrays for retrieving
the 'start' and 'end' coordinates, which is counter to the rest of the dataspace
API.
Solution:
Change the arrays to be hssize_t instead.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
FreeBSD 4.8 (sleipnir) w/parallel
h5committested
Misc. update:
Updated all docs for this change.
Added 1.4 compatibility #ifdef's
Code cleanup
Description:
Clean up older settings for strides of hyperslabs
Platforms tested:
h5committestted (although Fortran tests failed for some reason)
Code cleanup
Description:
Call srand(time(NULL)) before performing tests, to better randomize numbers
chosen for testing.
Platforms tested:
h5committestted (although Fortran tests failed for some reason)
Code cleanup
Description:
Free malloc'ed buffer of 0 bytes when H5_MALLOC_WORKS is defined, to make
purify happier.
Platforms tested:
h5committestted (although Fortran tests failed for some reason)
Code cleanup
Description:
Remove redundant "Testing" from test output.
Platforms tested:
h5committestted (although Fortran tests failed for some reason)
Bug fix
Description:
Failed tests were not being reported correctly to main test routine, so
they were not stopping a 'make check'
Solution:
Changed '1' to '-1' for failures.
Platforms tested:
h5committestted (although Fortran tests failed for some reason)
Purpose: Maintenance and bug fixes and test of latest szip library..
Description: Recently Quincey enabled MEDIUM test for istore. That caused
daily tests to fail on verbena. It looks like that test
creates a pretty big file, and afs write fails. Test passes
when run in /tmp.
Solution: Disable MEDIUM test and filed bug report to investigate the problem
little bit more carefully.
Platforms tested: verbena, arabica, arabica-64 (since I also tested newest szip)
Misc. update:
Small feature.
Description:
Change the wording for the use of HDF5_PARAPREFIX from Remark to hint.
Also made process 0 be the only one printing the hint rather all
processes duplicating the same hints.
Platforms tested:
Copper, both serial and parallel.
Did not do h5commit test since this is very localized and the above
tests covered both cases already.
Misc. update:
Code cleanup
Description:
Remove debugging information and match bug-fix changes to szip filter
code.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest not needed.
Code cleanup
Description:
Limit the scope on more function prototypes/macros/typedefs.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest not necessary.
New test
Description:
Added test to check for dangling objects being handled correctly by the
library.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committested
Bug fix
Description:
Iterating over the attributes of an object without any attributes was
returning FAIL instead of 0 as the RM states.
Solution:
Changed return value of H5Aiterate for objects without attributes to be 0
and added regression tests for this.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest not needed.
Description: when a datatype element size is bigger than I/O datatype
conversion buffer(1MB), library reports failure.
Solution: adjust conversion buffer to be at least equal to one element size
Platforms tested: h5committest
Add windows specified macro H5_TESTDLL for test routines.
Description:
See the previous CVS message.
Solution:
Platforms tested:
windows2000(will not affect other platforms)
Misc. update:
Code cleanup
Description:
Clean up warnings exposed by compiling on O2K. Also, revert some of Bill
and my changes to the H5S_mpi_opt_types_g, etc. and settle them back into their
original location.
Platforms tested:
h5committested.
Description: H5Sselect_hyperslab and H5Sselect_elements didn't check scalar
dataspaces.
Solution: put error detection in those functions.
Platforms tested: eirene(simple change).
Feature change
Description:
HDF5_PARAPREFIX has been default to various values like /tmp,
/var/tmp, ... None of these solve all problems and all of them
created new problems. For LLNL GPFS, '.' is more appropriate since
they can do the build right inside gpfs. Same for NCSA Copper.
The special setting for Janus is still retained since that is a
one of a kind machine and the uses could use all the help.
Platforms tested:
h5committested (using sol instead of arabica) plus eirene(pp).
Misc. update:
New feature/enhancement
Description:
Chunked datasets are handled poorly in several circumstances involving
certain selections and chunks that are too large for the chunk cache and/or
chunks with filters, causing the chunk to be read from disk multiple times.
Solution:
Rearrange raw data I/O infrastructure to handle chunked datasets in a much
more friendly way by creating a selection in memory and on disk for each chunk
in a chunked dataset and performing all of the I/O on that chunk at one time.
There are still some scalability (the current code attempts to
create a selection for all the chunks in the dataset, instead of just the
chunks that are accessed, requiring portions of the istore.c and fillval.c
tests to be commented out) and performance issues, but checking this in will
allow the changes to be tested by a much wider audience while I address the
remaining issues.
Platforms tested:
h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
Purpose: Cray T3E maintenance with Raymond's help
Description: fillval test failed for compact dataset since the
size of the dataset was bigger than 64K.
Solution: Reduced the dataspace of the compact dataset to 1024 elements.
Platforms tested: T3E; it was also tested with semi-manual h5committest.
(I had to built and test manually on modi4 parallel because
of some weird failure of h5committest on modi4)
Misc. update:
code warrior fix
Description:
eliminate the CW failure on getname.c
restrict the H5_NO_FILE_SHARING just to the test file_close of testhdf5 test
Solution:
the CW failure on getname.c can be eliminated if a unmount of the file is made before closing it
on tfile.c the failure is due to the file sharing flag of CW, and the test is maintained as before
Platforms tested:
Windows 2000 (octopus)
Linux 2.4 (rockaway)
SunOS 5.7 (arabica)
IRIX 6.5 (modi4)
Misc. update:
Revert last change (at least temporarily)
Description:
Revert last "NO_SHARED_WRITING" ifdefs after reviewing the tests that were
ifdef'ed out. I don't think that these tests should cause a problem, so I
would like them reviewed again to see if there is a file handle leak in the
library (or test).
Platforms tested:
FreeBSD 4.8 (sleipnir)
Triple check not needed.
Code restructure.
Description:
Restructured tests so they shouldn't depend on shared open()'s and can be
tested with CodeWarrior
Platforms tested:
FreeBSD 4.8 (sleipnir)
Triple check not needed.
code warrior port
Description:
added a flag H5_NO_SHARED_WRITING, it is defined only for CW in the H5pubconf.h
this avoids doing some tests for CW that fail on shared writing
Solution:
Platforms tested:
windows (cw and ms)
Linux 2.4 (rockaway)
SunOS 5.7 (arabica)
IRIX 6.5 (modi4)
Misc. update:
Purpase: Fortran Windows DLL support
Description: Fortran test uses functions h5_fixname and h5_cleanup from h5test.c.
Those were not exported, and Fortran could not link while using DLLs.
Solution: Added H5_DLL to functions prototype to export them from C DLL.
Platforms tested: Windows, h5committested.
Misc. update:
removed and change comments
Description:
removed the modification comment about the while loop, it is not sufficiently important to be there
changed the "Id to name" comment in the test description, it was incorrecly about other thing
Solution:
Platforms tested:
none , just comments
Misc. update:
Purpose: Windows maintenance and code cleanup
Description: There were a lot of places in the source code where varibale
was declared but never used.
Solution: Cleaned the source code to avoid warnings on Windows and Unix
platforms.
Platforms tested: arabica, modi4, Windows
Probably my environment is wrong on Linux, cannot
compile at all when fortran is enabled
If daily tests fails tomorrow, this will be my fault
but I want to go home now :-)
Misc. update:
Purpose: Bug fix
Description: on Cray T90IEEE compact storage test (in test_misc8)
fails since dataset dimensions are too big; dataset
will not fit into the message header.
Solution: Reduced dimension sizes from 100 to 50.
Platforms tested: h5committested on arabica and mod4; verbena failed
because of the F90 license problem. I tested on verbena
by hand and C only; Cray T90IEEE
Misc. update:
Purpose: Verify library behavior
Description: A file is first opened as read only. Then it's closed with
an object left open. A second open of the same file for read and
write should fail.
Platforms tested: arabica - simply test to verify correct library behavior.
Code cleanup
Description:
Christi Forsythe reported that the NGROUPS macro in this file was causing
a macro redefinition warning on the QT machine.
Solution:
Rename NGROUPS to UNLINK_NGROUPS
Platforms tested:
Eyeballed, too trivial for triple check.
Bug Fix
Description:
A resource leak happened if the H5Fget_access_plist() function was
called. What was happening: the driver ID and info parts of the
property list copied in H5Fget_access_plist were being overwritten,
but those properties were copied initially, so we lost information.
Added calls to the H5Fget_access_plist function to get the PList and
then immediately close it. It would cause an infinite loop if there
is a resource leak.
Solution:
Before copying over those values, call the H5F_acs_close() function
to close those values.
Platforms tested:
Modi4 (Parallel & Fortran)
Arabica (Fortran)
Verbena (Fortran & C++)
Misc. update:
Bug Fix
Description:
When using the STDIO driver, the dsets test would fail.
Solution:
Need to flush the data to disk before doing an HDopen call.
Platforms tested:
Modi4 (Parallel & Fortran)
Arabica (Fortran)
Verbena (Fortran & C++)
Misc. update:
Purpose: Windows port
Description: Windows cannot convert from _uint64_t to double. One of
the tests (test_set_local) used conversion to fill a data
buffer. Compilation failed on Windows.
Solution: Fixed the code not to use conversion
Platforms tested: CRAY T90IEEE, arabica, modi4 with parallel, Windows 2000
Only static tests (both debug and release) passed on Windows.
DLLs have multiple problems ;-)
Misc. update:
Code cleanup
Description:
Clean up comments, etc.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
New feature.
Description:
Added tests to verify correct operation of re-using file space.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
Code cleanup
Description:
Added macro for reporting line #'s of test failures more easily.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
Bug fix
Description:
Return correct value (1 instead of -1) on test failure.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
Code cleanup
Description:
Switched some system/library calls to use wrappers.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
Bug fix
Description:
This fixes a bug in the low-level metadata caching code in the library
which could possibly lose metadata during file I/O when a lot of objects are
inserted into a group.
This also fixes a couple of (similar) fencepost bugs in the B-tree
deletion code.
Solution:
For the metadata bug - call the low-level driver's 'write' routine instead
of H5FD_write.
For the B-tree bug - include the correct number of keys.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
(h5committest is still not working for me on burrwhite)
Misc. update:
Code cleanup & new tests
Description:
Updated szip and shuffle testing to reflect changes to API functions.
Added testing for new API functions: H5Pmodify_filter, H5Pget_filter_by_id
and H5Pall_filters_avail.
Added testing for "can apply" and "set local callbacks.
Cleaned up various things, also.
Solution:
Platforms tested:
FreeBSD 4.8 (sleipnir) w/szip
Linux 2.4 (sleipnir) w/szip
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel
Misc. update:
Purpose: This a fix for bug #921
Description: On platforms where big test runs, it creates a set of
"solid" 1GB files. Test will take forever (modi4) or will fail
if quotas are exceeded.
Solution: Default library behavior is to allocate dataset space earlier and
to write fill values. I changed the test to use late space allocation
and never write fill values.
Platforms tested: True64 (PSC), modi4 (sequential and parallel), arabica with 64-bit
option(test was skipped there). I also enabled szip and it passed :-)
Misc. update:
Code cleanup
Description:
Updated copyright.
Removed szip-specific testing in favor of standard testing, now that bugs
in the szip filter are fixed.
Updated to latest version of H5Pset_szip API
Solution:
Platforms tested:
FreeBSD 4.8 (sleipnir)
IRIX64 6.5 (modi4) w/parallel
Misc. update:
To add tests for szip compression in HDF5
Description:
Three tests were added:
1) szip filter itself
3) szip + shuffle + fletch32
2) fletch32 + shuffle + szip
Solution:
Since H5Dget_storagesize returns 0(Quincey can fix it or it may be gone),
I create another function called test_internal_filter_szip, which is the almost the same
as test_internal_filter but comments out H5Dget_storage_size function.
Platforms tested:
Since there are changes of configure.in and configure,I didn't use h5committest.
I tested with four platforms.
1) Linux 2.4 (eirene) 2) Solaris 2.7(arabic
3) windows 2000(VS 6.0) 4) SGI IRIX6.5-64(modi4)
For test 1)-3), only basic C tests were done For modi4 test, I tested 64-bit C,parallel and fortran.
All tests passed, except a warning message from szip library when checksum is used in some order, which doesn't cause any real problems.
Misc. update:
Update
Description:
Updated the Copyright statement
Platforms tested:
Linux (This change is only in the comments, so I just check that the
modules still compile)
Misc. update:
New test feature
Description:
Added the VFD_LIST definition to support the "make check-vfd" tests.
Platforms tested:
h5committested.
Since check-vfd is not invoked by default, I went to each machine
to invoke them by hand. The target worked fine but there were
errors reported from those driver tests. (Those errors were beyond
the scope of this make target test.)
Misc. update:
New internal feature
Description:
Add internal API for building and working with heaps (H5HP). This will be
used for the LRU algorithm in the new metadata cache code.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir)
Code cleanup
Description:
Added more information to information printed for test failure.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Code/comment cleanup
Description:
Made more information about reference-counted strings private to the
H5RS package by trimming the typedef used in H5RSprivate.h and switching
from using macros for a couple of operations to using functions.
Updated copyright information for a few of these files.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Code cleanup
Description:
Clean up miscellaneous warnings which have crept into the code.
Fix "_POSIX_C_SOURCE not defined" warning on FreeBSD.
Adjust gcc compiler flags to be more concise for production mode.
Refactor the H5O code so that there is a stronger boundary between code
in the H5O package and code in the library which just calls H5O routines.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel and gcc 2.95.4 & gcc 3.2.2
Misc. update:
Update MANIFEST if you add or remove any file.
