Bring r17599 from trunk to 1.8 branch:
Minor code cleanups, based on cleanups in the compress_group_fheap
branch.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk)
Description:
When copying a dataset using a vlen inside a compound, the various dataset
copying callbacks would allocate a background buffer but would not use it when
converting from disk to memory, only memory to disk. This caused an assertion
failure as compounds always need a background buffer. These callbacks have
been modified to use the background buffer for both conversions.
Tested: jam, linew, smirom (h5committest)
Bring r17553 from trunk to 1.8 branch:
Bring general fixes/improvements from file_free_space branch back to
trunk.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
r17543 | acheng | 2009-09-28 23:43:22 -0500 (Mon, 28 Sep 2009) | 8 lines
New test: (Bug ID 1656):
Add new tests (tcheck_version, testcheck_version.sh) to verify H5check_version()
does issue warnings and abort accordingly.
Changed H5check_version() to suppress the warning message totally if
$HDF5_DISABLE_VERSION_CHECK is 2 or higher. (Old behavior treated 3 or higher
the same as 1, that is to print a warning and allows the program to continue.
Tests:
H5committed tested plus jam serial tested.
Description:
At several places in H5Pint.c properties were being compared using memcmp, not
using the registered "cmp" callback. This could cause memory checkers to
report uninitialized memory errors, and could conceivably cause runtime errors
if memcmp reported false equality (for example if a value pointed to by the
property changed).
The code has been changed to always use the cmp callback. Tests have been added that check this in all the places that previously used memcmp.
Tested: jam, linew, smirom (h5committest)
Bring r17524 from trunk to 1.8 branch:
Switch to using system call wrapper macros instead of "raw" system calls.
Tested on:
Mac OS X/32 10.5.8 (amazon) w/debug & production
(too minor to require h5committest)
Add backward compatibility test to make certain that the 1.8 library
handles encountering a file with a fixed array chunk index gracefully.
Tested on:
FreeBSD/32 6.3 (duty) w/production
(too minor to require h5committest)
sure the stat function behaves as we expected. This test is skipped on some system because
the modification time from stat is the same as the last access time (We know OpenVMS behaves
in this way).
Tested on jam. I've tested the same change for the trunk on jam, smirom, and linew.
My account for OpenVMS expired. I'll test it once I have it back.
Test failed with libhdf5.so not found in MacOS which uses a different
suffix (*.dylib) for shared lib.
Solution:
Added code to setup shared lib file suffix according to OS types.
Tested:
Tejeda, jam, linew.
Description:
Build failed when embedded-info is not enabled. Fixed.
testlibinfo.sh output was ugly, did not prepare the case of embedded-info
not enabled. Fixed. Also changed NOT to test test binary even if static-exec
is enabled.
Tested:
jam (with and without embedded-info enabled). Did not test in other
platforms since these were script changes that are platform independent.
Stage 2 implementation of embedded library information feature.
H5.c: added code to print the embedded library information when there is
a library versions mis-match occurs. This ensures the library information
string is included in the executable.
Also modifies the code so that the Library mismatch warning string is
included only once in the executable.
H5private.h:
Added a global reference to the libinfo string variable to prepare
for possible stage 3 implementation of a public API.
test/testlibinfo.sh.in:
A new test added to verify the library information is indeed included
in the executables.
configure.in:
configure:
Added entry to auto-generate test/testlibinfo.sh.
H5detect.c:
Modified the libhdf5settings generating code to allow it to insert the
strings to a file other than stdout. This maybe needed in stage 3
implementation.
MANIFEST:
updated with the newly added file of testlibinfo.sh.in.
Tested:
h5committest passed. Also passed jam in serial mode.
returned from the system function stat is the same as the last access time, making it
impossible to test whether the file is modified.
Tested on jam for the same change in the trunk - simple change.
Bring r17463 from trunk to 1.8 branch:
Add another regression test for userblock+alignment usage, and correct
[another] issue with the combination. *sigh*
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk)
Bring r17461 from trunk to 1.8 branch:
Fix a few more problems when the user block is not aligned properly.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk)
Bring r17459 from trunk to v1.8 branch:
Correct bad interaction between non-zero userblocks with non-zero
alignments.
Also add some additional range checking and tests for invalid userblock
sizes.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk)
Updating autotools
Description:
Bring revisions 17345 and 17357 from trunk to 1.8, specifically:
- Automake upgraded to 1.11
- Autoconf upgraded to 2.64
- bin/reconfigure script edited to use new versions (on jam), and
run to generate new configure script and Makefile.in's.
- configure.in script edited to add "_cv_" to all AC_CACHE_VAL strings
(in order to comply with new autoconf standard).
- bin/install-sh script replaced with new version as provided
by automake.
Tested:
- All issues on trunk were resolved, so only tested on jam and linew. Any
other outliers should be caught by daily tests.
Bring r17408, 17411, 17412, 17413 & 17414 from trunk back to 1.8 branch:
r17408:
Move flush operation on mounted file hierarchy into H5Fmount module.
r17411:
Make H5AC_flush just flush the cache and make H5AC_dest perform the
proper parallel synchronization before destroying the cache. Also, further
discriminate between 'closing' and 'non-closing' actions in H5F_flush.
r17412:
Seperate 'flush' functionality from 'destroy' functionality at the
H5F level also.
r17413:
Remove vestigial intermediate routine for flushing file and move it
into API routine. Also, remove private, unused (now) 'H5F_FLUSH_DOWN' symbol
from public header file.
r17414:
Flush the core VFD's buffer before closing the file, also flush the
metadata accumulator before reseting it. Write the driver info message out
in the superblock flush routine more directly, instead of using wrapper
routine, since the wrapper routine won't work when the superblock is being
shutdown.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest performed on trunk)
detects the conversion working, a macro is set. If there's problem with this conversion like
Pathscale compiler, skip the test.
Tested on jam. Need to verify it on pathscale machine.
Bring r17393 and r17398 from trunk to 1.8 branch:
Bring back more changes from the file free space branch to the trunk. (17393)
First set of changes to move VFD 'truncate' call out of H5F_flush and defer
it until the file is closed. (17398)
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk)
Bring r17388 from trunk to 1.8 branch:
Correct error in freespace test which was relying on free space section
to be valid after the library had taken ownership of it (and therefore could
free it).
Also correct some checking for return values of H5FS internal routines
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest performed on trunk)
Bring r17365 from trunk to 1.8 branch:
Final merge of changes from sblock_mdc branch back to trunk. The
superblock is now managed by the metadata cache.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest performed on trunk)
Bring r17351 from trunk to 1.8 branch:
Clean up code (to align w/future sblock_mdc branch changes), tweak
tests for [slightly] easier debugging, fix memory leak when copying chunked
datasets with I/O filters, fix memory leak of free space section when it was
exactly the right size to use for extending an existing block in the file.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest performed on trunk)
Bring r17324 from trunk to 1.8 branch:
Bring more improvements/changes back from file_free_space branch
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest performed on trunk)
Bring r17313 from trunk to 1.8 branch:
Bring back various minor code cleanups from the file free space branch
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Clean up various compiler warnings from IRIX64 build
Tested on:
Mac OS X/32 (amazon) debug & production
(yes, I know it's not an IRIX64 system :-)
Too minor to require h5committest
Bring r17148:17149 from trunk into 1.8 branch:
Refactor how chunked dataset information is computed, moving it earlier and
avoiding more recomputation.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Bring r17146 from trunk to 1.8 branch:
Bring a bunch of misc. improvements & tweaks from the revise_chunks
branch back to the trunk, so that future merges won't be so painful.
Tested on:
FreeBSd/32 6.3 (duty)
(h5committested on trunk)
replaced it with H5Aopen in this round. I also updated some hard-coded numbers with some
macros.
Tested on jam only. I have tested the same change for the trunk.
the attribute structure wan't set correctly. It caused some confusion in H5A_read. This
flag was actually redundant because the library can alwasy check if the data buffer is
present. To fix it, I removed the "initialized" flag in the attribute structure and let
H5A_read check the data buffer.
I tested it on jam only but have tested the same change for the trunk on jam, smirom,
and linew.
Description:
Previously, when H5Z_filter_info was called for a filter that was not present,
it would succeed and return the information from one position past the end of
the pipeline, possibly causing a segfault. This affected at least
H5Pget_fitler_by_id1/2, and possibly other API functions. Fixed to properly
return failure.
Tested: jam, linew, smirom (h5committest)
Bring r17010,17017,17021-17022,17029-17031,17035 back from trunk:
"temporary" file allocation space changes.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Description:
When using H5T_copy on committed datatypes that are already open, H5T_copy would
properly use the already existing shared struct, but would still deep copy all
of the fields in that struct. This would cause memory leaks, and in the case of
a compound containing a vlen (or reference), the change in size would cause the
size of the resulting type to be set to an incorrect value. Changed H5T_copy to
properly avoid deep copies when using a reopened shared struct.
Tested: jam, linew, smirom (h5committest), purify on jam
Merge these trunk revisions which occurred during the 1.8.3 release code
freeze back to the 1.8 branch:
From Quincey: 16845 16847 16849 16851 16858 16869 16897
From Ray: 16859 16880
From Allen: 16863
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.6 (amazon) in debug mode
Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Description:
Previously, there was no versioning for H5Z_class_t. This prevented applications
written for 1.6 using custom filters from being able to use the 1.8 library.
There is now an H5Z_class1_t and H5Z_class2_t to enable compatibility. H5Zregister is
*not* versioned, it determines which version of the struct has been passed in by the
value of the first field (id or version, both are ints).
Tested: jam, linew, smirom (h5committest), jam (--with-default-api-version=v16)
Description:
When writing data to a dataset, the data transform was performed after type conversion.
This caused an error if the file type was non-native. This has been changed so data
transforms are always performed on the memory type.
Tested: jam, linew. smirom (h5committest)
- Updated bin/reconfigure to use latest version of automake (1.10.2).
Regenerated Makefile.in's by running bin/reconfigure.
- Added libtool version numbers to c++, fortran, hl, hl c++, and hl fortran
libraries.
Tested:
jam, liberty, smirom
source directory. Since the test opens the files with write mode, it's safer to make copies of
the original files. I added the copying step in test_family_compat in vfd.c. I changed the
Makefile.am to clean up the copied files. I created a new family_v16_00000.h5 with v1.6 library.
Tested on jam - supposed to be simple change.
Description:
The H5L interface was not marked as uninitialized when H5L_term_interface was
called. This caused the interface to not initialize itself later on. This
prevented external links from working after calling H5close, because they were
never re-registered.
Tested: jam, smirom, linew (h5committest)
