Updating autotools
Description:
Installed new autotools and used them to reconfigure HDF5.
- 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).
Tested:
Tested on machines jam, smirom, liberty, linew.
Tested w/ features c++, fortran, parallel.
Tested w/ compilers gcc, pgcc, icc.
Further testing via Daily Tests should catch any other outliers. Upon
passing DT's, I'll propogate the new tools into 1.8, hdf4, et cetera.
Fix BZ #1583
Description:
The --enable-static-exec flag was broken. Configure was adding the
-all-static linker flag to an environment variable which was subsequently
never used. (looks like it was used in 1.6 Makefile.ins, but never
moved to 1.8's Makefile.ams when we added automake support).
To fix, I've added this environment varibale to the link lines of all the
tools. Now, when --enable-static-exec is invoked, it will correctly
generate statically linked executables in the installed bin directory.
Tested:
I've tested manually to ensure that the generated execs are static when
the flag is used and dynamic when not. I've also tested when szip is
used, as this was a use case mentioned in the bug report.
Also: ran full tests with make check on jam and smirom for good measure.
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)
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
ISSUE: h5ltread_dataset_string_f causes library assertion with g95.
SOLUTION: convert the fortran string buffer to a C buffer with HD5f2cstring, and pass this string to the C function
TEST: added a test call in the fortran test lite program
DOCS: added the note in RELEASE.txt "- Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions had memory problems with the g95 fortran compiler. (PVN - 5/13/2009) 1522
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)
Description:
h5repack previously would not take named datatypes into consideration when copying
datasets and attributes. This would cause extra anonymous datatypes in the target file
at best, and cause errors halfway through the repacking at worst. h5repack should now
always handle named datatypes correctly. Named datatypes are also now converted to the
native type when -n is given.
Tested: jam, linew, smirom (h5committest)
- Updated bin/reconfigure to use latest version of automake (1.10.2).
Re-generated 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
Added a Make target of check-all-install to test the correctness of
installing via the prefix= or $DESTDIR options.
Platforms tested:
h5committested and jam serial mode. Then test check-all-install by hand.
- h5diff new flag, -c, --compare, list objects that are not comparable.
PVN - 2009/4/2 - 1368
- h5diff new flag, -N, --nan, avoids NaNs detection. PVN - 2009/4/2
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)
Description:
Versions of the library between 1.3.0 and 1.6.3 have a bug which prevents them
from opening any file that does not have the root group's symbol table
information cached in the root group's entry in the superblock. Prior to 1.8
this was not an issue as this information was always cached. However, 1.8.0
stopped writing this information (which is not required by the file format
specification), and these older versions can therefore not read files created or
last written by versions 1.8.0 to 1.8.2. This fix modifies the library to once
again add this information to the superblock (when using the old file format).
Tested: jam, linew, smirom (h5committest)
Description:
Changed Skip list package to use a deterministic skip list. This allows the
skip list package to avoid calling rand() and srand(), even on machines without
rand_r(). There is no longer a p-value or maximum level for skip lists.
Tested: jam, smirom, linew (h5committest)
Description:
Previously, H5Lcopy and H5Lmove would (through H5L_move) improperly apply the
"create intermediate groups" property to the source path traversal, and not the
destination. Fixed it to apply the property to the destination and not the
source. Also fixed H5Lcreate_ud to reject internal link classes without
throwing an assertion.
Tested: linew, jam, smirom (h5committtest)
Fortran High-Level APIs:
------
- Lite: The h5ltget_dataset_info_f function (gets information about a dataset)
was not correctly returning the dimension array (PVN - 2009/3/23)
