Add small 'h5mkgrp' tool to create groups in an HDF5 file from the command
line, allowing the group structure for a file to be created in a script. This
tool closely follows the 'mkdir' command line tool in UNIX/Linux.
Allow tool library applications to pass a FAPL to the h5tool_fopen() call,
giving some additional flexibility to tools which are adding objects to an
existing HDF5 file (like h5copy & h5mkgrp).
Fix missing files in MANIFEST from previous checkin(s).
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Add feature to h5copy to allow it to add an object to an existing file,
instead of blowing away existing file.
Modify h5tools_fopen() routine to take access flags, so it can be used
to open an existing file for writing.
Added check to h5copy test script that verifies it has produced a file
with the correct structure.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
Fixed#720 h5dump: improve how region references are displayed. h5dump now uses the new API function H5Rget_name to display the name of the dataset referenced instead of its ID. Added a case to the script test file
fix for bugzilla bug #551
several programming errors contributed to this bug
1) the parsing of subsetting was using atoi to convert the parameter to an int,
which caused problems for numbers greater that int. Substitute with atof
2) several index counters were declared as int, use hsize_t instead
3) the numerical format passed for printf was %lu, defined one compatible with
hsize_t instead (unsigned long long)
Fix several bugs
1) the parsing of subsetting was using atoi to convert the parameter to an int, which caused problems for numbers greater that int. Substitute with atof
2) the printing of indices in the subsetting case was not being done. Solution: calculate the element position at the start of the subsetting using the algorythm
Given an index I(z,y,x) its position from the beginning of an array of sizes A(size_z, size_y,size_x) is given by
Position of I(z,y,x) = index_z * size_y * size_x
+ index_y * size_x
+ index_x
And pass that position to the function that dumps data, h5tools_dump_simple_data.
3) several index counters were declared as int, use hsize_t instead
4) modified the test generation program so that it includes test cases for subsetting of 1d, 2d, 3d, and 4d arrays and add these tests to the shell script
fixed 2 initializations of char* with HDstrdup and HDcalloc
info->prefix = HDcalloc(1, 1);
fname = HDstrdup(argv[opt_ind]);
some were exposed by compiler warnings
Add new H5Lget_val_by_idx() routine & tests.
Also includes most of changes for H5Ldelete_by_idx() routine.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
the linkval buffer, per Elena and Frank's suggestions while revising
the documentation. Added error checking using this size, as well as a
couple of tests.
Tested on juniper, kagiso, and sol.
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
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
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).
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.
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
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:
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)
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:
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 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
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
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
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
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
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)
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.
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.
