| Commit message (Collapse) | Author | Age | Files | Lines |
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New version of the function h5tools_dump_simple_subset, to display subsetting. The new algorithm is:
Introduced an outer loop for cases where dimensionality is greater
than 2D. In each iteration a 2D block is displayed by rows in a inner
loop. The remainning slower dimensions above the first 2 are incremented
one at a time in the outer loop
Note: when blocks are introduced, the display is not correct. This is a bug that requires an improvement of the algorithm.
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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
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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)
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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
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added a size of array information when printing differences
modified print_pos and diff_datum for having one extra argument *dims
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introduced a new macro PDIFF to calculate differences for unsigned types
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introduced more ABS macro use
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fix some memory allocation problem with info->prefix
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compiler warning clean
../../../hdf5/tools/lib/h5tools_ref.c:257: warning: old-style parameter declaration
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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
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more compiler warning
../../../hdf5/tools/lib/h5diff_attr.c:214: warning: passing arg 4 of `diff_array' with different width due to prototype
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cleaned more warnings
../../../hdf5/tools/lib/h5diff_attr.c:214: warning: passing arg 4 of `diff_array' with different width due to prototype
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Cleaned warnings
h5diff_array.c:804: warning: passing arg 1 of `fabs' as floating rather
than integer due to prototype
introduced double precision arithmetic when possible instead of single
precision
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floating point comparison
../../../hdf5/tools/lib/h5diff_array.c: warning: comparing floating point with == or != is unsafe
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h5diff_array.c:127: warning: declaration of 'per' shadows a global declaration
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cleaned compiler warning
../../../hdf5/tools/lib/h5diff_array.c:139: warning: declaration of 'per' shadows a global declaration
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Added a relative error formula to deal with floating point uncertainty
in the comparison of floats and double types.
Added new tests for this feature to the file generator program and to
the shell script
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open/close in the cheking of objects when there are none requested by the user
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Basic support for H5Literate() routine. Still needs to be fleshed out and
refactored to simplify. Also, needs tests. :-)
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
Mac OS X/32 10.4.8 (amazon)
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The version of libtool used by HDF5 isn't directly affected by the reconfigure
script; instead, libtoolize --force must be used by hand. Libtool was the
source of the problem, so rolling its version back to 1.5.14 should solve the
issue (at least temporarily).
Reconfigure should still work on both heping and kagiso.
Tested on heping, kagiso, and tg-login3.
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Hopefully this will fix
issues on tg-login3.
bin/reconfigure should still work on both heping/mir and kagiso.
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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)
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Should disable linking against shared libraries in Fortran for compilers that
don't support shared libraries.
Should also fix problem when the wrong Fortran file extension was specified.
If these changes don't solve the Daily Test issues, I'll look at backing out
the autotool version change until I have time to fix them.
Tested on heping, kagiso, juniper.
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h5dump bug 701. Symptom: The creation of a hardlink pointing to the root group "/" causes h5dump to display it as a link pointing to itself.
Cure: the root group was not being inserted in the table that keeps track of object names and links.
Added a test for this in the test generation program, the creation of a hardlink to the root
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Linux machines.
Updated to the latest versions of autotools.
Tested on kagiso, heping, and juniper. Let me know if you have any problems.
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Changed H5Lget_linkval() to H5Lget_val(), per our design discussion last
Friday afternoon.
Tested on:
Linux/32 2.6 (chicago)
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Change H5Lget_linkinfo() to H5Lget_info() to better align with coming API
changes.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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the size of
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.
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added a new test for h5diff relative error for the file generator
program
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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
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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
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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
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only tested
if it is enabled.
Added Direct VFD status to the configure summary.
Removed a line left over from pablo support. Oops!
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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
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utility
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.
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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
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output to the
parallel part of h5diff
tested : heping parallel
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the number of atribute differences was not added to the total sum of
differences
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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).
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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
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VFD is being used
when a test is run.
Running reconfigure also regenerated error header files (because someone edited
them manually?).
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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.
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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.
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"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.
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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
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new feature
h5dump binary output. use little and big endian type conversions
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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
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Clean up some compiler warnings.
Tested on:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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