| Commit message (Collapse) | Author | Age | Files | Lines |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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)
|
|
|
|
| |
temporary fix for a daily test failure
|
|
|
|
|
|
|
|
|
|
|
|
| |
Add empty & "full" groups to source HDF5 file and test copying them.
Test renaming objects during copy
Test specifying root group path for source & destination objects
Tested on:
Linux/32 2.6 (chicago)
Too minor to require more tests
|
|
|
|
|
|
|
|
|
|
|
| |
Refactor h5copy testing script to abstract out some of the common behavior,
obey the "HDF5_NOCLEANUP" environment variable, delete any output file left
over from a previous run, add a "test variation" parameter to output file name
for adding next sequence of test variations, etc.
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)
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Fix core dump for iterating over attributes and not passing in a "starting
point".
Update output files missed in previous checkin. This change essentially
reverses a previous change of attribute ordering, leaving the output of h5dump
& h5ls compatible with 1.6.x
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
|
|
|
|
| |
replaced a dataset type from H5T_NATIVE_CHAR to H5T_NATIVE_SCHAR
|
|
|
|
| |
remove a test that was incorrectly added previously, that was not the feature that had to be tested
|
|
|
|
| |
added a test for the printing of long long numbers greater than 4GB
|
|
|
|
| |
2 tests that were previously incorporated inside the array indices test file were separated from it. These are a test with a dataset with dimensions greater tan 4GB and a test to read by hyperslabs
|
|
|
|
| |
replaced the path to XML schema from NCSA page to hdfgroup.org
|
|
|
|
|
|
|
| |
The problem
came from the EOA for the whole MULTI file. It's taken out because it's
meaningless for MULTI file. Instead, each individual file has its EOA.
|
|
|
|
|
|
|
|
|
|
| |
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.
|
|
|
|
| |
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 display order of attributes.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
| |
added a size of array information when printing differences
modified print_pos and diff_datum for having one extra argument *dims
|
|
|
|
| |
introduced a new macro PDIFF to calculate differences for unsigned types
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
| |
terminator is not correct
|
|
|
|
| |
remove and insert these files, somehow their end of line terminator is not correct
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
| |
changed the usage message relative to the relative error formula to a more
common and easy to understand form | (b-a) / a |
|
|
|
|
|
|
|
|
| |
h5repack revision:
1. added a new test due to the introduction of H5Ocopy in the copy of objects (compressed dataset with references, that still must go a second sweep of the file to be regenerated).
2. Moved all the source files from the h5repack test program to a new file h5repacktst.c and removed the old ones (testh5repack*.c).
3. Renamed the binary files from test*.h5 to h5repack*.h5 for easy reference.
4. Modified the shell script to use variables for file names instead of hard coded names
|
|
|
|
|
|
| |
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
|
|
|
|
|
| |
added a new test for h5diff relative error for the file generator
program
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
| |
added more tests for h5copy (compressed datasets, vl named datatypes )
|
|
|
|
| |
rewrote the -b option to make it more clear
|
|
|
|
|
|
| |
used can be different from the driver
used for standard output.
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
| |
added calls for the scale offset filter to the h5repack test script
|
|
|
|
| |
added new tests for h5copy script, generated in the test file generator program
|
|
|
|
|
|
| |
added new tests with different datatypes for h5dump binary output
tested: kagiso
|
|
|
|
|
|
|
|
|
| |
Further minor modifications to the file format for tracking links in groups.
This is tentatively the "final" file format for groups.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
|
|
|
| |
output to the
parallel part of h5diff
tested : heping parallel
|
|
|
|
| |
corrected usage message to have an example of the new binary parameters
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
| |
the number of atribute differences was not added to the total sum of
differences
|
|
|
|
|
| |
added a new output file for the case of missing file name, conforming to
the new usage message
|
|
|
|
|
|
|
| |
added a test file generator program for h5copy, modified test script to use
that file, added binary file to repo
tested on heping, shanti
|
|
|
|
| |
Add external link test file
|
|
|
|
|
|
| |
nosuchfile.ls is the expected output.
Tested: tg-ncsa and heping.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
|
| |
updated the usage message with new info for the binary output option
tested: linux
|