| Commit message (Collapse) | Author | Age | Files | Lines |
|
|
|
|
|
|
|
|
| |
Switch from H5P_DATASET_ACCESS_DEFAULT to H5P_DEFAULT for calls to
H5Rdereference2().
Tested on:
Mac OS X/32 10.6.8 (amazon) w/debug
(too minor to require h5committest)
|
|
|
|
|
|
| |
list to the function H5Rdereference. It's called H5Rdereference2 now. H5Rdereference function has been deprecated to H5Rdereference1. I also added some test cases in trefer.c.
Tested on jam, heiwa, and koala.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Revert the previous makefile change as release snapshot test failed with
MANIFEST check. Don't clean 'testfiles' dir via 'make distclean' for
the case of build&test in source dir.
In regular daily testings, we build&test in seperate dir from source dir,
so no issues occurred.
However for the release snapshot test, it seems that we build&test in
source dir.
The previous change can remove testfiles in source dir if build&test is
done in source dir becasue currently the dir name 'testfiles' is same in
source dir and test dir.
Other task (7602) may change to use different name for the test directory,
so 'make distclean' can do its job without interrupting MANIFEST.
|
|
|
|
| |
Tested: local linux (after clearing old testfiles)
|
|
|
|
| |
Tested: local linux
|
|
|
|
|
|
|
| |
- h5repack: h5repack failed to copy dataset if the layout is changed from chunked with
unlimited dims to contiguous. (PC -- 2011/07/15)
- h5diff: "--delta" option considers two NaN of the same type are different, which is wrong
based on http://www.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Diff. (PC -- 2011/07/15)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Purpose:
Remove H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS and
H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS #defines from source.
Description:
Two advanced parallel functionalities, special collective IO and
complex derived datatypes, are not supported by older
implementations of mpi, and thus our code limits the use of these
features with #ifdefs and has checks in configure to set them (or
not). Unfortunately, configure can't actually run a parallel check
to see if these features are working (nor not) so it resorts to
looking in the config files where they are explicity enabled or
disabled based on versions of mpi, sytems being built on, or for
no documented reason at all (i.e. just set to on or off as some
'default'). Overriding these settings is easy if need be, provided
it is known that it needs to be done to get improved performance,
and oftentimes it is not.
Most new MPI implementations successfully handle the functionality
requested when these #defines are set, and many of the "turn these
features off" cases in the config files are for old (> 5 years)
versions of MPI and retired systems (such as NCSA's tungsten).
Therefore, the decision has been made to remove the support for
these old versions of MPI and systems that cannot handle these
behaviors. The #ifdefs and supporting setup in the config/ files
and configure script has been removed, and the code executed when
these options were not set removed from the source.
In passing, this commit also cleans up some whitespace issues in
both t_mpi.c and H5Dmpio.c. Furthermore, in t_mpi.c, the special
collective IO test was not getting regularly run due to it being
written to work only with four processes (we regularly test with
six, previously with three), and thus it failed when actually run
due to an out of bounds data buffer assignment. It has been
modified to run at any number of processes greater than four, and
the memory problem has been fixed so the test passes.
Tested:
jam, h5committest, ember
|
|
|
|
|
|
| |
H5_SIZEOF_LONG_LONG. This is set if 64-bit integers are supported.
Tested: local linux
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
| |
Work for HDFFV-7600 - GMQS: h5diff - argument options -d, -p and --use-system-epsilon should be mutually exclusive.
Description:
Fixed h5diff to display instructive error message and exit with 1
when mutually exclusive options (-d, -p and --use-system-epsilon)
are used together.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
|
|
|
|
|
|
|
|
|
|
|
| |
Purpose:
Work for HDFFV-7602 - HDF5 command tools: Provide framework for reusable
test files among tools
Description:
Provide framework to share test files among tools for tools test.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE)
|
|
|
|
|
|
| |
status of check
Tested: heiwa
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
HDFFV-5878 - GMQS: h5dump - incorrect output format for array type with multiple elements in an index
Description:
Fixed h5dump to display the first line of each element into correct
position for multiple dimention array type.
Before this fix, the first line of each element in array were displayed
after the last line of previous element without moving to the next
line (+indentation)
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE)
|
|
|
|
|
|
| |
inside the test macro. Allows individual tests to be independently executed.
Tested: local linux
|
|
|
|
| |
Tested: Debug windows
|
|
|
|
|
|
| |
say which filter isn't registered. The fix is simple. Most of the effort is on the test. The file with filter enabled is created in gen_filter.c. The verification of the error message is in test_error.c. The output is compared against the standard output.
Tested on jam, koala, and heiwa.
|
|
|
|
|
|
|
|
|
|
|
| |
HDFFV-7607: h5ls - improve efficiency of test scripts - removing top 3 extra lines from expected output files
Description:
This is a subtask from 'HDFFV-7514 - gmqs: h5dump - improve effectiveness of testing scripts for handling expected output files'.
This is prerequisite for 'HDFFV-7602 tools - upgrade tools' test scripts to share test files among tools, providing framework for test file re-usability.'
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE), Cmake (jam)
|
|
|
|
| |
comparision of code changes
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring Coverity changes back to trunk:
r20340:
Address coverity issue 248. Set freed pointer to NULL if realloc fails, then check for NULL before attempting to close array of handles stored in memory addressed by pointer.
r20341:
Added initialization udata.path = NULL; udata.visited = NULL; to prevent unintialized use after done: label.
Do C-style initialization AFTER all variable definitions.
r20342:
Fix valgrind error in H5DUMP-XML-tall.h5
r20343:
Addressed Coverity issue 591 - check the return value of H5S_SELECT_ITER_RELEASE.
r20344:
Added initialization udata.path = NULL; to prevent uninitialized used after done: label
r20347:
Purpose: Fix memory leak in overhead.c
Description: Fixed leak in test() in overhead.c where array "had" was never
freed.
r20348:
Addressed Coverity issue 705 - added prototype for resize_configs_are_equal to cache_common.h.
r20392:
Purpose: Fix coverity issues 1677 and 1678
Description: Added return value checking for 4 funciton calls in
H5tools_get_symlink_info().
r20394:
Purpose: Fix coverity issues 1674 and 1675
Description: Modified H5Epush2() and H5E_printf_stack() to keep track of whether
va_start() has been called, and to call va_end() at the end if so.
r20395:
Should be H5MM_calloc(count * sizeof(void*)). Fixed --gh
r20396:
Should be H5MM_calloc(count * sizeof(void*)). Fixed. --gh
Tested on:
Mac OSX/32 10.6.7 (amazon) w/debug & production
(h5committested on branch)
|
|
|
|
|
|
| |
corrected test dependencies so that memcheck would process tests in correct order.
Tested: local linux - confirmed with valgrind
|
|
|
|
| |
Tested: local linux - Confirmed by Valgrind
|
|
|
|
|
|
|
|
|
|
|
| |
HDFFV-7514 - GMQS: h5dump - improve effectiveness of testing scripts for handling expected output files
Description:
Fist phase for h5dump test update. Next phase will be for h5ls.
This is prerequisite for 'HDFFV-7602 Tools - upgrade tools' test scripts to share test files among tools, providing framework for test file re-usability.'
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), linew (solaris-BE), Windows (32-LE), Cmake (jam)
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
| |
HDFFV-7594 - GMQS: h5dump shows wrong values for H5T_STD_I8LE dataset on Blue-gene (ppc64 linux BE +@)
Description:
For the STD_I8 type data, updated to use 'signed char' instead of 'char' as
'char' could be defined as unsigned on a certain system, which cause h5dump
to display data values incorrectly.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE)
|
| |
|
|
|
|
|
|
|
|
| |
passed in by value. The print functions needed an independent context with only the current indent level passed in by argument. Also synched the two routines logical flows and corrected a mem_space error.
h5dump (and h5stat, h5jam/h5unjam) help option not tested. Added h5dump parse_command_line technique for h5stat and h5jam/unjam and created testfiles.
Tested: local linux
|
| |
|
| |
|
| |
|
|
|
|
| |
Tested: local linux
|
|
|
|
|
|
| |
passed in by value. The print functions needed an independent context with only the current indent level passed in by argument. Also synched the two routines logical flows and corrected a mem_space error.
Tested: local linux
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Test scripts sometimes need to filter some system-specific messages from the
actual output so that it can match the correct expected output. These filtering
functions, ususally called "STDOUT_FILTER()" and "STDERR_FILTER()" were being
repeated in individual test scripts. This becomes a maintenance problem and
is error prone.
Solution:
Extract the two filter functions code to bin/output_filter.sh and then each
test script sources it in. This allows reuse of coding and is much easier to
maintain and to add new filtering.
Tested:
LLNL Zeus (linux64 cluster) and Dawndev (Blue-Gene cluster), both for serial
mode only.
--This line, and those below, will be ignored--
M tools/misc/testh5mkgrp.sh
M tools/h5dump/testh5dump.sh.in
M tools/h5diff/testh5diff.sh
M tools/h5copy/testh5copy.sh
M tools/h5ls/testh5ls.sh.in
M MANIFEST
A bin/output_filter.sh
|
|
|
|
|
|
|
|
|
|
|
|
| |
HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects
Description:
Improved performance by eliminating duplicated action for getting object
information in half from the previous fixe when comparing group vs group.
This is addition to the previous commit r20676.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
H5Dread() produces different output for invalid enum type values
on systems of different endiannes. On BE systems, it always
emits -1. On LE systems, the invalid value is emitted. This
difference caused the h5diff test to fail since it tests to
see if different invalid enum values are reported as different
(on BE systems they are not since -1 == -1).
This fix removes the "invalid vs. different invalid" test
while we fix the library bug. HDFFV-7527 will be reopened
in JIRA until the full test passes.
Tested on: jam, heiwa, linew
|
| |
|
|
|
|
| |
Tested: local linux
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
not represent a valid enum value.
Description:
The h5diff code compares enum values by converting them to strings and
then comparing them. When the enum value is out of range and can't be
converted to an enum string representation, the comparison was skipped.
The code now flags differences when one of the two enum values is out
of range (two out of range values are compared in memory). A test has
been added to the tools test script.
This fixes JIRA HDFFV-7527
Tested on: jam, koala, heiwa (h5committest)
|
|
|
|
| |
Add SOVERSION for linux
|
|
|
|
|
|
| |
Change case of tools subtests to not conflict with tools tests.
Tested: windows, local linux
|
| |
|
|
|
|
|
|
|
|
|
| |
removed option defines and #ifdef/#endif
refactored all printf to HDfprintf in h5dump.c
formatted and indention improvements
synched with 1.8 branch
Tested: local linux
|
|
|
|
|
|
| |
Autotools merge to come.
Tested: local Linux
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
- HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects
Description:
Fixed:
1) adding h5tools_is_obj_same() function to check if two given IDs or paths point to the same object. This function can be very useful for other tools and applications.
2) using h5tools_is_obj_same() at h5diff() and diff() in h5diff.c. If two paths point to the same object, there is no need to check the details of the object since we know there is no difference. The fix will increase the performance by skipping the content comparison. It also fixed the problem of reporting difference for some cases of comparing the same file, e.g. empty files or files with incomparable objects the same file.
Test update:
Updat prvious test cases (171, 172, 530) affected by this fix, so they
still perfrom originally intended testing without bypassing.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
|
|
|
|
|
|
|
|
| |
failure when it tried to display empty attribute data. I added
a check for empty attribute in h5dump.c. I also added a check for empty dataset in tools/lib/h5tools.c.
Tested on jam. But I tested the same changes in 1.8 on jam, linew, and amani.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
HDFFV-5948 - CHICAGO: Tools - implement missing external link test cases
Description:
Correct mistake in cmake script from previous commit r20595.
Add three test cases for h5dump and h5ls.
- h5ls: external link to soft link with follow symlink.
- h5dump: external link to soft link with follow symlink.
- h5ls: external link to soft link without follow symlink.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
HDFFV-5948 - CHICAGO: Tools - implement missing external link test cases
Description:
Add three test cases for h5dump and h5ls.
- h5ls: external link to soft link with follow symlink.
- h5dump: external link to soft link with follow symlink.
- h5ls: external link to soft link without follow symlink.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
|
|
|
|
|
|
| |
check in these 2 data files for the test.
Now test is needed.
|
|
|
|
|
|
|
|
| |
cases in the tests for h5dump and h5diff. I also added the
test cases in the CMAKE script.
Tested on jam, linew, and amani. Tested CMAKE on jam.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring Coverity changes back to trunk:
r20276:
Add recursive is vlen string function.
Cleanup resource leaks for issues: 200,202,329,688,811,812
r20277:
Check types and close by adding error section: issue 687
r20278:
Replaced implicit pointer conversion with (ocrt_info.new_obj != NULL).
r20280:
Addressed coverity issues 927-929 & 583. The real issue is failure to check
file name length -- at least at the H5FD interface level. This needs more work, but at least I have dealt with the issue in H5FDfamily.c
r20337:
H5O_type_t obj_type = H5O_TYPE_UNKNOWN;
r20338:
Added udata.name = NULL; to prevent potential uninitialized use after done: label.
r20339:
coverity issues: 686,828,1670-1673,1707-1711
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
FreeBSD/32 8.2 (loyalty) w/gcc4.6, in debug mode
FreeBSD/64 8.2 (freedom) w/gcc4.6, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) 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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Clean up various warnings & code formatting issues.
Bring changes from Coverity branch to trunk:
r20085:
Purpose: Fix coverity issue 793
Description: Modified H5S_hyper_project_simple_higher() to free the entire span
list in new_space on failure.
r20091:
This is a fix for coverity bug #1683.
Changed the two printfs to use %lu (unsigned long) for printing "dset_size".
r20162:
Purpose: Fix coverity issue 785
Description: Modified H5T_enum_nameof() to free "name" on failure if it was
allocated. Also clarified some code in H5S_hyper_rebuild_helper().
r20189:
Addressed coverity defect 783.
H5SL_new_node() in H5SL.c was failing to free space allocated in its
first alloc if the second alloc failed. Added a call to H5FL_FREE
to address this issue.
This is purely to keep coverity happy -- if this code is ever triggered,
we have much larger problems.
Note that this fix will trigger an unused return value complaint
from coverity next week.
r20190:
Fixed Coverity issues 1561 1565 and 1678 (UNUSED_VALUES) by moving checks of return values to after the function call.
r20191:
Fixed coverity issues 643 644 and 1678 (CHECKED_RETURN).
r20232:
Addressed coverity issues 923-925. Replaced calls to sprintf with calls
to HDsnprintf.
r20233:
Fix coverity issue 662. Don't try to sort 0 attributes in H5Aint.c.
r20234:
Fix coverity issue 664. Check for NULL before dereferencing in H5Gdeprec.c.
r20271:
Purpose: Fix coverity issue 784
Description: Modified H5_debug_mask() to keep a list of files opened for use as
a debugging output stream, and modified H5_term_library to close these files on
exit.
r20272:
addressed coverity issues 838 & 955. Issue was use of strcpy() -- existing
code was safe, but modified to use strncpy() to keep coverity happy.
r20273:
Addresed coverity issues 1388 and 1389.
Initialized sel_iter->type to NULL in H5S_select_iter_init.
r20275:
Purpose: Fix valgrind issue in mf.c
Description: Fixed bug (incomplete if statement) in test_mf_fs_alloc_free() so
the retrieved node gets freed.
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/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) 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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
|