2
0
mirror of https://github.com/HDFGroup/hdf5.git synced 2025-01-12 15:04:59 +08:00
Commit Graph

964 Commits

Author SHA1 Message Date
Neil Fortner
73d58f8b3c [svn-r20029] Purpose: Fix bug 2131
Description:
When using the scale-offset filter with floating point data or fill values, big
endian machines would save some metadata in the wrong byte order.  This caused
such datasets to yield incorrect data when read on little endian machines.
Fixed the scale-offset filter to always save this metadata in the right byte order (i.e. little endian).

Tested: jam, amani, heiwa (h5committedt); fedora, linew
2011-02-02 09:41:49 -05:00
Neil Fortner
c5988b31d3 [svn-r19967] Add note on parallel failures to RELEASE.txt 2011-01-19 10:51:20 -05:00
Jonathan Kim
562ba69f35 [svn-r19892] Purpose:
Bug 2089 - GMQS: h5diff segfault on a compound dataset with fixed length + 
    vlen string type order

Description:
    This is fix for the segfault when h5diff compares a compound dataset with 
    combination of fixed length string types and vlen string types in certain 
    orders. Optimized vlariable length string handling codes. The fix is 
    referred from h5dump handling vlen strings. 
    For testing, several compound datasets were added with various combinations.
    Previous failed cases:
     - Vlen string, Fixed length string, Vlen string, Fixed length string
     - Fixed length string, Fixed length string, Vlen string, Vlen string
     - Fixed length string, Vlen string, Fixed length string, Vlen string
     
Tested:
 jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
2010-12-28 13:08:40 -05:00
Albert Cheng
192339db91 [svn-r19816] Bug 2091: updated with the removal of Metraowerks compiler code. 2010-11-17 18:25:56 -05:00
Mike McGreevy
8897a3dcbd [svn-r19808] Purpose:
Add "--enable-unsupported" configure flag.

Description

    The "--enable-unsupported" configure flag allows a user to
    prevent configure from failing due to the use of incompatible
    options, such as c++ with parallel.

    Specifying --enable-unsupported will bypass all of configure's
    checks for incompatible and unsupported combinations of flags. 
    There are no guarantees that the library will be configured
    in any sort of working condition, but that's the risk of
    using the --enable-unsupported flag.

    I've changed all default error messages related to unsupported
    option combinations to indicate that using --enable-unsupported
    will allow configure to complete without error.

Tested:

    by hand on jam, tested all unsupported configure option 
    combinations with and without the new flag, making sure
    the flag allows configure to finish without error. 
    (h5committest wouldn't do any good here; it won't test
    the new option, and since we're enabling unsupported
    combinations, failures are likely to occur in build or
    tests with --enable-unsupported turned on anyways. 
    That's why they're unsupported!)
2010-11-17 13:07:51 -05:00
Mike McGreevy
39e3974628 [svn-r19798] Purpose:
Add additional error checking to catch erroneous user input.

Description:

    Attempting to retrieve a links's name by index in the case
    where the link is external and the file that the object is
    located in doesn't exist was causing a segmentation fault
    (in production) and an assertion failure (in debug).

    The segfault wasn't occuring until the metadata accumulator
    attempted a write, so I've added error checking higher in
    the pipeline in H5O_protect (where there was previously just
    an assert) to catch this. I've also added additional asserts
    in the H5F layer where there were none.

    Additionally, I added another case to the links.c test to
    test that this fails gracefully instead of segfaulting or 
    asserting out.

Tested:

    h5committest and gandalf (mac os x)
2010-11-17 10:08:33 -05:00
Jonathan Kim
40d56dd20c [svn-r19757] Purpose:
Improve h5diff performance.

Description:
    The following changes for improving h5diff performance:
    1) use HDmemcmp() before comparing each elements 
       (memcmp() is very fast at both linew and jam)
    2) replace the expensive H5Tequals() calls
    3) retrieve datatype information at dataset level not each element level 
       for compound datasets


Tested:
 jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
2010-11-11 10:23:44 -05:00
Jonathan Kim
40b3a8dee9 [svn-r19751] Purpose:
Fixed Bug# 1979 Output from h5ls -rdlS on nested compound datatypes is 
    difficult to parse.

Description:
    Update to add curly brackets for the nested compound members, when
    S (--simple) option is used with -l (--label), so user can tell 
    which members blong to which compound type.


Tested:
 jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32)
2010-11-09 16:13:53 -05:00
HDF Tester
97a3d197e1 [svn-r19740] Snapshot version 1.9 release 79 2010-11-07 08:31:35 -05:00
Jonathan Kim
e45cfcb9ee [svn-r19712] Purpose:
Fixed h5diff to handle variable-length strings in a compound dataset 
    correctly. Also variable-length string array in a compound dataset.
    Bug .
    

Description:
    Garbage values were displayed when h5diff compared variable-length 
    strings (or string array) in a compound type dataset. 


Tested:
 jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (Mac32)
2010-11-02 11:39:42 -05:00
HDF Tester
398aaea3e6 [svn-r19701] Snapshot version 1.9 release 78 2010-10-31 09:11:50 -05:00
HDF Tester
2efc06789a [svn-r19666] Snapshot version 1.9 release 77 2010-10-24 09:12:06 -05:00
Jonathan Kim
e926608485 [svn-r19633] Purpose:
Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.

Description:
 Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. This is expected to be failed.

Tested:
 jam, amani, heiwa
2010-10-18 18:06:53 -05:00
Jonathan Kim
07a4684190 [svn-r19605] Purpose:
Backout the previous changes (r19598):
 (Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.)

Description:
 Some failure occurred on talwit, so backout the changes and will put it back 
 after the fix.
 (Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. This is expected to be failed.
 Merged from hdf5 trunk r19598.)
2010-10-14 19:17:51 -05:00
Jonathan Kim
08e1300625 [svn-r19598] Purpose:
Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.

Description:
 Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. Expected to be failed.

Tested:
 jam, amani, heiwa
2010-10-14 15:47:20 -05:00
HDF Tester
ef168eb0d8 [svn-r19569] Snapshot version 1.9 release 76 2010-10-10 08:50:39 -05:00
Elena Pourmal
82be08b34a [svn-r19566] Maintenance: Added -O3 to be used with the C Intel v 11 compilers; set default to -O for all
unknown versions of the C Intel compilers.
             Modified apple config file to display Intel compiler information.
             Updated RELEASE.txt notes accordingly.
Platfroms tested: jam, amani and dubna (Mac 64-bit) with Intel C, Fortran and C++ compilers.
2010-10-08 15:57:17 -05:00
Allen Byrne
1f370978b4 [svn-r19525] Updated tested Windows platforms 2010-10-06 09:47:30 -05:00
HDF Tester
e1cd1485b8 [svn-r19512] Snapshot version 1.9 release 75 2010-10-05 08:37:04 -05:00
Raymond Lu
1c61b6fe13 [svn-r19481] I'm backing out my fix for bug 1707 because there're some unresolved issues - r19441 and 19467.
Bug 1707 is that H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API with 
the 1.8 library to compile.  

I created a branch off the trunk called set_auto to continue working on the problem.

Tested on jam - backing out, simple.
2010-09-27 14:02:48 -05:00
Neil Fortner
2087c6a9e4 [svn-r19461] Purpose: Fix bug 1864
Description:
Library versions 1.6.3 and earlier contain a bug which causes them to be unable
to perform certain operations on a group if that group's symbol table
information is not cached in the parent group's symbol table.  Versions 1.8.0
to 1.8.5 did not cache this information.  Modified library to cache this
information.

Tested: jam, amani, heiwa (h5committest)
2010-09-21 12:52:12 -05:00
Raymond Lu
d6c6a34a8f [svn-r19457] Bug fix for 1707 - H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API with the 1.8 library to compile. The cause is from the mismatch of H5Eprint1 and H5Eprint2 set
through H5Eset_auto.  I changed the union in the structure H5E_auto_t.  Another change is to 
make H5Eget_auto fail if H5Eset_auto is called to set the printing function.  I'll write a 
document for it.

Tested on heiwa, jam, and amani.

The property change in configure.in, config, and Makefile.am came from the merge of the 1.8 
library change.
2010-09-21 11:46:38 -05:00
Jonathan Kim
eb7b5b2cef [svn-r19406] Purpose:
Add --exclude-path option

Description:
 Specified path to an object will be excluded from comparing the two files or two groups. If group is specified all the member objects will be excluded.
 Related to "1890:  h5diff excluding object for file comparison via command line"

Tested:
 jam, amani and heiwa
2010-09-16 16:46:16 -05:00
Jonathan Kim
c561dc7183 [svn-r19400] Purpose:
Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object

Description:
 Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly.

Tested:
 jam, amani, heiwa
2010-09-16 12:48:06 -05:00
Jonathan Kim
a6b6b75a79 [svn-r19389] Purpose:
Fix for Bug1896 h5repack - changing layout to COMPACT does not work

Description:
Make h5repack be able to convert a layout to COMPACT for small size dataset as default.  Also add verifying layout changes in our test script.

Tested:
 jam, amani, heiwa
2010-09-15 13:32:07 -05:00
Neil Fortner
cb9a804f82 [svn-r19386] Purpose: Fix assertion failure caused by fractal heap header file pointer
Description:
The fractal heap header structure keeps a pointer to the file associated with
it.  However, it is possible for that file pointer to be closed while the
header is still in cache (through the shared file pointer).  Previously, the
header's file pointer was not updated and subsequently pointed to an invalid
file structure.  Modified fractal heap code to update the file pointer every
time the header is accessed.

Tested: jam, linew, amani (h5committest)
2010-09-15 10:29:38 -05:00
Allen Byrne
c55acc2d03 [svn-r19377] Added bug 1938 resolution 2010-09-13 10:54:55 -05:00
Mike McGreevy
b7c2d18029 [svn-r19367] Purpose:
Add windows threads support to HDF5.

Description:

    Added calls to the windows threads library to the H5TS layer, and wrapped
    most calls to either pthreads or windows threads library with portable
    H5TS-style defines. Modified tests to use portable function definitions
    as well.

    This can be configured via CMake with the HDF5_ENABLE_THREADSAFE
    option, and should work on windows vista and later operating systems.

Tested:

    h5committest, plus threadsafe with pthreads on jam and amani,
    and tested on a Windows Vista VM with threadsafe using windows threads.
2010-09-10 11:15:34 -05:00
Raymond Lu
073eb187d6 [svn-r19363] When mandatory filter failed to write data chunks, the dataset
couldn't close (bug 1260).  The fix releases all resources and closes
the dataset but returns a failure.

Tested with h5committest - jam, heiwa, amani.
2010-09-09 13:15:36 -05:00
Raymond Lu
ad0134f2a6 [svn-r19354] Quincey and I made H5Eset_current_stack also close the stack to be set. This is to avoid
H5Eclose_stack clearing the default stack.  Please see bug 1799.

Tested on jam - simple change.
2010-09-07 10:41:55 -05:00
Raymond Lu
9fbdf8f07a [svn-r19288] Bug 1934 - I added support of all data types for H5Tget_order. I added a new byte order
H5T_ORDER_MIXED specifically for compound types and its derived types.  They report mixed 
orders if they have members of different orders.

There is no change to configure.in, config, and Makefile.am in the top directory.  They have 
some property changes when I merged the code from 1.8.  

Tested on jam.  I tested the same change for 1.8 with h5committest.
2010-08-24 11:00:20 -05:00
Raymond Lu
e56b6f6c40 [svn-r19251] New feature(bug ): I made H5Tset_order support all data types with some restictions:
1. For enum type, members shouldn't be defined yet.
        2. H5T_ORDER_NONE only works for reference and fixed-length
           string.
        3. For opaque type, the order will be ignored.
        4. For compound type, all restrictions above apply to the
           members.

I'll change H5Tget_order and do another commit.

There is no change to configure.in, config, and Makefile.am.  There is some property change for
these files when I did a merge from 1.8.

Tested on jam.  But I tested the 1.8 on heiwa, and amani.
2010-08-19 10:27:56 -05:00
Raymond Lu
1fe94ec545 [svn-r19176] Bug fix for - The filter's public function CAN_APPLY should return htri_t not
herr_t.  To minimize the change of the library's behavior, in the function
H5Z_prelude_callback of H5Z.c, if the return value of can_apply is FALSE and
the filter is MANDATE, this function returns a FAILURE.  If the return value is FALSE
but the filter is OPTIONAL, this function returns a SUCCEED.  During the IO, the filter
will fail and return a size of zero.  But the pipeline will skip this filter.

Tested the same change for 1.8 on jam, linew, and amani.  Tested on jam with szip.
2010-08-05 12:14:39 -05:00
Neil Fortner
dd01261ac1 [svn-r19146] Purpose: Fix bug in direct IO driver
Description:

In certain circumstances, the direct I/O driver did not perform correctly when
data was unaligned.  The driver has been patched to fix this.  Also added some
potential performance improvements for the unaligned case, and strengthened the
test for whether the data needs to be aligned.

Tested: cobalt
2010-07-28 17:23:11 -05:00
Raymond Lu
51a30dbdb7 [svn-r19144] Update for bug fix . 2010-07-28 14:46:31 -05:00
HDF Tester
075f618e23 [svn-r19086] Snapshot version 1.9 release 74 2010-07-18 07:33:00 -05:00
Neil Fortner
c22b8a94f2 [svn-r19076] Purpose: Fix bug 1951
Description:
A bug introduced in 1.8.5 causes local heap data blocks to be mis-aligned when
sizeof_offsets + 2*sizeof_lengths is not a multiple of 8.  In this case, the
address of the data block as stored in the heap prefix is aligned but the actual
data block is not.  This causes files created with these sizes to be corrupted,
and prevents uncorrupted files with these sizes to be unreadable.  Modified
local heap code to account for alignment.

Tested: jam, amani, linew (h5committest)
2010-07-16 11:32:49 -05:00
Albert Cheng
aab23acc05 [svn-r19070] Document update: ID 1921 change mpirun to mpiexec
Changed the use of mpirun to mpiexec which is the MPI-2 official standard.
INSTALL_parallel:
Also bring in previous update of Red Storm support.
2010-07-14 12:07:50 -05:00
HDF Tester
3d3d95db07 [svn-r19064] Snapshot version 1.9 release 73 2010-07-11 12:06:05 -05:00
Jonathan Kim
af749bafb7 [svn-r19051] Purpose:
Add --no-dangling-links option to h5ls. 

Description:
Related to "Bug 1830 - Following an dangling external link in h5ls should set non-zero return code."
If --no-dangling-links option is specified and any dangling link is found, return exit code 1 (error).

Tested:
 jam, amani and heiwa
2010-07-07 13:52:04 -05:00
HDF Tester
be5d631410 [svn-r19047] Snapshot version 1.9 release 72 2010-07-04 12:06:29 -05:00
Jonathan Kim
eb5eba9aee [svn-r19034] Purpose:
Change h5ls not to manipulate special characters in object name or attribute name for smart display.

Description:
Related to "But1784 h5ls has input and output issues with links that have '\' characters in them."

Tested:
 jam, amani and linew
2010-06-28 15:34:32 -05:00
HDF Tester
732eaaf99b [svn-r19031] Snapshot version 1.9 release 71 2010-06-28 07:24:51 -05:00
HDF Tester
cb72139f74 [svn-r19022] Snapshot version 1.9 release 70 2010-06-20 12:05:42 -05:00
Neil Fortner
686d856802 [svn-r19006] Purpose: Improve performance of the the chunk cache
Description:
Previously, the chunk cache would, when looking for a chunk, alwaylook for the
chunk in the b-tree before checking the cache.  Reworked the functions that
look up chunks to always check the cache first and avoid the b-tree lookup if
the chunk is in cache.

Tested: jam, linew, amani (h5committest)
2010-06-15 16:21:03 -05:00
Albert Cheng
4e4c5d3e0f [svn-r18992] Bug Fix: (ID 1921)
PHDF5 changed to use "mpiexec", instead of mpirun, as the default MPI
applications startup command as defined in the MPI-2 definition, section
4.1.  Note that only mpich related (using mpicc command) definitions are
changed to mpiexec. Other favors like hcc, AIX, champion, are not changed
since I don't have a way to verify them yet.

Tested:
jam and amani, using both current and new mpich.
Did not h5committested since this affects PHDF5 configure only.
2010-06-11 18:37:33 -05:00
Jonathan Kim
1a02e37f16 [svn-r18943] Purpose:
Support follow symbolic links.

Description:
    Add '--follow-symlinks' option to follow symbolic links (soft and external).
    Update help page according to RM.
    Remove some warning messages from compiler.

Tested:
    jam, amani and linew
2010-06-02 10:13:13 -05:00
Allen Byrne
16bb687b00 [svn-r18940] Update Cygwin and Windows references
Removed support for MinGW
2010-06-01 15:34:26 -05:00
Elena Pourmal
3df3fc6176 [svn-r18881] Maintenance: Fixed a typo in the bug number (should be 1851 instead of 1855) 2010-05-22 12:49:58 -05:00
Elena Pourmal
18ae0c6e6d [svn-r18880] Bug fix:
Fixed a bug (1855) in H5DSattach_scale, H5DSis_attached and H5DSdetach_scale
    caused by using H5Tget_native_type function to determine the native
    type for reading REFERENCE_LIST attribute. The bug was exposed on Mac PPC.

Platforms tested: juniper (Mac PPC), jam, amani, linew
2010-05-22 12:30:45 -05:00
Jonathan Kim
a5ca9e6ba9 [svn-r18873] Purpose:
Rename '--follow-links' to '--follow-symlinks' 

Description:
    The '--follow-links' option is to follow symbolic links (soft and external).
    Make the name more intuitive and specific to the feature.

Tested:
    jam, amani and linew
2010-05-21 15:12:22 -05:00
Neil Fortner
2db0e8ecf3 [svn-r18868] Purpose: Fix bug in dataset shrinking algorithm
Description:
Previously, it was possible for a chunk to be flushed due to chunk operations in
the callback from H5B_iterate in H5D_chunk_prune_by_extent.  Because flushing
the chunk can force it to be reallocated if it is filtered, this can change the
contents of the chunk b-tree in the middle of H5B_iterate.  Because H5B_iterate
uses a locally cached copy of the b-tree, this causes subsequent operations
to be passed incorrect data.  Rewrote H5D_chunk_prune_by_extent to avoid
H5B_iterate entirely.

Also fixed a bug in the dataset expand algorithm that could cause extra chunks
to be created.

Tested: jam, linew, smirom (h5committest)
2010-05-20 16:55:55 -05:00
HDF Tester
49a6f7174d [svn-r18823] Snapshot version 1.9 release 69 2010-05-16 09:55:25 -05:00
Elena Pourmal
d7a89d6c7b [svn-r18818] Bug fix:
Fixed a bug in the H5DSdetach_scale function when 0 bytes
     were allocated after the last reference to a dim. scale
     was removed from the list of references in a VL element of the
     DIMENSION_LIST attribute; modified the function to comply
     with the Spec: DIMENSION_LIST attribute is deleted now when no
     dimension scales left attached.

Platforms tested: jam with electric fence, amani amd linew
2010-05-14 23:10:53 -05:00
Jonathan Kim
f336441f7c [svn-r18813] Purpose:
Add bug fixes for Tools.

Description:
    Added list:
    1726 - NPOESS: h5repack loses attributes for datasets of type H5T_REFERENCE
    1814 - NPOESS: h5repack doesn't handle references to the groups as an 
                   element of a dataset
    1817 - h5copy fail to copy dangling link by specifying link path directly
    1793 - h5ls on a non-existent file gives 0 return code

Tested:
    no, just text update.
2010-05-14 16:37:27 -05:00
Mike McGreevy
ed4885a485 [svn-r18804] Purpose:
Fix memory leaks

Description

    Added a routine to free memory which addresses a memory leak
    when variable length strings are used as fill values.

Tested:

    h5committest and valgrind (on jam/amani) to confirm freed memory.
2010-05-14 13:44:36 -05:00
Binh-Minh Ribler
3cd3de7612 [svn-r18803] Description:
Added notes about
        + PropList::PropList(id) pclass id/plist id
	+ new DataSet::getInMemDataSize
	+ CommonFG::getLinkval and CommonFG::getComment take default values 
	+ bugzilla 1061
	+ read/write methods of DataSet and Attribute
2010-05-14 10:14:05 -05:00
Mike McGreevy
f0ecd71307 [svn-r18709] Purpose:
Improve configure's large-file support control.

Description:

    Modified configure to now attempt to add defines necessary for
    supporting largefiles on all systems, instead of solely on linux. This 
    is in response to user requests to enable largefile support on Solaris 
    by default, as well as to give extra control on AIX (instead of just 
    jamming the necessary flag into the config files).

    The old --enable-linux-lfs flag has been removed in favor of the 
    --enable-largefile flag (enabled by default), which can be used on all
    platforms.

    On systems where large files cannot be supported in this manner,
    configure will report as such.

Tested:

    h5committest
    AIX (NCSA's blue_print machine)
    duty, liberty, and linew.
2010-05-05 12:34:26 -05:00
Binh-Minh Ribler
3bfd4dd393 [svn-r18687] Description:
Added notes about new functions:
	CommonFG::getObjTypeByIdx
	CommonFG::getObjnameByIdx
2010-05-02 20:34:48 -05:00
HDF Tester
54cd6ecec9 [svn-r18684] Snapshot version 1.9 release 68 2010-05-02 10:21:31 -05:00
HDF Tester
987bc92a01 [svn-r18589] Snapshot version 1.9 release 67 2010-04-18 08:59:45 -05:00
Mike McGreevy
0cf2a97cfb [svn-r18579] Purpose:
Autotool Upgrade / Libtool Bug Fix

Description:

    Updated autotools referenced in bin/reconfigure as follows:

    Autoconf 2.64 --> Autoconf 2.65
    Automake 1.11 --> Automake 1.11.1
    Libtool 2.2.6a --> Libtool 2.2.6b-mcg

    The referenced libtool version is a custom version of 2.2.6b. It 
    has been tweaked to fix a bug in libtool that occurs
    when using PGI 10.0 compilers. A check incorrectly categorizes
    the C++ compiler as version 1.0 instead of 10.0, and the link
    line is subsequently set up incorrectly and fails to compile.

    A patch has been made available and will be included in the next
    release of libtool, but in the meantime I've applied the patch to a custom
    installation as indicated above. This bin/reconfigure now references
    the custom installation, and the resulting configure script will correctly
    categorize the PGI 10.0 C++ compiler.

    Ran bin/reconfigure to regenerate configure and makefiles.

Tested:

    jam and amani with PGI 10.0 compilers.
    h5committest
2010-04-15 16:17:22 -05:00
HDF Tester
3a0f7b3bba [svn-r18545] Snapshot version 1.9 release 66 2010-04-11 12:03:28 -05:00
Neil Fortner
7270b677a5 [svn-r18535] Purpose: Fix bug 1815
Description:
Attempting to copy an object with NULL references (all bytes zero) with the
H5O_COPY_EXPAND_REFERENCE_FLAG flag set would cause a failure or an assertion
(depending on whether it was in debug mode).  Changed copy routine to detect
NULL references (object and region) and avoid attempting to expand the reference
in this case.

Tested: jam, linew, amani (h5committest)
2010-04-08 13:29:59 -05:00
HDF Tester
6ea7793875 [svn-r18508] Snapshot version 1.9 release 65 2010-04-04 08:43:55 -05:00
HDF Tester
c49b97ff38 [svn-r18465] Snapshot version 1.9 release 64 2010-03-28 08:41:02 -05:00
Neil Fortner
d3d4d8782b [svn-r18445] Purpose: Fix bug 1637
Description:
Modified algorithm for extending a dataset with early allocation so it only
deals with the new chunks.  Formerly, it would loop over all chunks, checking
to see if each existed in cache and on disk, causing major performance issues
with large numbers of chunks.

Tested: jam, linew, amani (h5committest)
2010-03-24 11:41:14 -05:00
HDF Tester
689868202c [svn-r18432] Snapshot version 1.9 release 63 2010-03-21 08:42:10 -05:00
HDF Tester
0a4eadc0b9 [svn-r18406] Snapshot version 1.9 release 62 2010-03-14 10:04:16 -05:00
Neil Fortner
2ece0d878a [svn-r18395] Purpose: Fix links.c failure
Description:
The core file driver previously matched files only based on the name used to
open them, even when a backing store is used.  This caused problems in the
failing test when it traversed an external link to itself, and did not recognize
that it was the same file.  Similar tests in links.c were skipped when the core
file driver was used.  The failure was previously masked by inappropriate file
flushes caused by external link traversal.  Added code to the core file driver
to keep track of low level file information of the backings store to allow for
accurate recognition of duplicate files.  Also re-enabled all links.c tests for
the core file driver.

Tested: Fedora (core and sec2 drivers; no time for full commit test, will
monitor daily tests)
2010-03-09 13:19:42 -05:00
Neil Fortner
1872925320 [svn-r18376] Purpose: Fix bug 1733
Description:
Support for expanding external links was not implemented in H5Ocopy, even though
a flag existed for H5Pset_copy_object to enable this.  This patch implements
this feature.

Tested: jam, amani, linew (h5committest); Fedora
2010-03-05 12:51:45 -05:00
Neil Fortner
179b54da83 [svn-r18374] Purpose: Fix bugs involving external links
Description:
Previously, the library would reopen the source file when traversing an external
link if unable to find the target file otherwise.  This has been corrected.
Also moved the call to H5F_flush from H5F_try_close to H5F_dest, so the file is
only flushed when the last identifier for the file is closed.  This prevernts
situations where the library could attempt to flush a file with protected
metadata.

Tested: jam, amani, linew (h5committest); Fedora
2010-03-05 12:24:17 -05:00
HDF Tester
ed2e263b3f [svn-r18350] Snapshot version 1.9 release 61 2010-02-28 08:37:04 -05:00
Jonathan Kim
ee757e449b [svn-r18273] Purpose:
bugzilla 1754: h5diff: support comparing through links.

Description:
    Fix incorrect (or hanging) behavior in parallel mode when specifying 
    invalid combination of command options. 
    (ex: -v and -q , --no-dangling-links without --follow-links)
    Add relate test case
    Update h5diffgentest.c due to add test files this and previous time

Note:
    svn  (prior to this)
    svn  (original check-in)

Tested:
    h5committest (jam, amani and linew)
2010-02-18 11:51:12 -05:00
Jonathan Kim
ad9e876b0c [svn-r18266] Purpose:
bugzilla 1754: h5diff: support comparing through links.
    (original check-in svn revision )
Description:
    fix the hang issue in parallel mode when compare external-link.
    add --no-dangling-links option. 
    add test cases (#450-#459) relate to the new option.
    improve test script to check exit code.
    update --help relate to the new options.
    correct some indentations.

Tested:
    h5committest (jam, amani and linew)
2010-02-16 14:43:05 -05:00
Neil Fortner
7c82bbf030 [svn-r18262] Purpose: Fix bug in b-tree code
Description:
In certain cases, removal of an object in a v1  b-tree would cause the leftmost
key in the right neighbor to be overwritten.  While this did not pose a problem
for group b-trees, with chunked datasets it would overwrite the offset value
of the neighbor's leftmost child, causing corruption.  Reworked the code to
differentiate between b-trees whose children are fundamentally associated with
their left key and those who are associated with their right key.

Tested: jam, linew, amani (h5committest)
2010-02-16 12:18:38 -05:00
HDF Tester
9daa1a55cd [svn-r18217] Snapshot version 1.9 release 60 2010-02-07 07:35:22 -05:00
HDF Tester
1c05d48b93 [svn-r18199] Snapshot version 1.9 release 59 2010-01-31 07:29:07 -05:00
Jonathan Kim
1afb0667d2 [svn-r18167] Update MANIFEST and RELEASE.txt for svn r18164 and r18165 2010-01-25 20:33:09 -05:00
HDF Tester
1e25bc217f [svn-r18120] Snapshot version 1.9 release 58 2010-01-17 07:25:27 -05:00
HDF Tester
a65b70ccc7 [svn-r18100] Snapshot 2010-01-10 07:33:23 -05:00
HDF Tester
a65f27f30f [svn-r18059] Snapshot 2010-01-03 07:39:26 -05:00
HDF Tester
06ce6af638 [svn-r18047] Snapshot 2009-12-20 07:32:29 -05:00
HDF Tester
dc974e3de2 [svn-r18012] Snapshot 2009-12-13 07:35:57 -05:00
Raymond Lu
5d0fdb855d [svn-r17985] I put in the bug fix info for . No test is needed. 2009-12-10 11:39:58 -05:00
HDF Tester
94a00c768c [svn-r17973] Snapshot 2009-12-07 09:18:34 -05:00
Albert Cheng
497a6fcc85 [svn-r17936] Updated AIX compilers information. 2009-11-27 11:12:18 -05:00
Albert Cheng
d65fa708c0 [svn-r17934] Updated with new ibm compiler configure changes. 2009-11-26 13:10:28 -05:00
Jonathan Kim
8bcc914263 [svn-r17905] Purpose:
Fix Bug1672 - Display garbage value on LE machine for BE data.

Description:
	Casuing by calling diff_dataset twice when -r or no option was given.
	Change to call it once which fix the problem. 
	It also improves the performance. (diffing time in half)
	According further test, it also occurred on BE machine as well and it 
	seems occruing only with the BE data attached to Bugzilla. 
	Don't know how the file was created. Anyway this fix will prevent 
	from diffing with garbage values in similiar potential case. 
	
Tested on:
	linux32 (jam) , linux64 (almani), solaris (linew)
2009-11-20 13:56:01 -05:00
HDF Tester
5a821b959b [svn-r17902] Snapshot 2009-11-17 09:27:25 -05:00
Elena Pourmal
5793231260 [svn-r17835] Maintenance: More cleanup in the configuration table. 2009-11-04 19:07:53 -05:00
Elena Pourmal
ce42be8e9c [svn-r17834] Maintenance: Updated system information for Solaris and Mac Intel 2009-11-04 19:06:00 -05:00
Mike McGreevy
9e170a0be0 [svn-r17819] Purpose:
Updating RELEASE.txt

Description:

    Clarifying explanation of --enable-static-exec behavior.

Tested:

    Doc only, none needed.
2009-11-04 09:39:45 -05:00
Albert Cheng
ec06f9913a [svn-r17818] Removed Zeus and ubgl entries since they were not tested any more.
Added AIX known problem of testcheck_version.sh failure.
2009-11-03 23:32:18 -05:00
Neil Fortner
63cb9f4d61 [svn-r17811] Update RELEASE.txt for fractal heap filtering changes (r17623) 2009-11-03 11:33:30 -05:00
Albert Cheng
8357259887 [svn-r17801] Added known problem of h5repack in AIX -q32 platform.
(forgot to add the text in the last commit.)
2009-11-02 10:02:52 -05:00
Albert Cheng
48869af67a [svn-r17800] Removed support and known problems of the IRIX, IRIX64 and Tungsten platforms
since they have retired.
Added known problem of h5repack in AIX -q32 platform.
2009-11-02 09:31:32 -05:00
Neil Fortner
2f423f0a47 [svn-r17771] Add bug number to note in RELEASE.txt. 2009-10-28 10:10:10 -05:00
Neil Fortner
529eb825c2 [svn-r17764] Purpose: Fix bug 1483
Description:
H5HG_load made improper assumptions about the ordering of object indices, namely
that they are in order.  Not only is this not guaranteed by the file format
spec, but this condition can be violated if id's "wrap around" which can happen
when overwriting VL data.  H5HG_load has been fixed to handle any order of
indices.  Also fixed some other bugs involving allocation of global heaps in
memory.

Tested: jam, linew, amani (h5committest)
2009-10-27 21:52:05 -05:00
Neil Fortner
8552aed7bb [svn-r17763] Minor formatting change in RELEASE.txt. 2009-10-27 17:52:05 -05:00
Neil Fortner
376a788840 [svn-r17760] Purpose: Fix problem with H5TB API
Description:
The H5TB API makes some improper assumptions about the order of compound
datatype members.  Namely, it assumes that members remain in the order in which
they were inserted.  Unfortunately, this assumption is inherent in the design of
the interface.  The library has been patched so that this assumption holds in
situations relevant to H5TB.

Tested: jam, linew, amani (h5committest)
2009-10-27 17:23:49 -05:00
HDF Tester
4af649f03d [svn-r17742] Snapshot version 1.9 release 50 2009-10-25 01:45:59 -05:00
Larry Knox
27a68642f1 [svn-r17670] Snapshot version 1.9 release 49 2009-10-18 11:40:34 -05:00
Larry Knox
64ffab6881 [svn-r17628] Snapshot version 1.9 release 48 2009-10-11 07:49:32 -05:00
Peter Cao
82efaff584 [svn-r17619] Add comments about h5diff change made for epsilon. 2009-10-08 14:40:42 -05:00
Mike McGreevy
7ec079a515 [svn-r17616] Purpose:
CFLAGS overhaul

Description:

    Modified the way configure handles CFLAGS.

    (note: all changes also apply to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS).

    1. The configure process will now always preserve a user's CFLAGS
    environment variable setup. Any additional flags necessary for compilation
    added at configure time will be passed into the Makefiles as AM_CFLAGS,
    which is an automake construct to be used in addition to CFLAGS.

    This will allow a user to have the final say, as CFLAGS will always appear
    later in the compile line than AM_CFLAGS. Additionally, setting CFLAGS
    during make will no longer completely erase all flags set by configure,
    since they're maintained in AM_CFLAGS.

    2. Additionally, where possible, flags previously being assigned directly
    into CFLAGS (and thus propagating into h5cc) have now been redirected into
    H5_CFLAGS, so they're used ONLY for compiling hdf5, and not embedded into
    the h5cc wrapper script as well.

    *Note that H5_CFLAGS ultimately is assigned into AM_CFLAGS for use in the
    Makefiles. Complete description of changes and build process will be
    included in a Configure Document that Elena and I are working on.

    3. Removed unsupported config files. This includes:

       config/dec-osf*
       config/hpux11.00
       config/irix5.x
       config/powerpc-ibm-aix4.x
       config/rs6000-ibm-aix5.x
       config/unicos*

     4. Modified configure summary to display additional values. Specifically,
     appropriate AM_* variables are being shown, as well as H5_FCFLAGS and
     H5_CXXFLAGS, which were for some reason not already present.

Tested:

    - H5committest
    - Tested on all THG / NCSA machines, using several combinations of the more
      prominent configure options (c++, fortran, szip, threadsafe, parallel,
      et cetera). (Thanks to Quincey for rysnc testing setup!)
    - With regards to new automated testing, anything *necessary* for
      compilation will be caught by the daily tests as it stands now. (i.e.,
      if LDFLAGS is not properly set when szip is used, linking will fail).
      Additionally, with regards to which flags get into h5cc, if any
      *necessary* flags have been improperly removed, then daily tests should
      fail during make installcheck. Additional machine-specific desired
      behaviors and/or checks may have to be set up separately within the
      daily tests, so this is something to work on.
2009-10-08 10:17:30 -05:00
Albert Cheng
047ac8f136 [svn-r17615] Updated with H5Pget_preserve fix information. 2009-10-08 09:11:32 -05:00
Albert Cheng
8d8f365711 [svn-r17606] Code Cleanup:
TFLOPS machine has retired long ago. Removed all code specific for its
support.

Test:
h5committested.
2009-10-07 00:08:05 -05:00
Larry Knox
be2d2abf86 [svn-r17589] Snapshot version 1.9 release 47 2009-10-04 07:56:18 -05:00
Neil Fortner
eed2ea424b [svn-r17585] Purpose: Fix bug 1597
Description:
When copying a dataset  using a vlen inside a compound, the various dataset
copying callbacks would allocate a background buffer but would not use it when
converting from disk to memory, only memory to disk.  This caused an assertion
failure as compounds always need a background buffer.  These callbacks have
been modified to use the background buffer for both conversions.

Tested: jam, linew, smirom (h5committest)
2009-10-02 15:40:01 -05:00
Mike McGreevy
1abb6b133b [svn-r17571] Purpose:
Makefile Bug Fix

Description:

    Added $(EXEEXT) extension to H5detect when it's executed to generate
    H5Tinit.c so it works correctly on platforms that require the full
    extension when running executables.

Tested:

    h5committest, mingw, and user-verified (via submitted patch).
2009-10-01 14:51:57 -05:00
Mike McGreevy
8c754e8385 [svn-r17567] Purpose:
Configure Fix

Description:

    Modified configure to set FC and CXX to "no" when fortran and c++ are
    not being compiled, respectively. This will prevent configure from running
    some checks on these compilers when they are not being used.

    This fixes a problem that was occuring when FC and/or CXX are set to
    a nonexistant or invalid compiler. Even if the languages were disabled,
    a libtool test would fail, thus preventing libtool from properly linking
    any libraries, yet configure would not flag an error message due to this
    because the languages were disabled.

Tested:

    - h5committest (jam, smirom, linew)
    - manually eyeballed configure output and logfile.
2009-10-01 12:05:38 -05:00
Allen Byrne
98f6b609ad [svn-r17566] Fix for Bug 1562. H5DSis_attached needed to account for platform dependent types. Added test and test files for LE and BE dimension scales. Reworked part of test_ds file as part of debug.
Added missing H5Tclose in region reference routines.
H5DS.c checked for other locations which need to account for platform dependent types in dealing with ds_list_t. Added generator program for test files of LE and BE dimension scales.

Tested: local linux, h5committest
2009-10-01 11:17:17 -05:00
Albert Cheng
531f086cbc [svn-r17550] Updated with H5check_version tests. 2009-09-29 11:49:34 -05:00
Albert Cheng
8feb521bbb [svn-r17544] 2009-09-28 23:45:46 -05:00
Albert Cheng
0f2901843c [svn-r17543] Bug fix (ID 1656):
Changed H5check_version() to suppress the warning message totally if
$HDF5_DISABLE_VERSION_CHECK is 2 or higher. (Old behavior treated 3 or higher
the same as 1, that is to print a warning and allows the program to continue.

Tested:
h5committested, extra jam serial, --disable-embedded-libinfo.
2009-09-28 23:43:22 -05:00
Larry Knox
96318e678f [svn-r17538] Snapshot version 1.9 release 46 2009-09-27 07:42:31 -05:00
Neil Fortner
a57f2246b2 [svn-r17535] Purpose: Fix bug 1620
Description:
H5Ppublic.h listed H5Pget_filter_by_id1 and H5Pget_filter_by_id2 as returning
H5Z_filter_t, when in fact they return herr_t.  The header file has been
corrected to indicate that they return herr_t.

Tested: jam
2009-09-25 14:13:22 -05:00
Neil Fortner
2f3d788b2c [svn-r17534] Add note to RELEASE.txt for changes in r17530 2009-09-25 14:08:41 -05:00
Allen Byrne
c1f98f4763 [svn-r17451] Added new features for h5dump in tools section. Moved h5dump bug fix to bug fixed section. 2009-09-04 15:38:40 -05:00
Larry Knox
458358f0bd [svn-r17446] Snapshot version 1.9 release 45 2009-09-03 13:02:46 -05:00
Quincey Koziol
e6c9d34f58 [svn-r17394] Description:
Update release notes with note about fixing Bz#1473.
2009-08-20 14:17:51 -05:00
Allen Byrne
0ac57cc17b [svn-r17369] Added h5dump/h5ls display buffer resize fixed in tools library. 2009-08-17 09:19:59 -05:00
Mike McGreevy
4598a59f86 [svn-r17345] Purpose:
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.
2009-08-12 13:55:25 -05:00
Larry Knox
eb3fc461a4 [svn-r17343] Snapshot version 1.9 release 44 2009-08-12 08:27:39 -05:00
Peter Cao
1f34be9bba [svn-r17334] Add notes about bog fix (1563) 2009-08-11 18:14:40 -05:00
Albert Cheng
eccec94aec [svn-r17328] Added the recognization of PathScale compilers. Also added the known
problem of PathScale MPI failure when accessing a Panasas file system.
2009-08-11 15:13:07 -05:00
Mike McGreevy
6a00b1b6ff [svn-r17228] Purpose:
Fix BZ 

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.
2009-07-23 15:04:18 -05:00
Albert Cheng
114dd0ecb0 [svn-r17201] Changed default Gnu fortran compiler from g95 to gfortran since
gfortran is more likely installed with gcc now.
2009-07-19 18:47:30 -05:00
Larry Knox
818e0698cc [svn-r17159] Snapshot version 1.9 release 43 2009-07-06 10:42:14 -05:00
Larry Knox
e70b32f7b5 [svn-r17135] Snapshot version 1.9 release 42 2009-07-01 12:23:31 -05:00
Neil Fortner
1846ea8d50 [svn-r17120] Add bug number for yesterday's fix. 2009-06-26 14:53:12 -05:00
Neil Fortner
02dc89e00b [svn-r17108] Purpose: Fix bug in H5Z_filter_info
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)
2009-06-25 13:56:00 -05:00
Larry Knox
312d6350fe [svn-r17047] Snapshot version 1.9 release 41 2009-06-14 10:41:49 -05:00
Allen Byrne
cce29e5642 [svn-r17034] Updated performance section to note that the perf_serial test works on windows. 2009-06-11 14:29:54 -05:00
Neil Fortner
4d2449d382 [svn-r17025] Purpose: fix bug 1593
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
2009-06-10 14:17:26 -05:00
Larry Knox
c87c334876 [svn-r17012] Snapshot version 1.9 release 40 2009-06-07 10:41:52 -05:00
Larry Knox
126dae2440 [svn-r16995] Snapshot version 1.9 release 39 2009-06-01 13:50:44 -05:00
Pedro Vicente Nunes
8745d8b7cc [svn-r16947] 1. (B1) h5ltread_dataset_string_f error with g95
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
2009-05-13 14:10:25 -05:00
Christian Chilan
9e45b7d2d6 [svn-r16885] Update to include the modification in parallel tests. 2009-04-29 01:39:10 -05:00
Neil Fortner
8c074d5c03 [svn-r16807] Purpose: Fix bug 1533
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)
2009-04-20 14:12:19 -05:00
Neil Fortner
c7aa94f4ec [svn-r16803] Purpose: Fix bug 1548
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)
2009-04-20 11:54:52 -05:00
Neil Fortner
6d13b7a243 [svn-r16800] Purpose: Fix bug 1516
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)
2009-04-20 11:37:47 -05:00
Scot Breitenfeld
22acfa9fe1 [svn-r16799] corrected typos in fortran API 2009-04-20 11:26:17 -05:00
Mike McGreevy
bc36a358d1 [svn-r16792] Description:
- 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
2009-04-20 01:00:11 -05:00
Scot Breitenfeld
0ef325886d [svn-r16781] Added information about new fortran wrappers added:
H5D_h5dget_access_plist_f
   H5I_h5iis_valid_f
   H5P_h5pset_chunk_cache_f
   H5P_h5pget_chunk_cache_f
2009-04-17 12:58:05 -05:00
Neil Fortner
b04489e6ce [svn-r16766] Fix a comment in H5Pdapl.c, update RELEASE.txt with chages to factory free
lists.

Tested: kate
2009-04-16 16:06:37 -05:00
Albert Cheng
773f3686f0 [svn-r16749] New feature (Bug ID: 1345):
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.
2009-04-14 17:07:24 -05:00
Allen Byrne
2049a2691c [svn-r16745] Added fixed bug 1536, about the include for the _getcwd() function. 2009-04-14 09:06:22 -05:00
Larry Knox
0eacb97a15 [svn-r16738] Snapshot version 1.9 release 38 2009-04-11 08:24:23 -05:00