Minor code safety issue in test/fheap.c and whitespace in other files.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug
(Too minor to require h5committest)
This occurs due to the istore test creating very large files on systems which
do not have POSIX-like sparse file semantics. The large amount of I/O causes
the test to run for a very long period of time.
The fix was to copy the "big" test's sparse file check and only run the
largest sparse file test when POSIX-like sparse file semantics are found.
Tested on:
jam (nfs)
ostrich (nfs)
loyalty (ufs)
64-bit linux VM (ext4)
64-bit OS-X Lion (hfs, detected as not POSIX sparse)
64-bit Windows 7 (NTFS, detected as not POSIX sparse)
The OS-X failure to pass the sparse check is likely an error and will be
entered as a new bug.
The parser mistaked "-" as substraction. I fixed it and also fixed another problem
with some special cases like 100-x and 2/x.
Tested on jam, koala, and ostrich.
Description:
When using the new object header format, it was possible for corruption to occur
if the first object header chunk changed size such that the lenght of the "chunk
0 size" field changed. This only occurred if there were messages that had not
been decoded. The original algorithm that changed the object header chunk size
marked all messages as dirty, causing those that had not been decoded to have
both the raw and native form invalidated. Changed the algorithm to avoid
marking messages dirty and added assertions to catch the case where messages
are dirtied without being decoded (or recently created) first.
Tested: jam, koala, ostrich (h5committest), durandal
Description:
When using the new object header format and adding an attribute with a size near
64K, it was possible for file corruption to occur. This happened only if the
first object header chunk was smaller than 256 bytes and then grew to larger
than 64K after the attribute was added.
Tested: ostrich, jam, koala (h5committest), durandal
Correct corner case for creating a contiguous dataset with a zero-sized
dataspace, when the allocation time is set to early.
Also clean up a few compiler warnings in the dataspace code.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug & parallel
Remove some leftover uses of the __FUNCTION__ macro, replacing them with
FUNC macro, as used everywhere else.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
(too minor to require h5committest)
Add FUNC_ENTER macros for package-private routines and begin process of
switching package routines to use them. All H5G routines are currently
finished.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
Description:
When shrinking a chunked dataset, the library fills in the unused parts of
chunks that have been shrunk. The fill value buffer allocated for this purpose
had a maximum size of 1 MB, but the fill was performed in a single operation.
Therefore, if the amount of unused space in a chunk after being shrunk was
greater than 1 MB, the library would read off the end of the fill value buffer.
Changed the maximum fill buffer size to be equal to the chunk size.
Tested: durandal; jam, koala, heiwa (h5committest)
Don't check dataset storage size for compressed datasets with region
reference datatypes. (The address of the region reference type in the file
varies and affects the compressed size)
Tested on:
Mac OS X/32 10.7.2 (amazon) w/debug & production + check-vfd
Recalculate the size of destination attribute message when the source and
destination versions are different during an object copy operation.
(Jira: HDFF-7718)
Tested on:
Mac OS X/32 10.7.2 (amazon) w/debug
(h5committest upcoming)
Description:
Added new H5SL_TYPE_GENERIC skip list type, which uses void *'s as keys and a
client-supplied callback for key comparison. This was added to support the
upcoming "merge named datatype" feature for H5Ocopy, but may be used in other
places as well. Also added testing.
Also fixed a potential bug with the H5SL_TYPE_OBJ implementation, and added
testing for that.
Tested: jam, koala, heiwa (h5committest), durandal
Correct error in loading local heap prefix & data block from the file.
Sometimes the local heap's prefix could be loaded before the data block (e.g.
using H5Oget_info), but then when the data block was loaded later, the free
list information would get lost, causing the heap's size to grow larger than
necessary. This is Jira bug #HDFFV-7767
Tested on:
Mac OS X/32 10.7.2 (amazon) w/debug
(h5committest coming up)
Description:
H5Ocopy could get confused when copying a named datatype containing an
attribute which used that named datatype as its datatype. This happened
because H5Ocopy would recurse into the attribute's datatype before the object
the attribute was in was fully copied (i.e. before the "post-copy" pass).
Modified H5Ocopy to avoid recursing before the post-copy step in this case.
Required many changes, including to how non-committed shared messages are
copied.
Tested: jam, koala, heiwa (h5committest); durandal
Some machines, like LLNL udawn, a blue-gene machine, requires all executables,
be launched by some command like mpirun.
Solution:
Added $RUNSERIAL to launch the executable.
Tested: LLNL uDawn.
them is in the INIT_INTEGER macro definition in dt_arith.c. It complained about line 150 where it tried to subtract 1 from
the negative minimal value of "int", causing it to overflow (or underflow). So I revised the code to avoid it.
Tested on jam, koala, linew, and Mac OS Lion with CLANG compiler.
temp_point->l = (unsigned long long)((i * 100 + j * 1000) * n);
The value can overflow the signed int before being converted to unsigned long long. So I changed it to
temp_point->l = (unsigned long long)((i * 40 + j * 400) * n);
to keep it under the maximal value.
Tested on jam. Simple change.
Ran bin/reconfigure to update the Makefile.in in directories not part of the fortran directory check=in. Updates Makefile.in due to changes made in configure.in for the Fortran 2003 additions.
Tested on all platforms run under daily tests.
i_mask = ~((unsigned)~0 << (precision[0] + offset[0])) & ((unsigned)~0 << offset[0]);
in line 3680 left shifted a 32-bit integer for 32-bit. The result is undefined by C language. A user
discovered it using clang compiler with -fcatch-undefined-behavior option (see Issue 7674
in Jira). So I changed it in a funny way to avoid it.
Tested on jam, koala, and heiwa.
Further patches for Jira 7638, to ensure that H5D/Aget_type will
be attached to the correct top file. (This change to the library should
reverted when Jira 7638 is finally finished)
Tested on:
FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode
FreeBSD/64 8.2 (freedom) w/gcc4.6, 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 (koala) 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
Mac OS X/32 10.6.8 (amazon) in debug mode
Mac OS X/32 10.6.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
1. Quincey changed H5P_DATASET_ACCESS_DEFAULT to H5P_DEFAULT for the tests that call H5Rdereference. Inside H5R_dereference, I assigned H5P_DATASET_ACCESS_DEFAULT to OAPL_ID if it is H5P_DEFAULT.
2. I added the test for invalid OAPL_ID in trefer.c.
Tested on jam, koala, heiwa.
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)
Check in ugly version of fix for Jira #7638. I'm going to leave the issue
open in Jira and when the library has been refactored to use shared file
pointers (instead of top file pointers) for file operations, I'll uncomment
the check in src/H5Oshared.c
Tested on:
Mac OS X/32 10.6.8 (amazon) w/debug
(too small for h5committest)
super block. We took it out in v1.8 library because it's meaningless
for the MULTI file. v1.8 library saves the EOA for the metadata file,
instead. But this caused some backward compatibility problem.
v1.8 library couldn't open the file created with v1.6 library. I
fixed the problem by checking the EOA value to detect the file
created with v1.6 library.
Tested on jam, koala, and heiwa.
data, overflowing values are retained. When conversion happens, the values become -1. The conversion function puts -1
when overflow happens. I added two new dataset transfer property to control whether to fill 0xff in the destination
data or convert to the destination data when overflow happens. The two new functions are H5Pset(get)_enum_conv_overflow. I also added test cases in enum.c and dtypes.c.
Tested on jam, koala, and heiwa.
Description:
When closing an object that had two open id's, the library would previously fail
to account for the status of the "holding_file" field, potentially causing the
file's "nopen_objs" field to become inconsistent. This caused problems when
opening the same object twice through an external link using th external file
cache. Modified the library to properly account for the status of the
"holding_file" field when closing an object id, even when the underlying
"shared" object isn't closed.
Tested: jam, koala, heiwa (h5committest)
The problem was that the test was a clone of the SEC2 test. The SEC2 test accepts a file descriptor (int) via a void pointer from H5Fget_vfd_handle() whereas the STDIO test needs to accept a FILE pointer. Storing the FILE pointer in an integer failed on some systems. The STDIO test now stores the file handle in FILE pointer and checks it for NULL instead of < 0.
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
Add explicit test that checks that the 'fileno' field in H5O_info_t
is the same for objects in the same file, whether the file was opened twice
or not.
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
Description:
Added internal tesitng routines to traverse a file and verify that symbol table
information is *always* cached, whenever possible. Added this check to the end
of many tests to check all the test files, right before the call to h5_cleanup.
Tested: jam, amani, heiwa (h5committest)
Correct several problems with compound datatypes that don't have any
fields added:
- Change assertion to error report when a file is encountered which has this
situation.
- Added check to attribute creation to avoid creating attributes with a
datatype like this (datasets and named datatypes already have the check)
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
General shared library improvements for CYGWIN / AIX
Description:
Shared libraries are disabled on both CYGWIN and AIX due
to inability to build them correctly. Part of the problem
in both of these situations is the lack of the libtool
flag -no-undefined, which tells libtool that all needed
symbols are defined at link time (a requirement on these
systems) and that it's okay to build shared libraries.
Another problem are lack of dependencies between wrapper
libraries and core C HDF5 library.
This patch addresses both of these by fixing configure to
add in -no-undefined flag for libtool during linking and
adds automake dependencies in the Makefile.am files.
After testing, both CYGWIN and AIX now generate shared
libraries, but there are still some test failures in each.
(cache_api, dt_arith, and testerror.sh on CYGWIN, and
fortran tests on AIX).
Even though the shared libraries are not quite perfect,
this is a general improvement to what we had before, so
I'm applying the patch anyways. Note that default behavior
of shared libraries on these systems being disabled has
NOT been changed and requires the use of the
--enable-unsupported to attempt to build them.
We will need to address the test failures in each
architecture prior to formally supporting shared
libraries on each.
Tested:
h5committested & CYGWIN tested (on bangan)
(AIX tested by Albert on bp-login2)
Add "silent make" mode configure option.
Description:
Automake 1.11 has a new option available that allows for a
silent make mode. This functionality needs to be explicitly
enabled in configure.in via the use of the automake macro
AM_SILENT_RULES, which is what this commit is adding.
This introduces a new configure option:
--{en|dis}able-silent-rules
This option is on by default, and simplies compile and link
line outputs when building the library. Disabling this option
will print full "verbose" output (i.e., full compile and
linking lines for each target).
Tested:
This was tested on jam & h5committested
forbid setting the dimension size bigger than existing maximal size. In this checkin, I restored it to the previous
behavior that any change will wipe out previous record of dimensionality.
Tested on jam - a simple change.
r20440 and r20469:
1. The dataspace code has another bug - when the maximal dimension isn't passed in for H5Sset_extent_simple, it
is supposed to be same as the dimension. The current library sets NULL to it. I corrected it and added a
test case to it.
2. I corrected the tests of Fortran and C++ for this problem.
Tested on heiwa, jam, and amani.
Remove global variable for the path name in the group traversal code. Also
clean up a bunch of compiler warnings.
Tested on:
Mac OS X/32 10.6.7 (amazon) w/debug & production
FreeBSD/32 6.3 (duty) w/debug
FreeBSD/64 6.3 (liberty) w/debug
Solaris/32 2.7 (linew) w/debug
- Revise shared Fortran library disabling scenarios in configure
- Improve configure output summary
Description:
Shared Fortran libraries are not supported on Mac, but were being
disabled by configure in a way that also forced the C libraries
to be static-only. This has been fixed, so now only shared Fortran
is disabled while shared C can remain.
This prompted two additional changes:
1. While working on the check that addresses whether or not
shared Fortran libraries are allowed, removed old and no
longer needed check(s) that disable shared Fortran
libraries with HP, Intel 8, PGI, and Absoft compilers.
(Essentially, Mac is the only situation in which Fortran
shared are disabled by configure.)
2. Having two different states of libraries (i.e. shared C
library with static-only Fortran library) was not apparent
in the configure summary, which labeled all libraries as
either shared and/or static. I've added lines to both the
C++ and Fortran output sections to list shared/static-ness
of these libraries specifically.
Additionally, I've made sure that the new --enable-unsupported
configure option correctly overrides configure if it tries to
disable a shared library.
Tested:
jam, fred, & h5committest
1. I added a test case of extending dataset of zero dimension size and shrinking back to zero dimension size.
2. I updated the Makefile to include the new data file to be cleaned up.
Tested on jam - relatively simple.
Progress on bug 2138 (bugzilla) / HDFFV-4298 (JIRA)
Description:
- Added basic VFD tests (i.e. cloned the SEC2 test) for the Windows, STDIO and log VFDs.
- Added H5Pget_driver() sanity check to all VFD's tests.
- Added log output file to list of files to clean up in Makefile.am.
Tested on:
- h5committest script platforms (jam, amani, heiwa)
- Windows 7 (32- and 64-bit)
Description:
Implements a cache of files opened through external links. Adds the public
functions H5Pset_elink_file_cache_size(), H5Pget_elink_file_cache_size(), and
H5Frelease_file_cache().
Tested: jam, amani, heiwa (h5committest), fedora 64.
Bring changes from Coverity branch to trunk:
r19930:
Fix memory leaks involving VL attributes in h5repack and h5diff. The buffers in
copy_attr and diff_attr were not checked for the presence of a vlen before being
freed, and vlen storage was never reclaimed. Added checks and calls to
H5D_vlen_reclaim().
r19933:
Purpose: Fix memory leak in H5L_move_cb()
Description: H5L_move_cb copied the source link using H5O_msg_copy() but freed
it manually using H5MM_xfree(). Since H5O_link_copy allocates the link using
H5FL_MALLOC, this causes the link to be allocated from the free list but is
never put back on the free list when it is freed. This prevents the link free
list from shutting down properly. Modified H5L_move_cb() and H5L_move_dest_cb()
to free the link properly using H5O_msg_free().
r19973:
Fix resource leaks by freeing string created by HD5f2string
r19974:
Issue #345: Inialize buf variable to null
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
(h5committested on Coverity branch)
Clean up Coverity warnings, and fix some style issues:
r19735:
Fix for memory leak in test/mf found by valgrind.
r19736:
Fix memory leak in h5repack. The buffer in copy_objects, when copying the
entire dataset at once, was not checked for the presence of a vlen, and vlen
storage was never reclaimed. Added check and call to H5D_vlen_reclaim().
r19772:
Change H5assert() to
if (H5T_VLEN != src->shared->type || H5T_VLEN != dst->shared->type)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a H5T_VLEN datatype")
r19774:
removed unused priv.
r19775:
removed unused variables
r19778:
Fix memory leak comparing for variable length data types.
r19834:
Fixed memory leaks found by valgrind. Memory errors remain for another day.
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
(h5committested on branch)
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
"*buffer_size = j + 1;" was mistakenly taken out by someone. It is necessary to update the new size. I
put it back and made 2 test cases for integer and float to verify the correct dataset size.
I'm bringing the fix from 1.8 branch. The changes to configure.in, tools/misc, config, Makefile.am are only property changes.
Tested on jam. But I tested 1.8 on jam, heiwa, and amani.
Changed the test to run Huge Dataset (tens of GB), Xtra large dataset(4GB big),
Large dataset (2GB big), or merely 1GB big, depending on if the file system
supports sparse file or if it supports larger than 32bigs I/O.
Tested: h5committest, jam (serial), Windows (Bangan which is Windows 7, 32bits).
file name listed for DISTCLEANFILES should be testlinks_env.sh
2. Add comments to test_4() in test/external.c about the link name "/ link".
3. Fix memory leak as reported by valgrind in src/H5Lexternal.c:
free memory pointed to by tmp_env_prefix for HDF5_EXT_PREFIX case.
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)
Also updated root CMakeLists.txt to output a message when unsopported options are configured with the PARALLEL option. CMake will still generate files.
Tested: windows and local linux
1) Move the test for H5D_EXT_PREFIX in links.c to a separate file: links_env.c
2) links_env.c will be used by testlinks_env.sh to test for the environmental
variable H5D_EXT_PREFIX in searching for the external linked file.
Add another test for shutting down open object IDs without using the
standard "close" routines.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(too minor to require h5committest)
double to (unsigned) long and from (unsigned) long to long double. I added tests in configure.in
to detect these algorithms. Before I can figure out them, I disable the tests in dt_arith.c.
There are property changes to tools/misc, config, and Makefile.am when I brought the fix from 1.8.
Tested on jam, heiwa, amani, IBM Power6 Linux machine in Holland (huygens.sara.nl).
Do some extra range-checking on H5Pset_elink_acc_flags() calls.
Clean up some minor compiler warnings also.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(too minor to require h5committest)
Bring Coverity revisions from branch back to trunk, and clean up some other
misc. compiler warnings also.
r19500:
Fix coverity items 1446 and 1447. Moved up calls to memset in test_cont in
ohdr.c so the test never tries to close uninitialized locations.
r19501:
Fix coverity items 1398-1445. Various uninitialized variable errors in fheap.c.
r19502:
Fixed coverity issue 579 and some additional warnings in the file as well.
r19503:
Bug fix: This fix addressed the "RESOURCE_LEAK" problems #789 and 790, run 26
r19504:
minor mods to try to keep coverity from flagging false positives.
r19505:
Fixed coverity issues 566 - 571. Declared variables that are passed to functions that use them as arrays to be arrays of size 1.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug, production & parallel
(h5committested on trunk)
- Fix a bug in each of the metadata accumulator source and test code
Description:
- In accum.c test file, switch dxpl_id used in H5F_accum_*
function calls to H5P_DATASET_XFER_DEFAULT (instead of
H5AC_dxpl_id), to fix compilation on windows.
- Changed boundary checking from <= to < when checking
if a read from disk with overlapping dirty metadata in the
accumulator has the read ending such that it aligns exactly
with the dirty accumulator (line 234 of H5Faccum.c).
Tested:
- h5committested
Merge accum_tests branch back to the trunk.
Description:
Changes consist of addition of tests for H5Faccum.c source code,
as well as some fixes that address some discovered bugs in the
metadata accumulator on several corner cases.
Tested:
h5committested
Address issue with object headers being created getting evicted from
the metadata cache cache before they are completely initialized. This is
done by pinning the object header in the cache until it is completely
initialized and attached to a group.
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
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
with the 1.8 library to compile. The cause is from the mismatch of H5Eprint1 and H5Eprint2
set through H5Eset_auto. I changed the structure H5E_auto_t. I added a IS_DEDAULT flag in
it. Both H5Eprint1/2 are the default now. If the user sets his/her own printing function.
Then a call to H5Eget_auto1/2 will have to match H5Eset_auto1/2.
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.
flag IS_DEDAULT in the H5E_auto_t structure. Both H5Eprint1/2 are the default now. If the user
sets his/her own printing function. Then a call to H5Eget_auto1/2 will have to match
H5Eset_auto1/2.
Tested on jam, heiwa, and amani.
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.
Create a new, more streamlined method of generating I/O sequences when
there is only a single block defined by a hyperslab. This improves the
performance of Ger Van Diepen's (LOFAR team) benchmark by about 20%.
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
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-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Description:
The AIX platform does not install the lib*.so for some reason but libhdf5.a
acts like a shared library. Until we can find out how to fix this, patch
up tetlibinfo.sh to not look for an lib*.so in AIX. (Note the test results
look wierd as it says libhdf5.a passed and skipped.)
Tested: NCSA BP for both enable and disable-shared.
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.
Correct Bz#1968 (Problem when opening new format file with
H5F_LIBVER_EARLIEST) by initializing symbol table leaf information in a
more universal way. Also cleaned up other superblock initialization a
little bit while I'm here.
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
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Clean up the internal usage H5I_dec_ref() to eliminate the sequence of
flags that has been creeping in.
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
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Bring back various modifications to the v2 B-trees that were introduced
in the revise_chunks branch but aren't dependent on any file format or API
changes.
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
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
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)
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.
