| Commit message (Collapse) | Author | Age | Files | Lines |
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Bring Coverity changes into the trunk: (also other minor cleanups)
r17991:
Fix Coverity items 175 and 176. Fixed memory leak on error in print_enum in
H5LT.c.
r17993: (r17992 was not a Coverity change)
Close Coverity issue #206: inconsistently checking whether dt->shared was
non-NULL after H5T_alloc() returned a valid 'dt' value (which should guarantee
that dt->shared is valid).
r17994:
Fix Coverity item 149. Fixed file handle leak on error in H5FD_stdio_open.
r17995:
Fixed Coverity issues 154 to 161:
Added H5MP_close routine to error handling in the event *mp has not been
freed before error.
r17996:
Close Coverity issue #126: potentially leaking merged_spans on routine failure.
r17997:
Fix Coverity items 147 and 148. Fixed resource leaks on error in H5FDloc.c.
r17998:
Coverity issue 269-272:
Added integer result variable to functions that could return negative.
Assigned to unsigned after checking.
Added H5E_BEGIN_TRY block around H5Tclose and removed H5E_THROW in the
catch block.
Checked buffer is NULL before free. Changed HGOTO_ERROR outside of the if
block to H5E_THROW.
r17999:
Close Coverity issue #127: release temporary spans in more generic manner.
(Also add error checking to previous fix)
r18000:
Resolved Coverity issues 211 and 212 in H5T.c. Added comments to ignore
Coverity warning regarding not checking pointer for NULL, as we are using
an assert which catches the issue.
r18001:
Fix Coverity item 146. Fixed resource leak on error in H5O_layout_copy.
r18002:
Fix Coverity items 143 and 145. Fixed resource leaks on error in
H5D_compact_copy and H5D_contig_copy.
r18003:
Close Coverity issue #192: close file on error
r18004:
Fix Coverity issue #125: release temporary spans on error
r18005:
Resolved Coverity issues 5, 25, and 83 (in H5T.c):
Separated embedded functions in order to check for NULL on return of
H5I_object before passing into H5T_copy.
Check to see if new_dt is NULL within error handling before
dereferencing it.
Ignore Coverity's dead code warnings as the checks that lead to the code
are machine dependent.
r18006:
Coverity 63,70,73: Checked result of function before assigning to an unsigned
variable.
r18007:
Coverity 78,79: added continue statement if H5Pget_filter2 returns negative.
r18008:
Fixed Coverity issue # 138:
Added support in error handling to free dst pointer (if allocated) on error.
r18009:
Whitespace & coding style cleanup
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Abstract "print header" code into separate routine.
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug
(too minor to require h5committest)
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Bring Coverity changes into the trunk:
r17877:
Error 266: Uninitialized memspace set to -1. Changed malloc and free to HDmalloc and HDfree. Removed unused dtype var.
r17878:
Error 265: Uninitialized mem_space set to -1. Changed malloc and free to HDmalloc and HDfree.
Error 267: Uninitialized smspace set to -1. Changed malloc and free to HDmalloc and HDfree.
r17879:
Error 242: Uninitialized aid set to -1.
Error 243: Uninitialized sid set to -1.
Uninitialized tid set to -1 for consistency
r17880:
Error 242: reinitialized aid to -1 after close to be ready for reuse.
Error 243: reinitialized sid to -1 after close to be ready for reuse.
reinitialized tid to -1 for consistency after close to be ready for reuse.
r17881:
use valgrind to check there is a memory leak. The fix is to free ptrstr in line 5838 at xml_dump_group() of h5dump.c after it is used. run the valgrind after the fix, no memory leak for that part of the code.
r17882:
Fix Coverity items 256 and 269.
r17883:
Error 222-230: initialized hid_t vars to -1 after close to be ready for reuse.
Also added H5Tclose for tid in gent_bigdims
r17884:
Bug fix (Coverity run2, view 23, dead code)
(this is pair-program done by Albert, Elena and Larry).
Confirmed and fixed the deadcode in hyperslab read branch of function
diff_datasetid.
(Discovered other bad code that diff_datasetid() should be recoded.
Bug 1693 is entered for this.)
r17906:
Fix Coverity item 260.
r17907:
262: Initialized hid_t's dtype, dtype_tmp and file to -1. Initialized H5T_t * dt to NULL.
r17908:
Fix Coverity item 261.
r17909:
Fix Coverity item 248.
r17910:
Revise fix for Coverity item 248.
r17911:
Resolved coverity issues #s 263, 162, 163, 164. All issues in dsets.c. Initialized fid and did hid_t's. filter_corrupt function was returning in the middle of an if statement, bypassing free calls. Updated error handling to free buffers and hid_t's appropriately.
r17912:
(done by Larry and Albert)
Cleanup Coverity view warnings (#231-241) about
using uninitialized variables. Initialized all
of them.
r17913:
Resolved issue 251 and 264. Initialized tid2 to -1 and initialized buffers that were freed in case of an error.
r17914:
Resolved coverity issues 66, 220, and 221:
66: Negative Return assignment ignored
220,221: Initialized hid_t's.
r17915:
Fix Coverity item 247.
r17916:
Fix Coverity item 246.
r17917:
Fix Coverity item 245.
r17918:
Fix Coverity item 244.
r17919:
Coverity Issue #84: Moved asserts in H5T_cmp to the top of the function, and converted them to HDassert. Coverity complaining about using potentially NULL pointer without checking it. Want to see if Coverity will accept Assertions as acceptable checking before using the value.
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 (smirom) 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, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Fix potential problem similar to Bug1672 (getting garbage values)
Description:
This will resolve the potential problem like Bug1672 when comparing
attributes. It improves the performance by not calling diff_array
twice. (diffing time in half). Little clean up on comment lines.
Refer to the Bug fix 1672. (also svn revision 17905 on trunk)
Tested on:
linux32 (jam) , linux64 (almani), solaris (linew)
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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)
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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.
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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
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Bring most of Vailin's changes to the fixed array data structure back
to the trunk, including new regression test for data structure.
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/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) 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, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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references.
Changed default Error handling init to successful as all error macros set the return to failure
Tested: local linux
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Tested: local linux
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functions in the tools lib. Bring back from NPOESS. Added missing tests to h5dump test script for region references.
Tested: local linux
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" Use "--use-system-epsilon" for system EPSILON
" Use "-p" or "-d" for whatever user's choice of epsilon
" Use "-p 0" or "-d 0" for strict equality (same as default)
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processing to use boolean.
Tested:
local linux
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Correct a 'hsize_t *' to 'hsize_t' and vice versa.
Tested on:
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
(too minor to require h5committest)
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changes from NPOESS
Tested: local linux smirom
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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.
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Added test cases
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functions: va_start(), HDvsnprintf(), and va_end(). When the boundary of the string buffer was reached and resized, the HDvsnprintf() function recalled without the other two functions in the code loop. This usage exposed bug 1520 by a user.
Tested: linux
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The file used for input is located in the common source tools for testfiles, in tools/testfiles
Modified the h5repack shell script to read files from this location (h5repack reads its input files from a dedicated testfiles location in h5repack/testfiles)
Changed the h5diff open file call to use h5tools_fopen, so that it can open all file drivers
Tested: windows, linux, solaris
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tested: windows, linux
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the case of different classes
tested: windows, linux
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tested: linux
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- 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
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tested: linux
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Description:
Changed Skip list package to use a deterministic skip list. This allows the
skip list package to avoid calling rand() and srand(), even on machines without
rand_r(). There is no longer a p-value or maximum level for skip lists.
Tested: jam, smirom, linew (h5committest)
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output in frebsd (liberty)
removed the call to the file generation in the test generation program
removed the binary h5 and ddl from svn
tested: linux
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H5TOOLS_BUFSIZE limit.
ISSUE : the tools use the following formula to read by hyperslabs: hyperslab_size[i] = MIN( dim_size[i], H5TOOLS_BUFSIZE / datum_size) where H5TOOLS_BUFSIZE is a constant defined of 1024K. This is OK as long as the datum_size does not exceed 1024K, otherwise we have a hyperslab size of 0 (since 1024K/(greater than 1024K) = 0). This affects h5dump. h5repack, h5diff
SOLUTION: add a check for a 0 size and define as 1 if so.
TEST FOR H5DUMP: Defined a case in the h5dump test generator program of such a type (an array type of doubles with a large array dimension, that was the case the user reported). Since the written file commited in svn would be around 1024K, opted for not writing the data (the part of the code where the hyperslab is defined is executed, since h5dump always reads the files). Defined a macro WRITE_ARRAY to enable such writing if needed. Added a run on the h5dump shell script. Added 2 new files to svn: tools/testfiles/tarray8.ddl, tools/testfiles/tarray8.h5. NOTE: while doing this I thought of adding this dataset case to an existing file, but that would add the large array output to those files (the ddls). The issue is that the file list is increasing.
TEST FOR H5DIFF: for h5diff the check for reading by hyperslabs is H5TOOLS_MALLOCSIZE (128 * H5TOOLS_BUFSIZE) or 128 Mb. This makes it not possible to add such a file to svn, so used the same method as h5dump (only write the dataset if WRITE_ARRAY is defined). As opposed to h5dump, the hyperslab code is NOT executed when the dataset is empty (dataset is not read). Added the new dataset to existing files and shell run (tools/h5diff/testfiles/h5diff_dset1.h5 and tools/h5diff/testfiles/h5diff_dset2.h5 and output in tools/h5diff/testfiles/h5diff_80.txt).
TEST FOR H5REPACK: similar issue as h5diff with the difference that the hyperslab code is run. Added a run to the shell script (with a filter, otherwise the code uses H5Ocopy).
tested: linux (h5commitest failed , apparently it did not detect the code changes in /tools/lib that fix the bug: the error in an assertion in the hyperslab of 0. I am sure that making h5ccomitest --distclean will detect the new code , but don't want to wait more 3 hours :-) )
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Bug Fix
Description:
Fixing BZ #1381. The --includedir=DIR configure option, which is used
to specify the installation location of C header files, did not work
correctly as the path was hard-coded in config/commence.am. I'm presuming
this is because an older version of automake didn't know where to put
c header files. In any case, removing this line now defaults the includedir
to the same directory that it is currently hard-coded to, and also fixes
the configure flag to allow customization of this value.
Tested:
jam, liberty
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big or little endian machine. Configure.in was modified to export a variable carrying endianess information to testh5ls.sh. This script then compares the current run with 2 expected outputs, one for a big-endian machine (linew was used to generate the output), other for little endian (jam was used to generate the output)
the way h5ls prints types, it starts searching for NATIVE types first. One solution would be h5ls not to detect these native types, using for example the same print datatype function that h5dump does, that would make the output look the same on all platforms ("32-bit little-endian integer" would be printed instead). Drawback, this "native" information would not be available. Other solution is to have not one but 2 expected outputs and make the shell script detect the endianess and compare with one output or other
tested: h5committest
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causing compilition error on AIX
tested: h5commitest
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tested: h5committest
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replacing all instances with long long.
Tested:
h5comittest
fedora 10 x64
Vista 32, VS2005, IVF101
XP32, Cygwin
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members was not done
Solution: for compound types, recursively apply that check
Two new cases are added
1) the compound type has a different number of members. Message printed is
<obj1> has X members <obj2> has Y members
Where X and Y are the number of members of each compound type being compared
2) the compound type has not comparable types (for example a double and an int at the same index)
In this case the message
Comparison not possible: object1 is of class1 and object2 is of class2
Is replaced with
Comparison not possible: object1 has a class1 and object2 has a class2
Modified the test generator program to have these 2 cases
Added a shell run for these 2 cases
Tested: windows, h5committest
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tested: linux serial and parallel
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a new line was not inserted at the end of output, causing diff to complain between linux and frebsd
tested: linux , freebsd
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tests to fail
tested: linux parallel
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Implemented RFC. The new option is <-c, --compare List objects that are not comparable>
added some test cases
tested: windows, linux
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Changed 'THG' to 'The HDF Group' in various HDF5 source files,
most of which are <subdirectory>/COPYING.
-- Closes Bugzilla entry 1403.
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tested: windows, linux
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-N, --nan Avoid NaNs detection
Note: there is no shell script run for datasets with NaN because the output is non portable (different results and NaN strings for different systems)
Tested: windows, linux
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PG compiler complains about array out of bounds (a rank of zero was not checked)
Adding a scalar dataset to the test generator program. this case is run on a previous existing run, the case was added to 2 existing files
Tested: windows, linux
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h5diff return value (not done for 1.8)
* Pedro Vicente, pvn@hdfgroup.org, Nov 4, 2008
* Compare the graph and make h5diff return 1 for difference if
* 1) the number of objects in file1 is not the same as in file2
* 2) the graph does not match, i.e same names (absolute path)
* 3) objects with the same name are not of the same type
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difference is found instead of a non-existing array position
Tested: windows
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Introduced a new feature in the tools library regarding command line parsing
In the definition of arguments, an "*" means that the switch can or can not have an optional argument. This "*" is put in the code regarding the letter definition, and it is transparent to the user (e.g b* instead of the previous b: ), where ":" notes a required argument after the letter (and no ":" or "*" notes no argument, mandatory)
Used for the h5dump binary option -b
It can be now
1) -b (defaults to NATIVE)
2) - b NATIVE
3) - b FILE
4) -b LE
5) -b BE
Note: the keyword NATIVE replaces MEMORY
This feature (-b with no argument) was tested with the sequence of h5dump to binary (NATIVE) then h5import to generate an HDF5 file from the binary file and h5diff to compare the 2 HDF5 files
Tested: linux
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regarding the return value of h5diff (0, no difference in files, 1 difference )
objects with the same name must be of the same type
tested: linux
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Regarding use of unsigned long long print format
Tested: linux
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Regarding h5diff, h5copy
Tested: linux
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Eliminate -c option and make that behavior the default and return 2 instead of -1 on error status
tested: linux
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long long)
tested: windows, linux
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