Bring r18109 from trunk to 1.8 branch:
Bring r18076-18096 from hdf5_1_8_coverity branch to trunk:
r18076:
Correct Coverity issue #1 by removing dead code
r18077:
Fix coverity item 142. When an error occurred while copying a linked list in
H5S_point_copy, the library would not free the partially allocated list. Added
code to free the list in this case.
r18078:
Correct Coverity issue #2 by removing impossible to reach code.
r18079:
Correct #3 by removing impossible to reach code.
r18080:
Correct Coverity issue #4 by removing impossible to reach code.
r18081:
fix coverity 26 , check (dblik->parent) before calls H5HF_man_iblock_detach().
r18082:
Fixed coverity issues 321 and 316.
321: freed sm_buf in error handling to remove resource leak.
Also set sm_buf to NULL after other instances in which
it is freed to prevent double free.
316: initialized nmembs to 0.
r18083:
Correct Coverity issue #6 by removing debugging knob from error reporting code.
r18084:
Fix coverity item 269 + others. When a error occurred in a function using the
h5tools error framework, the "past_catch" variable would not be set to true
because that statement was before the label that goto jumped to. This could
cause a failure in the cleanup section to go back to the start of the section,
freeing variables twice, etc.
Moved the label infront of past_catch=TRUE.
r18085:
fixed coverity #27, check if (heap) before use heap->obj....
r18086:
fixed coverity #28, check curr_span not null before use it at if(curr_span &&
(io_bytes_left==0 || curr_seq>=maxseq))
r18087:
Correct Coverity issue #7 by cleaning up correctly on error
r18088:
Correct Coverity #8 by removing unchanged variable checking code.
r18089:
Correct Coverity issue #9 - remove impossible to reach code.
r18090:
Correct Coverity issue #11 by removing impossible to reach code. Also clean
up some minor style issues.
r18091:
Fix coverity items 314 and 318. Changed the improper assertion of the return
value of a library function to a check, and a return(void) on failure.
r18092:
Fix coverity item 70. Changed the improper assertion of the return value of a
library function to a check, and a return(void) on failure.
r18093:
Correct Coverity issue #12 by removing dead code.
r18094:
Correct Coverity issue #16 by removing debugging code.
r18095:
Fixed coverity issue # 271.
Removed redundant checking and freeing of sm_buf1 and sm_buf2.
r18096:
Correct Coverity issue #17 by refactoring test to remove dead code.
Also, removed previous "coverity" statements in comments, we'll review
those issues again and see if we can figure them out, now that we have more
experience with Coverity.
Tested on:
Mac OS X/32 10.6.2 (amazon) debug & prod
The mixed use of RUNTEST (original) and RUNTESTS (new) caused
confusion. E.g., the timings in test/ was still using the old
$RUNTEST. It made more sense to use $RUNTEST which is used
by the dejagnu feature of automake. So, I changed all
$RUNTEST or $RUNTESTS to $RUNEXEC.
config/commence.am & config/conclude.am are the two files
that got changes. Also fixed an error in test/Makefile.am.
The rest are changed by bin/reconfigure.
Tested: h5committested.
h5tools error framework, the "past_catch" variable would not be set to true
because that statement was before the label that goto jumped to. This could
cause a failure in the cleanup section to go back to the start of the section,
freeing variables twice, etc.
Moved the label infront of past_catch=TRUE.
Tested: Fedora
321: freed sm_buf in error handling to remove resource leak.
Also set sm_buf to NULL after other instances in which
it is freed to prevent double free.
316: initialized nmembs to 0.
Bring r18011 from trunk to 1.8 branch:
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
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug & production
(h5committested on trunk)
Bring r17981 from trunk to 1.8 branch:
Abstract "print header" code into separate routine.
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug
(too minor to require h5committest)
Bring r17953 from trunk to 1.8 branch:
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) w/debug
(h5committested on trunk)
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. (svn revision 17921 on 1.8 branch)
Tested on:
linux32 (jam) , linux64 (almani), solaris (linew)
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)
Merge from Trunk
Description:
Merging all of my CFLAGS-related changes from trunk to 1.8
This includes revision #s: 17616, 17625, 17627, 17639, and 17643.
Tested:
h5committest and some additional checks on our FreeBSD as well
as NCSA's machines.
Stage 2 implementation of embedded library information feature.
H5.c: added code to print the embedded library information when there is
a library versions mis-match occurs. This ensures the library information
string is included in the executable.
Also modifies the code so that the Library mismatch warning string is
included only once in the executable.
H5private.h:
Added a global reference to the libinfo string variable to prepare
for possible stage 3 implementation of a public API.
test/testlibinfo.sh.in:
A new test added to verify the library information is indeed included
in the executables.
configure.in:
configure:
Added entry to auto-generate test/testlibinfo.sh.
H5detect.c:
Modified the libhdf5settings generating code to allow it to insert the
strings to a file other than stdout. This maybe needed in stage 3
implementation.
MANIFEST:
updated with the newly added file of testlibinfo.sh.in.
Tested:
h5committest passed. Also passed jam in serial mode.
" 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)
Updating autotools
Description:
Bring revisions 17345 and 17357 from trunk to 1.8, specifically:
- 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).
- bin/install-sh script replaced with new version as provided
by automake.
Tested:
- All issues on trunk were resolved, so only tested on jam and linew. Any
other outliers should be caught by daily tests.
Add a run to the h5repack shell script to read a family file
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: linux
- Updated bin/reconfigure to use latest version of automake (1.10.2).
Regenerated 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
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)
1. #1501 (B1) tools bug if dataset is larger than 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).
FURTHER ISSUES: the type in question ("double") has a different output cross platforms (e.g on liberty some garbage number is printed at some array locations)
SOLUTION: defined an "int" type for this test. However the printing of such an array has a bogus output at least in one platform (FreeBsd), so eliminated the test run altogether and filed a bug report on this
Bug Fix
Description:
Fixing BZ #1381. The --includedir=DIR configure option, which is used to
spceify installation location of C header files, did not work correctly as
the path was hard-coded into 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 which allows for customization of this value.
Tested:
jam, liberty
have 2 expected outputs for 2 h5ls runs depending if run on a 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: jam, linew
Bug fix: for compound types, the not comparable test for 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: h5committest
bug fix
a new line was not inserted at the end of output, causing diff to complain between linux and frebsd
tested: linux (freebsd tested on the trunk)
#1368 (E1) h5diff: implement "not comparable" messages. Implemented RFC. The new option is <-c, --compare List objects that are not comparable>
added some test cases
tested: windows, linux
Added an option to avoid dealing with NaNs
-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
Bug fix
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
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: windows, linux
use of
H5_PRINTF_LL_WIDTH
in the definition of
#define HSIZE_T_FORMAT "%"H5_PRINTF_LL_WIDTH"u"
the printing of "unknow u" in tg-login3.
for unsigned long long was a configure bug fixed by rev 15942
tested: tg-login3
for some reason , the use of H5_PRINTF_LL_WIDTH to convert to a unsigned long long format, is not working in ia64 linux (tg-login3)
extra characters are printed, this time in h5ls
hardcoded the format defined in HSIZE_T_FORMAT to "%llu"
tested: windows, linux (kagiso), solaris, ia64 linux (tg-login3)
