Fix for HDFFV-8001 - h5unjam: segfault when used -V (show version) option
Description:
h5unjam has an option '-V' to display version information.
"h5unjam -V" caused segfulat for 1.8.9 pre-release.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
Work for:
HDFFV-7515 - GMQS: h5unjam - incorrect help page and should display when
no file is given.
and
HDFFV-5941 - h5jam: specifying a user block file with a proper HDF5 magic
number will result in a corrupted HDF5 file.
Description:
- Revised command help pages of h5jam and h5unjam. The descriptions
were not up to date and some were missing. (HDFFV-7515)
- Fixed h5jam not to allow specifying an HDF5 formatted file as input
file for -u (user block file) option, because the original HDF5 file
will not be accessible if allows. (HDFFV-5941)
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam, Wondows)
h5dump (and h5stat, h5jam/h5unjam) help option not tested. Added h5dump parse_command_line technique for h5stat and h5jam/unjam and created testfiles.
Tested: local linux
Bring changes from Coverity branch to trunk:
r19975:
Fixed potential mem leak at H5O_attr_open_by_name
r19980:
Fix coverity issue 792.
Free tmp_env_prefix in H5Lexternal.c line 365 if it is not NULL but its contents are 0 when it goes out of scope.
r20039:
Eliminate warnings about nested extern and implicit declarations of parallel_print and address Coverity defects 712-781 by #including h5tools_utils.h in h5diff_array.c, h5diff_attr.c, h5diff_dset.c and h5diff_util.c.
r20046:
Purpose: Address TOCTOU warnings in h5jam and h5unjam
Description: Coverity is afraid that the state of the input file could change
between the call to stat() and the call to open(). This is called a time-of-
check time-of-use (TOCTOU) vulnerability. Modified stat calls to fstat which
uses an open file pointer so it (hopefully) won't complain any more.
r20047:
Addressed coverity issues 135-137, 462-464. Local pointers that needed to be freed in case of error were moved out of a switch statement in src/H5Tnative.c, set to NULL, and checked before freeing.
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
(h5committested on Coverity branch)
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.
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.
Enable tools lib to be built as a dll on windows. Added two get/set functions for progname and d_status.
Also add windows import/export declarations to functions.
Updated error_mesg() and warn_mesg() to remove progname argument and use get functions
Tested:
Windows, linux
Bring revisions from Coverity fixing branch to trunk:
r18184:
Fixed Coverity issue 373. Allocated memory freed in line 762 in case of error.
r18185:
Fixed Coverity issues 357 & 358. Added check for NULL pointer before use.
r18186:
Fix coverity item 65. Added code to h5unjam to correctly handle failures in
read() and write, and also to correctly handle writes that write less than
requested.
r18187:
Fix coverity items 115 and 116. Added code to H5Tenum.c to correctly close
opened datatypes in case of failure.
r18188:
Fixed Coverity issue 46. Check that dataset->shared is not null when freeing
memory after error.
r18190:
Fix coverity item 95. Added code to H5T_create_vlen to correctly close
allocated datatype in case of failure.
r18191:
Fixed Coverity error 59. Checked sfirst for -1 value before use in line 10533.
r18192:
Fix Coverity items 121 and 28
Added Asserts:
121: assert that all dimensions of count have values greater than zero.
28: assert curr_span pointer is not null before dereference.
Note: still need too add checks in hyperslab APIs that fail
when count values are zero, and appropriate tests.
r18194:
Fixed Coverity issues 61 & 62. Checked variable snpoints for value < 0 in line
218.
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug & production
(already daily tested on coverity branch)
Description:
In library code, we try not to use system calls directly, but instead use the HD{function} macro instead. This way, we can map special versions of the call on particular systems. Previously, it was all done in H5private.h. However, in an effort to clean up platform-specific definitions, we move all of the Windows macros into a separate file, win32defs.h. This way, we can use the non-Posix versions that Visual Studio sends warnings about.
Some macros are set specifically in the platform-specific header files. Then, any macros left unset will be set by the "default" implementation in H5private.h.
This checkin also cleans up various source files to use the HD* macros when possible.
Tested:
VS2005 on WinXP
VS.NET on WinXP
h5committest (kagiso, linew, smirom)
Description:
In h5unjam.c, there was a call to "open", rather than "HDopen". This isn't a problem on most platforms, as the are equivalent. However, on Windows, we use the HDopen macro to unconditionally set the O_BINARY flag. This is needed to safely seek within a file.
Tested:
VS2005 on WinXP
h5committest (kagiso linew smirom)
Rename new error handling API routines from H5E<foo>_stack() to
H5E<foo>2().
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
Code cleanup
Description:
Tweak recent "forward compatibility" changes to the H5E* API (which allowed
for the old H5E API functions to remain unchanged) by allowing for the error
stack callback function (H5E_auto_t) to also remain unchanged from the 1.6
branch. This required changing the H5E{get|set}_auto routines to have the
old style H5E_auto_t type (which didn't have a stack ID parameter) and the new
H5E{get|set}_auto_stack routines to have a newer "H5E_auto_stack_t" type (which
has a stack ID parameter). This should make the H5E API changes as forwardly
compatible as possible.
One side-affect of this change was that it was impossible to determine if
the current auto error callback was the old style (H5E_auto_t) or the new style
(H5E_auto_stack_t) of callback, so a new API function (H5Eauto_is_stack) was
adde to query this.
Platforms tested:
FreeBSD 4.10 (sleipnir)
IRIX64 6.5 (modi4)
h5committest
Description: Restore 6 old error API functions back to the library to be backward
compatible with v1.6. They are H5Epush, H5Eprint, H5Ewalk, H5Eclear, H5Eset_auto,
H5Eget_auto. These functions do not have error stack as parameter.
Solution: Internally, these functions use default error stack.
Platforms tested: h5committest and fuss.
Misc. update: RELEASE.txt
Update.
Description:
Make some minor change so that h5jam.c is compatible with Windows.
Solution:
1. unistd.h is not available in windows system. Add a macro for this header file as:
#ifdef H5_HAVE_UNISTD_H
#include <unistd.h>
#endif
2. Change open, read, write, lseek functions to HDopen, HDread, HDwrite, and HDlseek,
as these HD functions are more comtatible with Windows system.
3. add #include H5private.h
4. remove #include <stdlib.h>
Platforms tested:
Windows 2000
Windows XP
eirene
(Note: I talked with Bob and Kent about these changes before check-in)
Misc. update:
Bug fix
Description:
Correct compilation errors w/--enable-hdf5_v1_6 and using the C++ compiler
as a C compiler
Platforms tested:
FreeBSD 4.10 (sleipnir) w/above flags
Not tested with h5committest
Adding new 'jam' utility
Description:
New utility, plus changes to makefiles
Solution:
See http://hdf.ncsa.uiuc.edu/RFC/Jam
Platforms tested:
verbena (fortran,C++), arabica, hirdls (SGI Irix64)
Misc. update:
Manifest will be done in next checkin.
