configure fixes for HDFFV-9068,9069,9096,9097,9135 from autotools_rework branch:
- Remove Infering parallel compilers (C and Fortran) from configure.ac
- Remove restriction to build shared with parallel
- Cleanup parallel sections in configure.ac
- remove large file support checks
- MPE fixes.
Merge changes that correspond to the 64-bit ID changes (without the actual
switch to 64-bit IDs) to the 1.8 release branch. (Plus a few minor cleanups
and alignments with the trunk that aren't on the branch)
Tested on:
Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN
(h5committested on branch already for a week)
- remove configure checks for MPI_File_get_size and Big MPI_File_set_size as they are supported by MPIO implementations today.
- fix bug in t_mpi.c (HDFFV-8856)
tested with h5committest.
Added instead configure variable hardcode_into_lib=no. This removes rpath from lib files on Linux and solaris machines.
Tested with h5committest on jam, koala, ostrich and platypus (cmake), and on emu and kite.
Merge of r24937 from the trunk
Adds H5free_memory to the API. This function should be used to free
memory allocated by the library (e.g., returned values from
H5Tget_tag, H5Pget_class_name, etc.).
This is mainly to help Windows applications deal with multiple CRT
instances, but can also be helpful when a debug memory manager is
being used or when the HDF5 API is being wrapped for managed languages
like Python and Java.
Tested on:
32-bit LE linux (jam) with fortran and C++
64-bit BE linux (ostrich)
64-bit LE linux (koala)
Bring r24864 from trunk to 1.8 branch:
Remove all traces of MPI-POSIX VFD and GPFS detection/code.
Remove remaining traces of stream VFD.
Remove testpar/t_posix_compliant test (it's not actually verifying anything).
Clean up H5D__mpio_opt_possible() further.
Moved environment variable that disables MPI collective operations into
MPI-IO VFD (instead of it being in src/H5S.c).
A few other small code cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
(daily tested on trunk)
Bring r24803 & r24804 from trunk to 1.8 branch:
r24804:
Brought changes from Coverity branch back to trunk, and cleaned up misc.
other warnings & formatting issues:
r20833:
Fixed Coverity 667 and 668 with real integer overflow tests this time.
r20834:
Use HDstrncpy and HDstrncat. --gh
r20835:
Change to use strncpy - use base_len + 1 for line 156, use HDstrlen(path) + 1 for line 159
r20836:
Fixed coverity 585 by casting output of fgetc() to a char.
r20837:
Changed sprintf calls to snprintf with size 1 less than the allocated buffer to address coverity issue #967.
r24803:
Rename GCC_DIAG_OFF/ON macros to H5_GCC_DIAG_OFF/ON and move from
src/H5private.h to src/H5public.h. Wrap typedef of hsize_t and hssize_t
in DIAG_OFF(long-long) macros.
Clean up a bunch of "macro '-' is unused" warnings.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(too minor to require h5committest)
Bring r24726 & r24727 from trunk to 1.8 branch:
Description:
Revert some earlier usage of strncpy, which was incorrect.
Bring Coverity changes from branch back to trunk:
r20821:
Use HDstrncpy. --gh
(Fixed already, with strdup)
r20822:
(Not merged, incorrect use of HDstrncpy())
r20823:
(Not merged, incorrect use of HDstrncpy())
r20824:
Maintenance: Bug fix: addressed CID 666.
Value stored at *expression_len should be used in the call to
HD5packFstring to avoid overflow (and unnecessary arithmetic
calculation and casting)
r20825:
Issue 642: Added check for error and handler with print to stderr and exit.
r20826:
Undo revision 20818, as that issue has already been fixed in the 1.8 branch
and trunk (but not coverity branch)
r20827:
(Not merged, incorrect use of HDstrncpy())
r20828:
Use HDstrncpy. --gh
(Corrected use of strncpy())
r20829:
Check return of H5Lget_val(print_udata->fid, path, targbuf,
linfo->u.val_size + 1, H5P_DEFAULT) and if error set trgbuf[0] to 0.
Check if H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL,
&filename, &objname) was successful and allow print. Otherwise filename
and objname are not created. (init those to NULL)
r20830:
resolved coverity issues 939, 940, 941, 944, and 947.
all were complaints about use of sprintf, and in all cases, the
buffers used were large enough for all eventualities.
Resolved issue by replacing calls to sprintf with calls
to snprintf.
r20831:
Maintenance: Addressed CID 852
Replaced sprintf with snprintf
r20832:
Purpose: Fix valgrind issues with hl/examples/ex_image2
Description:
Modified hl/examples/ex_image2 to free global "gbuf" before exit.
Tested on:
Mac OSX/64 10.9.1 (amaon) w/C++, FORTRAN & Threadsafety
(too minor to require h5committest)
Switched default to link to shared lib files when HDF5 is configure with --disable-static.
This addressed HDFFV-8141, h5cc failed because it defaulted to link to lib*.a files which
aren't built with --disable-static.
-help message also updated.
Tested in trunk.
Merged code tested with h5committest.
Bring r24020 from trunk to 1.8 branch:
Clean up compiler warnings
Tested on:
Mac OSX/64 10.8.4 (amazon) w/C++ & FORTRAN
(too minor to require h5committest)
The previous change set exec_prefix, libdir and includedir to actual values.
That removed the option for user to hand edit just the first prefix=...
to make "everything" to work.
Changed h5redeploy to do this by default:
## Installation directories: ##
## prefix architecture-independent files. ##
## exec_prefix architecture-dependent files, default is <prefix>. ##
## libdir libraries, default is <exec_prefix>/lib. ##
## includedir header files, default is <prefix/include>. ##
############################################################################
This allows users to just change the first line of prefix=<...> and the
effect will change libdir and includedir too.
This was also try to accommodate the -prefix option of h5XX. Unfortunately,
after changing h5redeploy, I found out the h5XX code to support -prefix
actually does not provide the stated efffect. This will be fixed in the
release.
Tested: h5committested plus hand test.
Change h5redeploy to change all 4 lines, prefix=..., exec_prefix=...,
libdir=..., and includedir=... This way, it reset all 4 lines. Should work
for both version of h5cc created by configure or by rpm.
Tested: hand tested in jam.
Bring r22921 from trunk to 1.8 branch:
Review Coverity changes and bring them back to trunk. (QK & JK)
r20402:
Added #includes for h5tools.y or h5tools_utils.h as required to remedy implicit
function declarations which caused compiler warnings and coverity issues 703-4
and 708-11.
r20414:
This is related to the previous checkin r20399. There were incorrect updates
which caused incorrect behavior when no file was given. Also possible segfault
when handling hyperslab options. Simplify the code changes.
r20449:
Description: Modified H5E_walk2_cb to check return value of H5I_object_verify.
r20450:
fixed coverity 813
Tested on:
Mac OSX/64 10.8.2 (amazon) w/C++, FORTRAN, debug & threadsafe
(too minor to require h5committest)
Convert configure.in to configure.ac.
Align TESTS usage with autotools convention.
Update all references from configure.in to configure.ac
Tested: h5committest
Bring r22646 from trunk to 1.8 branch:
Changes resulting from Klocwork static analysis tool, from Mark Miller
@ LLNL (miller86@llnl.gov).
Tested on:
Mac OS X/64 10.7.4 (amazon) w/debug, C++ & FORTRAN, using gcc 4.7.x
(too minor to require h5committest)
Bring r22287 from trunk to 1.8 branch:
Clean up more FUNC_ENTER/FUNC_LEAVE macros and move H5D & H5T code toward
the final design (as exemplified by the H5EA & H5FA code).
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug & parallel
If a link is specified on the command with the -d option, call the handle_links function on error from the H5Dopen command.
Updated test file results with error stack when link not found.
Tested: trunk
Merge 1.8 and h5dump/tools and tests based on tools library from trunk.
Reduced warnings.
HDFFV-7949:
Remove duplicated functions in h5ls
Tested: local linux,h5committest
Fix HDFFV-7592
"Remove PACKEDBITS option from autotools files"
Description:
The code for h5dump's packed bits feature was
conditionally compiled in via this option during its
'beta' release in 1.8.5. Now that the feature is fully
supported, h5dump has since been changed to always
compile the packed bits code (having removed the #ifdef
H5_HAVE_H5DUMP_PACKED_BITS checks), so this option in
configure is no longer needed.
This commit removes the --enable-h5dump-packed-bits
configure option, including the help summary from
'./configure --help' and the libhdf5.settings output
summary, the PACKED_BITS Makefile variable, and the
definition of H5_HAVE_H5DUMP_PACKED_BITS define in
appropriate pubconf header files (which has already
been removed from use in source code as of r20722).
Note that this option was never added to the trunk,
thus this commit only need occur on the 1.8 branch.
Tested:
- Configure output, help, & summary verified on jam
- h5committested
Test scripts sometimes need to filter some system-specific messages from the
actual output so that it can match the correct expected output. These filtering
functions, ususally called "STDOUT_FILTER()" and "STDERR_FILTER()" were being
repeated in individual test scripts. This becomes a maintenance problem and
is error prone.
Solution:
Extract the two filter functions code to bin/output_filter.sh and then each
test script sources it in. This allows reuse of coding and is much easier to
maintain and to add new filtering.
Tested:
LLNL Zeus (linux64 cluster) and Dawndev (Blue-Gene cluster), both for serial
mode only.
Bring r20535 & r20536 from trunk to 1.8 branch:
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.
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
