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.
HDFFV-9046: reorganize hdf5/perform, step 2
Last changes had caused problems with Windows platform:
1. H5private.h in io_timer.h is not accessible in the distributed shared library of tools.
Need to move it to io_timer.c.
2. debug_start_stop_time() would not be available outside of h5perf. Some favor of compiler
does not like it. Screened it out for now.
3. mere "extern" is not good enough for Windows shared library. Must mark them as DLL. Need to mark them as
"H5TOOLS_DLL".
4. STANDALONE mode is broken. Screened out the code for now.
Tested: h5committest.
HDFFV-9046: reorganize hdf5/perform, step 2
Move timing measurement routines used by h5perf and h5perf_serial to tools/lib
so that they can be used by other tools too.
tools/lib/io_timer.c
tools/lib/io_timer.h
tools/perform/io_timer.c
tools/perform/io_timer.h
renamed perform/io_timer.[ch] to lib/io_timer.[ch]
tools/lib/Makefile.am
tools/lib/Makefile.in
tools/lib/CMakeLists.txt
tools/perform/Makefile.in
tools/perform/Makefile.am
tools/perform/CMakeLists.txt
MANIFEST
updated due to the move.
Tested; h5committest and jam (serial)
HDFFV-8902: merge the source code of h5perf and h5perf_serial, stage 1.
tools/perform/sio_timer.h:
tools/perform/pio_timer.c:
tools/perform/io_timer.h:
tools/perform/io_timer.c:
Renamed pio_timer.[ch] as io_timer.[ch];
merged content of sio_timer.[ch] into io_timer.[ch] so that both h5perf and h5perf_serial
call the combined io_timer.[ch].
Moved the debug printing code segment in set_time() in [sp]io_timer.c to as debug_start_stop_time() in [sp]io_perf.c where it belongs.
Screened out set_timer_type() and get_timer_type() which were not used by any code.
tools/perform/Makefile.am:
tools/perform/Makefile.in:
tools/perform/CMakeLists.txt
Adjusted to use io_timer.c for both h5perf and h5perf_serial.
tools/perform/pio_perf.c:
tools/perform/sio_perf.c:
tools/perform/pio_perf.h:
tools/perform/sio_perf.h:
Renamed [sp]io_time_destory() to same io_time_destroy();
Moved the debug printing code segment in set_time() in [sp]io_timer.c to as debug_start_stop_time() in [sp]io_perf.c where it belongs.
tools/perform/pio_engine.c:
tools/perform/sio_engine.c:
Removed #include io_timer.h since it was already #include by [sp]io_perf.h.
MANIFEST:
Updated the merge of [sp]io_timer.[ch] into io_timer.[ch].
Tested: h5committest and jam in extra.
Benchpar.c is retired/deleted. If it is ever needed, it can be retrieved from the SVN repository
or even previous version of HDF5 source code.
Tested: jam parallel make passed.
Previously, ph5diff may hang in a test in Linux 32 platform(HDFFV-587).
No solution was available and a patch to bypass the test is implemented.
Since the company is changing domain name soon, the patch would not be valid any more.
Tests were done (repeat 100 mpiexec -np 6 ./ph5diff -v h5diff_hyper1.h5 h5diff_hyper2.h5)
and the previous hanging problem did not occur. It is likely the newer versions of
mpich no longer have this problem. Therefore, it is decide to remove this patch
to make the test script cleaner, if nothing else.
Tested: ran build and test in Jam (linux 32) and the repeat 100 command mentioned above.
All passed.
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.
Bring r25215 from trunk to 1.8 branch:
Bring changes from Coverity branch back to trunk:
r20914:
Use HDstrncpy and HDstrncat! --gh
r20915:
Use HDstrncpy and HDstrncat! --gh
Tested on:
MacOSX/64 10.9.3 (amazon) w/gcc 4.9, FORTRAN, C++, multi-threads & parallel
(h5committested on the trunk)
Bring r25197 from trunk to 1.8 branch:
Bring changes from hdf5_1_8_coverity branch back to trunk:
r20878:
Issue 76: Check if H5Tget_nmembers(type) fails and simply return(FALSE). Also move printf to after check.
r20880:
Issue 192: Create ret_val var set to -1. Add out label for failures to jump to, return ret_val at bottom.
r20882:
Fixes for coverity:
1) bug #1679: remove dead code in test/mf.c
2) bug #1680: remove dead code in tools/lib/h5diff_dset.c
r20883:
Fix coverity issue 585
Description:
Changed variable "c" in processStrData in h5import.c to an int, to match fgetc
return value, and removed call to feof, instead checking if c == EOF.
Tested on:
MacOSX/64 10.9.3 (amazon) w/C++, FORTRAN & parallel
(too minor to require h5committest)
Make the exit status from ph5diff always be 0, as it is on the trunk. Also
a few coding standard cleanups to the test generation code.
Tested on:
MacOSX/64 10.9.2 (amazon) w/FORTRAN & parallel
(h5committest not necessary)
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.
h5diff issues "unable to read attribute" error message when comparing
two files
Description:
h5diff did not handle attributes of variable length strings
correctly. It created the wrong memory type if one but not both
compared attributes are of the variable strings type. It ended in
H5Aread() failure.
Solution:
We decided to treat the case when one type is variable length string
and the other is not as incomparable. That bypassed the above error.
We still need to figure out the proper way, if possible, to compare
variable string with non-variable string types.
Tested: h5committested plus tested in Swallow (OS X 10.8).
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)
h5diff segfaults with user's files
Solution:
Added a variable to indicate if real data are in the buffer and will call H5Dvlen_reclaim()
only when real data are in the buffer.
Tested: with the user provided data files and no more segmentaion fault.
Also h5committ tested.
Bring r24869 & r24875 from trunk to 1.8 branch:
Clean up more compiler warnings, plus merge a few Coverity bug fixes from
the hdf5_1_8_coverity branch back to the trunk:
r20877:
Purpose: Fix coverity issue 1723
Description:
Modified test_generate in hl/test_image to close file "f" before exit, even if
an error occurs.
r20879:
Issue 63: change check of return of H5Tget_nmembers to <=0. No need to go
futher if call fails as well as empty.
r20881:
Coverity #659 in Run 46: I changed the Line 442 where it tries to check whether
FLAG_PRINTED is TRUE. But it had just been set to FALSE. I took out the
condition check in the print statement.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & Parallel
(daily tested on trunk)
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)
Fix ph5diff worker command handling so it can correctly respond to
situations where there's no work to perform. Also, a few minor code cleanups.
Tested on:
Mac OSX/64 10.9.0 (amazon) w/parallel
The h5dump tests only looked at headers and never the data. Data reads would fail with invalid number of params (7 expected 20).
Regenerated file and replacement ddls updated.
New h5dump test will be added to read the data.
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 r24101 & 24111 from trunk to 1.8 branch:
r24101:
=======
Description:
Clean up warnings, enable new compiler warning flag(s) and bring back
changes from Coverity branch:
r20813:
Remove the dead code as listed for coverity bug #1722. h5committested.
r20814:
Issue 69: Check return value and throw error if negative return. Also free datatype id on error
r20815:
Use HDstrncpy. --gh
r20816:
Replaced one last HDstrcat call with HDstrncat to resolve coverity issue 832.
r20817:
Use HDstrncpy and HDstrncat. --gh
r20818:
Purpose: Fix valgrind issues with h5jam
Description:
Modified h5jam to free strings strdup'd in parse_command_line before exit. Note
that they may still not be freed in case of error, due to the widespread use of
exit().
r20819:
Issue 80: change loop to use int as loop index.
r20820:
Maintenance: Fixed the bug found by coverity CID 788
There were two problems with this function:
1) it tried to unnecessary free NULL pointer
2) it tried to allocate c_name buffer that is done by H5Pget_class_name
r24111:
=======
Description:
Restrict GCC diagnostic pragmas to only gcc 4.6+
Tested on:
Mac OSX 10.8.4 (amazon) w/gcc 4.8.1, C++ & FORTRAN
(too minor to require h5committest)
