- Add an install rule to copy compiled fortran module files
- Only build the xlatefile utility if testing and tools are enabled
- Don't do MPI HAVE_XXX checks until MPI_FOUND is true
- Install needs H5version.h & H5overflow.h to be copied
- Add debug information flags to debug compile and link lines for win32 Intel compiler
Fixed a bug (1855) in H5DSattach_scale, H5DSis_attached and H5DSdetach_scale
caused by using H5Tget_native_type function to determine the native
type for reading REFERENCE_LIST attribute. The bug was exposed on Mac PPC.
Platforms tested: juniper (Mac PPC), jam, amani, linew
Fixed a bug in the H5DSdetach_scale function when 0 bytes
were allocated after the last reference to a dim. scale
was removed from the list of references in a VL element of the
DIMENSION_LIST attribute; modified the function to comply
with the Spec: DIMENSION_LIST attribute is deleted now when no
dimension scales left attached.
Platforms tested: jam with electric fence, amani amd linew
Improve configure's large-file support control.
Description:
Modified configure to now attempt to add defines necessary for
supporting largefiles on all systems, instead of solely on linux. This
is in response to user requests to enable largefile support on Solaris
by default, as well as to give extra control on AIX (instead of just
jamming the necessary flag into the config files).
The old --enable-linux-lfs flag has been removed in favor of the
--enable-largefile flag (enabled by default), which can be used on all
platforms.
On systems where large files cannot be supported in this manner,
configure will report as such.
Tested:
h5committest
AIX (NCSA's blue_print machine)
duty, liberty, and linew.
Autotool Upgrade / Libtool Bug Fix
Description:
Updated autotools referenced in bin/reconfigure as follows:
Autoconf 2.64 --> Autoconf 2.65
Automake 1.11 --> Automake 1.11.1
Libtool 2.2.6a --> Libtool 2.2.6b-mcg
The referenced libtool version is a custom version of 2.2.6b. It
has been tweaked to fix a bug in libtool that occurs
when using PGI 10.0 compilers. A check incorrectly categorizes
the C++ compiler as version 1.0 instead of 10.0, and the link
line is subsequently set up incorrectly and fails to compile.
A patch has been made available and will be included in the next
release of libtool, but in the meantime I've applied the patch to a custom
installation as indicated above. This bin/reconfigure now references
the custom installation, and the resulting configure script will correctly
categorize the PGI 10.0 C++ compiler.
Ran bin/reconfigure to regenerate configure and makefiles.
Tested:
jam and amani with PGI 10.0 compilers.
h5committest
Re-run bin/reconfigure to catch up with recent rearrangements, remove some
unused srcdir headers and duplicated code in main test header.
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug & prod
Linux/32 2.6 (jam)
Clean up srcdir querying code more, extracting it into single header file,
to avoid compiler warnings.
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug & prod
Linux/32 2.6 (jam)
Unify srcdir handling for test executables and allow them to use the srcdir
setting from configure time without requiring the 'srcdir' environment variable
be set (although you still can, to override the built in setting). Attempted
to get this right for Windows builds also.
Also add dependency between src/H5Tinit.c and src/libhdf5.settings, so
that the test/testcheck_version.sh script works correctly.
Tested on:
Linux/32 2.6 (jam)
Mac OS X/32 10.6.2 (amazon)
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)
Bring Coverity fixes from 1/22/10 session to trunk:
r18137:
219: Initialized hid_t to -1 and added close to error block.
189-191: Initialized line to NULL and added free line, and close fp to error block.
r18138:
19: Moved code block for printing that the number of enums is empty to the error block. (Would never have been executed otherwise)
r18139:
Fix coverity item 58. Moved code related to displaying the parent of a repeated
group to the else(isRoot) section, as the root group has no parent.
r18140:
218: Initialized ret_value variable to -1. Because of throw Exception in default case of switch, the coverity problem would not have executed anyway. Good pratice is to initialize variables.
r18141:
Fix coverity item 92. Added code to H5E_register_class to free cls in case of
an error.
r18142:
Fix coverity item 91. Added code to H5E_create_msg to free msg in case of an
error.
r18143:
fixed issue 14,
took away "if" and used #ifndef_xxx.
r18144:
Fix coverity item 110. Added code to H5Eget_minor to free msg_str in case of
an error.
r18145:
fixed coverity #18 removed "aligned", it is always NULL.
r18146:
Fix coverity item 109. Added code to H5Eget_major to free msg_str in case of
an error.
r18147:
Fixed coverity #81 and #82, Check for bad pointer(s), but can't issue error, just leave
r18148:
Fix coverity item 97. Added code to H5FD_fapl_open to free copied_driver_info
in case of an error.
r18149:
Fix coverity item 96. Added code to H5FD_dxpl_open to free copied_driver_info
in case of an error.
r18150:
Fix Coverity issue #29: Protected cache_ptr dereferences with "if(pass)"
block
r18151:
Fix coverity item 93. Added code to H5FL_fac_init to free factory and new_node
in case of an error.
r18152:
Fix coverity items 98 and 99. Added code free allocated space in case of
error.
r18155:
124: Freed head pointer before jumping to done. There was no error handling block and normal exit used same path out.
120-123: Freed list of lists in error handling block.
r18156:
Fix coverity issues 179, 180, 181, 182, 183, 184, 186, 320, 407. These were resource leak issues where allocated memory was not freed, generally in the case of tests that failed.
Tested on:
Mac OS X/32 10.6.2 (amazon) debug & production
Bring back changes from Coverity session on 1/15/10:
r18111:
Fix Coverity issue #130: make certain that the cache gets freed on error.
r18112:
Fix Coverity issue #43 by making cache testing calls protected by 'pass'
variable.
r18113:
Fix Coverity issue #129 by releasing the cache on error.
r18115:
Coverity #45 fix: patched an error check in H5Screate_simple to prevent future dereferencing of a NULL point.
Added a verification in test/th5s.c.
r18116:
Fix Coverity issue #43 by releasing cache on error.
r18117:
Coverity #362,363 by adding HGOTO_DONE, freeing allocations and associated changes. REsolving coverity results #364-368, 369, 370-372, 377, 379, and 380.
r18118:
Fix Coverity issue #42: assert that cache & test specification pointer are
valid.
r18122:
Coverity #362,363 by adding HGOTO_DONE and freeing allocations. This also takes care of #357,358.
r18123:
Coverity #359-361, 373-376: Added HGOTO_DONE(FAIL) statement after checking allocation for NULL. Verified allocation is freed in done block.
r18128:
Fixed coverity issue #10 -- removed dead code.
Tested on:
Mac OS X/32 10.6.2 (amazon)
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.
Bring r18030 from merge_metadata_journaling branch to trunk:
Bring "brush clearing" changes (whitespace & style issues, mostly) from
metadata_journaling branch to the "merging" branch, to converge the trunk and
the metadata_journaling branch.
Also, some other minor cleanups along the way.
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
Bring "brush clearing" changes (whitespace & style issues, mostly) from
metadata_journaling branch to the "merging" branch, to converge the trunk and
the metadata_journaling branch.
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
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
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.
Fix several errors in code, which was not compiling... :-(
Tested on:
FreeBSD/32 6.3 (duty) in debug 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
Configure Fix
Description:
Modified configure to set FC and CXX to "no" when fortran and c++ are
not being compiled, respectively. This will prevent configure from running
some checks on these compilers when they are not being used.
This fixes a problem that was occuring when FC and/or CXX are set to
a nonexistant or invalid compiler. Even if the languages were disabled,
a libtool test would fail, thus preventing libtool from properly linking
any libraries, yet configure would not flag an error message due to this
because the languages were disabled.
Tested:
- h5committest (jam, smirom, linew)
- manually eyeballed configure output and logfile.
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
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.
Bring r17266 from 1.8 branch to trunk:
Clean up various compiler warnings from IRIX64 build
Tested on:
Mac OS X/32 (amazon) debug & production
(yes, I know it's not an IRIX64 system :-)
Too minor to require h5committest
Fix BZ #1583
Description:
The --enable-static-exec flag was broken. Configure was adding the
-all-static linker flag to an environment variable which was subsequently
never used. (looks like it was used in 1.6 Makefile.ins, but never
moved to 1.8's Makefile.ams when we added automake support).
To fix, I've added this environment varibale to the link lines of all the
tools. Now, when --enable-static-exec is invoked, it will correctly
generate statically linked executables in the installed bin directory.
Tested:
I've tested manually to ensure that the generated execs are static when
the flag is used and dynamic when not. I've also tested when szip is
used, as this was a use case mentioned in the bug report.
Also: ran full tests with make check on jam and smirom for good measure.
ISSUE: h5ltread_dataset_string_f causes library assertion with g95.
SOLUTION: convert the fortran string buffer to a C buffer with HD5f2cstring, and pass this string to the C function
TEST: added a test call in the fortran test lite program
DOCS: added the note in RELEASE.txt "- Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions had memory problems with the g95 fortran compiler. (PVN - 5/13/2009) 1522
Bring r16846 from revise_chunks branch back to trunk:
Fix broken (for how long?) H5_ASSIGN_OVERFLOW macro to actually detect
overflows during assignments, along with several errors it [now] detected.
Cleaned up a fix minor warnings and/or pieces of code also.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest not needed - multi-platform test performed on branch)
- 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
ISSUE2: the scale index input/output parameter value passed to H5DSiterate_scales was not always incremented (it returns the scale index current iteration).
SOLUTION FOR ISSUE2: modified the cycle in H5DSiterate_scales so that the scale index is always incremented
TEST: added some test cases with calls to invalid indices and H5DSiterate_scales with return scale indices and visitor data
tested: windows, linux
ISSUE: When some functions are called with an invalid dimension index (for example, greater than the rank of the dataset) the function does not immediately fail, rather asserts down the code.
SOLUTION: added this check for H5DSdetach_scale, H5DSset_label, H5DSget_label (the other functions have this check) . H5DSiterate_scales also added a check for an invalid dimension scale index
TEST: added some test cases with calls to invalid indices
DOCS: Nothing added
ISSUE: Purify (Windows Visual Studio 6) complains of a memory leak in H5DSdetach_scale call regarding a H5Aread call (stack is H5A_read, H5T_convert, H5T_conv_vlen, H5T_vlen_seq_mem_write, H5MM_malloc).
SOLUTION: When a scale is detached from a dataset, the variable length structure length field is decreased in one entry. The associated pointer must be reallocated with the new length.
DOCS AND TEST: Nothing added
tested: windows with purify, linux
1. #1487 (B1) DS memory leaks ISSUE 1: On a "go to" error condition, previously allocated buffers were not freed. NOTE: these are "potential" memory leaks because typically the error conditions do not occur, so the potential memory leaks also do NOT occur. ISSUE 2: A function used to read dimension scales realistic data (topography of the North Atlantic, latitude and longitude) was being called without the data buffer being freed. SOLUTION FOR ISSUE 1: added "free" calls for the allocated buffers on the error sections. SOLUTION FOR ISSUE 2: added a "free" call after the read_data function, after using the buffer (on a H5Dwrite and H5Screate_simple). The read_data function reads both data and dimensions from the ASCII data files. DOCS: no docs added. Done for 1.9 and 1.8 STATUS: Closed bug
tested: h5committest
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
Remove another call to H5E_clear_stack() from within the library.
Clean up lots of compiler warnings.
Tested on:
Mac OS X/32 10.5.6 (amazon)
(followup on other platforms forthcoming)
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
Description:
- Remove need to set LD_LIBRARY_PATH when using shared szip library.
- Libtool 2.2.6a is now used to generate libraries.
- 'make check install' dependency bug is fixed, and should no longer
break the build.
- removed hard coding of shell in config/commence.am, as this causes
problems on Solaris with the new version of libtool.
- RELEASE.txt with appropriate changes.
Tested:
- kagiso, smirom, linew (merged from 1.8, pretty quick tests)
The custom rules for installing h5cc, h5fc, and the fortran modules in fortran
and in hl/fortran don't use $(DESTDIR). Added it to all those rules.
Tested: kagiso both serial and parallel with fortran and cxx enabled.
Tested by:
make install
make DESTDIR=/tmp/acheng install
diff -r /tmp/acheng/.../hdf5 hdf5
Remove trailing whitespace from C/C++ source files, with the following
script:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Tested on:
Mac OS X/32 10.5.5 (amazon)
No need for h5committest, just whitespace changes...
Description:
The daily test failure caused by the C++ API was fixed, so put
the packet table test back.
Platforms tested:
SunOS 5.10 (linew)
Linux 2.6 (kagiso)
FreeBSD (duty)
the file didn't have the data. It happened because each handle had its own
object structure, and the empty one overwrote the data with fill value. This is
fixed by making some attribute information like the data be shared in the
attribute structure.
Tested on smirom, kagiso, and linew.
