replace functions like h5_clean_files() that also do things like
reset the error handler and close fapls.
Existing tests have not yet been updated to use these new
functions.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
autotools serial
Complete revamp of package initialization/shutdown mechanism in the library.
Each package now has a single init/term routine.
This new way should avoid packages being re-initialized during library
shutdown and is also be _much_ more proactive about giving feedback for
resource leaks internal to the library.
Introduces a new "module" header file for packages in the library
(e.g src/H5Fmodule.h) which sets up some necessary package configuration macros
for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly
modified version of this header, src/H5FDdrvr_module.h)
Also cleaned up a bunch of resources leaks all across the library and tests,
along with addressing many warnings, as I encountered them.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
Linux/64 3.10.x (kituo) w/serial & parallel
Linux/64 2.6.x (ostrich) w/serial
- Updated the preprocessor logic that defines the H5_ATTR_* macros. The Solaris
Studio compiler understands __attribute__ but not the specific attributes
that we use. The H5_ATTR_* macros are now defined as blank with that
compiler which significantly cleans up the warnings, making debugging
easier.
- Replaced a few lingering __attribute__ macros with H5_ATTR_* markup.
Tested on: h5committest
Solaris w/ Solaris Studio (emu)
Bring generic improvements from encode/decode property list branch to
the trunk. This includes a better version of the property list comparison
routine, cleaned up compiler warnings, and some cleaned up property list
callbacks. Also, started on changes to clean up parallel test output, so that
it doesn't report successful tests from each process.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug, GCC 4.7.x, FORTRAN, C++, threadsafe and parallel
Linux 2.6/32 (jam) w/debug
Solaris 2.7/64 (linew) w/debug
Remove some leftover uses of the __FUNCTION__ macro, replacing them with
FUNC macro, as used everywhere else.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
(too minor to require h5committest)
Correct error in loading local heap prefix & data block from the file.
Sometimes the local heap's prefix could be loaded before the data block (e.g.
using H5Oget_info), but then when the data block was loaded later, the free
list information would get lost, causing the heap's size to grow larger than
necessary. This is Jira bug #HDFFV-7767
Tested on:
Mac OS X/32 10.7.2 (amazon) w/debug
(h5committest coming up)
Description:
Added internal tesitng routines to traverse a file and verify that symbol table
information is *always* cached, whenever possible. Added this check to the end
of many tests to check all the test files, right before the call to h5_cleanup.
Tested: jam, amani, heiwa (h5committest)
Add in override for testing timeout alarm to allow "HDF5_ALARM_SECONDS"
environment variable to change the timeout value from the default value.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(Too minor to require h5committest)
Description:
honest3 v1.8 failed in parallel test. It got stuck in the same
testpar/testphdf5 subtest (cbhsssdrpio). This is an old problem.
Upon closer inspection, the testphdf5, when terminated, had clocked
up 1hr 9min 46 sec wall clock time. Honest1 system also sent a message
that an mpi process has used up 30+ CPU minutes which exceeded their login
node cpu time limit and they killed the process. I also did a hand-run
of testphdf5. All subtests before cbhsssdrpio completed in a few minutes.
Therefore, it is safe to say the majority of the 70 minutes of wall clock
time are spent in the sub-test cbhsssdrpio. It also used up lots of CPU
time. cbhsssdrpio is likely infinite looping.
Since MPI application is prone to infinite looping due to message deadlock,
the testphdf5 has a built-in protection to give each subtest at most 20 minutes
of wall-clock time to run. When the 20 minutes wall-clock time is exceeded,
the testphdf5 will attempt to terminate itself. This prevents unnecessary
CPU time consumption in infinite looping.
But that clock limit was changed to 30 and then 60 minutes. I should have
but failed to, noticed the change mentioned by Quincey. IMO, 20 wall clock
time is more than sufficient for each subtest of testphdf5 to complete.
If a subtest takes longer than 20 minutes, it is likely infinite looping.
Giving it more time will not help.
If a subtest of testphdf5 takes more than 20 minutes, it should be broken
down to small tests that will finish way under 20 minutes so that it is
much easier to see progress and identify any deadlock problems.
In view of this, I am changing the testphdf5 time limit back to 20 minutes.
This will at least stop the CPU TIME exceeding limits and annoying the
system administrators.
Maybe there could be a provision, such as environment variable like
$HDF5_ALARM_SECOND to modify the alarm duration on individual execution.
Even so, that should be used temporary to see if an execution just needs
a little more time.
Tested: just eyeballed as the change is trivia.
Fix const pointer issues for projection construction routine and also
bump time before alarm kicks in to terminate a test from 20 minutes to 30
minutes, to give the PGI compiler tests w/debugging enabled a chance to finish.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug
Linux/32 2.6.18 (jam) w/PGI & debug
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)
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)
The previous implementation did not work for WIndows.
Moved the macro definition of HDGetTestVerbosity from testhdf5.h
to h5test.h.
Removed as much as possible macro definitions that use HDGetTestVerbosity
directly.
Tested: Jam (serial and parallel). Did not run h5committest since this
is a trival change that is portable.
Call h5_fixname (with an array of test filenames) for generating the
filename to create and then call h5_cleanup() when the tests pass, to delete the files
created and close the FAPL from h5_fileaccess().
Defined a macro
#define TESTING2(WHAT) {printf(" Testing %-62s",WHAT); fflush(stdout);}
Similar to TESTING, except that it has a initial indentation space.
The effect is for nested loop tests
Testing with old file format:
Testing with fill value, no compression PASSED
tested: windows, linux
Fix various problems with a the core & sec2 VFDs.
Improve the h5_get_file_size() routine to handle files created with
VFDs that use multiple files.
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, 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 production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
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...
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.
File format is not stable, don't keep files produced!
Description:
First stage of checkins modifying the format of groups to support creation
order. Implement "dense" storage for links in groups.
Try to clarify some of the symbols for the H5L API.
Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest
file format options (including "dense" link storage in groups)
Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation
order tracking in groups (although no index on creation order yet).
Remove --enable-group-revision configure flag, as file format issues are
now handled in a backwardly/forwardly compatible way.
Clean up lots of compiler warnings and other minor formatting issues.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-v1.6 compa
Mac OSX/32 10.4.8 (amazon)
AIX 5.3 (copper) w/parallel & FORTRAN
Feature
Description:
Sometimes the parallel prefix is given in the form of nfs:/mnt/pfs which
if given to a non-MPIO VFD like the default H5Fcreate, it would fail.
Added a new routine h5_rmprefix which would return the non-prefix component
part of the file name which would be okay for the default H5Fcreate and
such.
Platforms tested:
Tested in heping parallel.
Description:
The file size test in C++ library failed on Copper because the
value returned by h5_get_file_size was intepreted incorrectly
due to different interger sizes.
Solution:
H5private.h: Added check to use stat64 and off64_t where appropriate.
h5test.c and h5test.h: used h5_stat_size_t in place of off_t.
tattr.cpp: used h5_stat_size_t in place of off_t.
Platforms tested:
Linux 2.4 (heping)
AIX 5.1 (copper)
SunOS 5.8 64-bit (sol) - still on going
feature
Description:
Added the GetTestExpress and SetTestExpress to support the TestExpress mode
according to $HDF5TextExpress. For now, it is just defined or not, the
actual value does not matter.
Platforms tested:
heping(serial), mir (PP).
Bug fix.
Description:
getenv_all will be called even when it is NOT an MPI application.
Solution:
Moved the use of getenv_all("HDF5_NOCLEANUP") to fix_name so that it will
be invoked only if a parallel driver is used.
Platforms tested:
hand tested in copper.
new features
Description:
add support for compiling the library and testphdf5 in Windows
Solution:
Platforms tested:
Linux
AIX
Solaris
Windows VC6
Misc. update:
Feature.
Description:
Added ALARM_ON, ALARM_OFF feature to terminate tests that run more than
the default time limit. So far, the feature is applied in the standard test
frame.
Platforms tested:
heping PP.
Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Description: Renamed test/dt_atomic.c to test/dt_arith.c(an abbreviation
of "arithmetic data types") to better describe the program. This checkin
broke down into three sections when the floating-point numbers are the
source, normalized, denormalized, and special values. If there's any
difference of destination values, only normalized value test reports
failure. The other 2 report only as warning.
Platforms tested: h5commitest and fuss
Misc. update: MANIFEST
