Commit Graph

20826 Commits

Author SHA1 Message Date
Allen Byrne
d9a5a49e65 Update CMake compiler flags to use same set of warnings 2020-03-23 15:10:33 -05:00
Allen Byrne
477c96f06f Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'e916acd018d5a307e7690a7978a1b73e83508f2b':
  Move the GNU warnings configuration under config/gnu-warnings/ and trim the filename prefixes.  Update config/gnu-flags to suit.
  By default, demote warnings promoted to errors back to warnings.
  Incorporate the H5_ECFLAGS into the library CFLAGS.  Now a bunch of errors will occur.  Next commit will demote the warnings promoted to errors back to warnings again.
  Break out warnings into more files that autoconf and CMake can share.  This change temporarily disables the warnings that were promoted to errors, but I will add those warnings back as warnings, not errors, in the next commit.
2020-03-23 12:25:48 -05:00
David Young
e916acd018 Merge pull request #2402 in HDFFV/hdf5 from ~DYOUNG/werror:break-out-warnings to develop
* commit '2f09d8f3c8a4a44932c1b8ffb0f6ea2219059a5c':
  Move the GNU warnings configuration under config/gnu-warnings/ and trim the filename prefixes.  Update config/gnu-flags to suit.
  By default, demote warnings promoted to errors back to warnings.
  Incorporate the H5_ECFLAGS into the library CFLAGS.  Now a bunch of errors will occur.  Next commit will demote the warnings promoted to errors back to warnings again.
  Break out warnings into more files that autoconf and CMake can share.  This change temporarily disables the warnings that were promoted to errors, but I will add those warnings back as warnings, not errors, in the next commit.
2020-03-23 11:55:07 -05:00
vchoi
afdcac28b8 A fix in the cleaning up code for datatype when datatype initialization via H5D__init_type() fails.
This is triggered by the tests for revised references when the libver bounds setting does not allow version
4 datatype message to be created.  The test failure is abort core dumped.
This is due to the datatype initialization fails before the datatype ID is registered.
The datatype cleanup code should provide for the above situation.
The code to fix the problem is the same as what is done in H5D__open_oid().
2020-03-23 01:16:32 -05:00
Quincey Koziol
b51585a911 Revise API for H5get_alloc_stats() to take a struct instead of separate values. 2020-03-20 16:39:55 -05:00
Quincey Koziol
66350c3356 Merge remote-tracking branch 'origin/develop' into alloc_stats 2020-03-20 15:50:24 -05:00
Allen Byrne
13da6d137f Allow use of INTEL icl/icl++ for clang 2020-03-19 10:57:21 -05:00
Allen Byrne
26fecb8c5a Merge pull request #2457 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '6be711bbd2b86de5bcd8f092d8f27d6b2251c111':
  Fix threadsafe for new test
2020-03-19 09:23:02 -05:00
David Young
2f09d8f3c8 Move the GNU warnings configuration under config/gnu-warnings/ and trim
the filename prefixes.  Update config/gnu-flags to suit.

I also made changes to config/cmake/HDFCompilerFlags.cmake, but I'm not
sure they're correct.
2020-03-18 21:12:53 -05:00
Dana Robinson
eecddd9f3e Merge pull request #2456 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor to develop
* commit 'ce7936d2b256bdd5e61a5ef018f35e9562667cac':
  Fixed the RELEASE.txt note for HDFFV-11057
  Fix shutdown errors when using the HDF5_VOL_CONNECTOR environment variable to set a dynamically loaded plugin as the default VOL connector. Fixes HDFFV-11057
  Very minor comment change in H5VLconnector.h.
2020-03-18 17:07:37 -05:00
Quincey Koziol
ae5f556415 Merge remote-tracking branch 'origin/develop' into alloc_stats 2020-03-18 16:18:09 -05:00
Dana Robinson
ce7936d2b2 Fixed the RELEASE.txt note for HDFFV-11057 2020-03-18 14:08:47 -07:00
Dana Robinson
693008ecaf Fix shutdown errors when using the HDF5_VOL_CONNECTOR environment
variable to set a dynamically loaded plugin as the default VOL
connector. Fixes HDFFV-11057
2020-03-18 13:58:02 -07:00
Allen Byrne
6be711bbd2 Fix threadsafe for new test 2020-03-18 15:31:27 -05:00
Dana Robinson
f0a687f133 Merge branch 'develop' into develop_minor 2020-03-18 13:06:15 -07:00
Jordan Henderson
fa087c3919 Update Tools library to be better compatible with VOL connectors
Modify h5repack to integrate with VOL connectors

Update tools library to accomodate VOL connectors

Update logic in h5tools_fopen for VOL connectors

Add command-line options to h5repack for specifying in/out VOL
connectors

Implement h5tools_set_vol_fapl

Fix library shutdown issue

Integrate ROS3 and HDFS VFDs into new h5tools_get_fapl() scheme

Avoid H5Ocopy in h5repack when using different VOL connectors

Update h5tools_test_utils.c for ROS3 and HDFS integration
2020-03-17 14:25:36 -05:00
Vailin Choi
9c93c1bb00 Merge pull request #2451 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/develop_seg_fault_sel_compat to develop
* commit '81b1ed4e1724b8a6a731ab2b8fb03234a8b49d15':
  Fix issues when deserializing point/all/none selection with version beyond the library's supported version: (1) Verify the decoded version before proceeding further with deserialization (2) Close the dataspace if errors occurred after opening the dataspace
2020-03-16 14:06:57 -05:00
Vailin Choi
81b1ed4e17 Fix issues when deserializing point/all/none selection with version beyond the library's supported version:
(1) Verify the decoded version before proceeding further with deserialization
(2) Close the dataspace if errors occurred after opening the dataspace
2020-03-13 11:22:22 -05:00
Dana Robinson
3d29cbb27f Very minor comment change in H5VLconnector.h. 2020-03-12 13:21:11 -07:00
Quincey Koziol
545d0f4db3 Merge remote-tracking branch 'origin/develop' into alloc_stats 2020-03-12 14:36:14 -05:00
David Young
7613f7e1aa Merge pull request #2378 in HDFFV/hdf5 from ~DYOUNG/werror:dont-crash-on-close to develop
* commit '093c2c7e69bc4a40e9d49eece1d6fdcf54e8ecb0':
  Avoid a crash, don't check if we're flushing when the file is closing: there's no need to check if the metadata cache is flushing if we already know the file is closing, because the condition we rely on is "closing OR flushing."  Further, the cache may have already gone away, so sometimes calling into the cache to see if it's flushing will crash the program.
2020-03-12 14:00:07 -05:00
Vailin Choi
a24b0c4a84 Merge pull request #26 in ~VCHOI/my_third_fork from develop to bugfix/develop_seg_fault_sel_compat
* commit '9abbdeaa66c70a00b6a7bedee9c76d2493a8e947': (31 commits)
  Remove system command from valgrind reports
  Whitespace
  Fix incorrect FUNC_LEAVE macro (should match FUNC_ENTER_*_TAG).
  Add semicolons to more PASSED() invocations.
  So that I can use PASSED(); anywhere a statement can go, #define PASSED() with a do-while wrapper.
  revert type cast
  Switch the 'get offset' operation from a dataset 'get' callback to a [native] dataset 'optional' operation.
  Modfy expression to match mpicc build with Intel as intel compiler, not gcc.
  Complete the comment on thread_main(), explaining why the barrier is used.
  Fixed issue building HDF5 with NAG Fortran 7.0.
  The first implementation seemed to allow for the possibility that a thread could block at the barrier, wake and exit the barrier, re-acquire the barrier lock and increase `nentered` before the other blocked threads woke and checked `nentered % count == 0`.  Then the other blocked threads would check `nentered % count == 0` and, finding it false, go back to sleep in the barrier.  This new implementation waits for a looser condition to obtain so that threads don't go back to sleep in the barrier.
  Add java version and reference libsettings
  Test the right condition for the EBUSY return in pthread_barrier_destroy().
  s/exit_failure/EXIT_FAILURE/g
  Implement pthread_barrier(3) for Darwin using a counter, condition variable, and mutex.  Untested.
  Update examples and fix old version references.
  Move MODEL check to before usage in CTestScript.cmake.
  Copy generated files instead creating twice
  Fix standalone link
  Fix Fortran macro use and jni comment
  ...
2020-03-11 16:23:56 -05:00
Quincey Koziol
04b8cc82a8 Add routines to query the library's free list sizes and allocation stats. 2020-03-10 18:37:55 -05:00
David Young
9abbdeaa66 Merge pull request #2351 in HDFFV/hdf5 from ~DYOUNG/werror:b-bye-HDpthread_self to develop
* commit '224cb4a03406ed72e02d026efeab47fdf7f6b33b':
  Use a naked pthread_self() call in the HDF5 thread wrappers.
2020-03-05 11:06:39 -06:00
David Young
7350db497b Merge pull request #2424 in HDFFV/hdf5 from ~DYOUNG/hdf5:passed-do-while to develop
* commit 'b53eb6fb29e556c482ce20fa7a21485c99beea74':
  Add semicolons to more PASSED() invocations.
  So that I can use PASSED(); anywhere a statement can go, #define PASSED() with a do-while wrapper.
2020-03-05 11:05:29 -06:00
Allen Byrne
7413557dd5 Merge pull request #2434 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '24298a031f0b7f6a04364cfbfbdd9c8b6cc1a038':
  Remove system command from valgrind reports
  Whitespace
2020-03-04 09:29:03 -06:00
Allen Byrne
24298a031f Remove system command from valgrind reports 2020-03-02 14:11:25 -06:00
Allen Byrne
5fc283da8e Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'a01ac97ba509e51905b816e8a29b5d0b2bc8be87':
  Fix incorrect FUNC_LEAVE macro (should match FUNC_ENTER_*_TAG).
2020-03-01 09:24:12 -06:00
Jake Smith
a01ac97ba5 Merge pull request #2427 in HDFFV/hdf5 from ~JAKE.SMITH/hdf5:develop to develop
* commit '2d9a81878d05732725f96d7d9b20ada8dfd2a146':
  Fix incorrect FUNC_LEAVE macro (should match FUNC_ENTER_*_TAG).
2020-02-29 23:39:00 -06:00
Allen Byrne
5abf6785cb Whitespace 2020-02-29 14:01:55 -06:00
Kimmy Mu
6e565dd271 Merge pull request #2431 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/type_cast to develop
* commit 'b5cf422799797cf0b573cc9992f866381bd63054':
  revert type cast
2020-02-28 22:12:16 -06:00
Jacob Smith
2d9a81878d Fix incorrect FUNC_LEAVE macro (should match FUNC_ENTER_*_TAG). 2020-02-28 17:14:45 -06:00
David Young
b53eb6fb29 Add semicolons to more PASSED() invocations. 2020-02-28 16:52:22 -06:00
David Young
3e93aa9514 So that I can use PASSED(); anywhere a statement can go, #define PASSED() with
a do-while wrapper.
2020-02-28 16:51:55 -06:00
kmu
b5cf422799 revert type cast 2020-02-28 14:47:13 -06:00
Quincey Koziol
885aa08ec4 Merge pull request #2419 in HDFFV/hdf5 from revise_get_offset to develop
* commit '38af6ee3d59a8e836f4c62dd533ddabd914c7abb':
  Switch the 'get offset' operation from a dataset 'get' callback to a [native] dataset 'optional' operation.
2020-02-28 14:27:16 -06:00
Quincey Koziol
38af6ee3d5 Switch the 'get offset' operation from a dataset 'get' callback to a [native]
dataset 'optional' operation.
2020-02-28 14:06:28 -06:00
Larry Knox
d7eec7d6ec Merge pull request #2411 in HDFFV/hdf5 from ~DYOUNG/werror:darwin-barriers to develop
* commit '803d805c74466a9d736455930b17de2d9f5cb02d':
  Complete the comment on thread_main(), explaining why the barrier is used.
  The first implementation seemed to allow for the possibility that a thread could block at the barrier, wake and exit the barrier, re-acquire the barrier lock and increase `nentered` before the other blocked threads woke and checked `nentered % count == 0`.  Then the other blocked threads would check `nentered % count == 0` and, finding it false, go back to sleep in the barrier.  This new implementation waits for a looser condition to obtain so that threads don't go back to sleep in the barrier.
  Test the right condition for the EBUSY return in pthread_barrier_destroy().
  s/exit_failure/EXIT_FAILURE/g
  Implement pthread_barrier(3) for Darwin using a counter, condition variable, and mutex.  Untested.
2020-02-28 06:22:13 -06:00
Larry Knox
cfc52fc273 Merge pull request #2415 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit '811988f82c182012704942d333ee7800f4a78349':
  Modfy expression to match mpicc build with Intel as intel compiler, not gcc.
2020-02-27 22:03:28 -06:00
Larry Knox
811988f82c Modfy expression to match mpicc build with Intel as intel compiler, not
gcc.
2020-02-27 17:06:41 -06:00
Scot Breitenfeld
0a581b0ac0 Merge pull request #2414 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:develop to develop
* commit 'dde7e73d9fe8cc3b849767790aa9b13ee2d600cd':
  Fixed issue building HDF5 with NAG Fortran 7.0.
2020-02-27 16:23:06 -06:00
David Young
803d805c74 Complete the comment on thread_main(), explaining why the barrier is used. 2020-02-27 16:14:44 -06:00
Allen Byrne
a8755bfe2b Merge pull request #2412 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '6686cac564f5d0015a32b92e4478002069c973ee':
  Add java version and reference libsettings
2020-02-27 14:55:48 -06:00
M. Scot Breitenfeld
dde7e73d9f Fixed issue building HDF5 with NAG Fortran 7.0.
Accounted for the additon of half precision floating-point with a KIND=16.

HDFFV-11033
2020-02-27 12:19:29 -06:00
David Young
4be589813a The first implementation seemed to allow for the possibility that a thread
could block at the barrier, wake and exit the barrier, re-acquire the barrier
lock and increase `nentered` before the other blocked threads woke and checked
`nentered % count == 0`.  Then the other blocked threads would check `nentered
% count == 0` and, finding it false, go back to sleep in the barrier.  This new
implementation waits for a looser condition to obtain so that threads don't go
back to sleep in the barrier.
2020-02-27 11:27:45 -06:00
Allen Byrne
6686cac564 Add java version and reference libsettings 2020-02-27 10:51:13 -06:00
David Young
11d22f3ea5 Test the right condition for the EBUSY return in pthread_barrier_destroy(). 2020-02-27 10:17:24 -06:00
David Young
802bf2dc1e s/exit_failure/EXIT_FAILURE/g 2020-02-27 10:16:49 -06:00
Allen Byrne
9a0e84fb47 Merge pull request #2409 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '13f5b3aee20d1d65f56dc08f088e0f218da5cf37':
  Update examples and fix old version references.
  Move MODEL check to before usage in CTestScript.cmake.
2020-02-27 08:56:44 -06:00
David Young
b87d9cb50e Implement pthread_barrier(3) for Darwin using a counter, condition variable,
and mutex.  Untested.
2020-02-26 20:38:57 -06:00