Commit Graph

6824 Commits

Author SHA1 Message Date
Larry Knox
5ea58acf8a Merge pull request #2525 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit '43424a1392b662a29542bb70014c253162ccfe48':
  Add missing ')'.
  Add C++ warnings treated as error for autotools builds.
  Move macro ADD_H5_CFLAGS to cmake_ext_mod/HDFMacros.cmake and remove duplicate versions.
  Address PR suggestions and add overlooked GCC compiler version flags.
  Don't add general warnings flags for unsupported old versions of gcc and g++ (older than gcc/g++ 4.2). Correct gnu-cxxflags to determine warnings flags to be added based on C++ compiler version instead of C compiler version.
2020-04-23 13:41:34 -05:00
Larry Knox
de51001fcd Add C++ warnings treated as error for autotools builds. 2020-04-23 13:14:56 -05:00
Quincey Koziol
9e5dbf6906 Trim trailing whitespace 2020-04-20 18:12:00 -05:00
Dana Robinson
384693d8e5 Fixed some minor cmp callback bugs and cleaned warnings. 2020-04-17 00:46:46 -07:00
Dana Robinson
9ecca22dd1 Fixed problems with S3 and HDFS VFDs.
* Updated info struct parameter to correct info_string
* Fixed Makefile.am where the S3 VFD was listed twice, causing
  duplicated symbols errors.
2020-04-16 17:07:21 -07:00
Jake Smith
f1893e9404 Merge pull request #2452 in HDFFV/hdf5 from ~JAKE.SMITH/hdf5:feature/vfd_splitter_mirror_a to develop
Add Splitter VFD and Mirror VFD.

* commit '664fc6af47e369152727ff66d68d8532feb0e210':
  Add enable-mirror-vfd flag to configure options.
  Tidying of Mirror VFD.
  Add function header comment for `mirror_writer:run_writer()`.
  Add Splitter VFD to library.
2020-04-11 11:53:41 -05:00
Dana Robinson
0fdbbcfc0b Merge pull request #2502 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor to develop
* commit '35c0d5cdfcfaa84f59e1c596ba1ccaeb28e3d83d':
  Fix for passthrough VOL not passing tools tests due to incorrect optional callback queries.
2020-04-09 10:30:09 -05:00
Dana Robinson
35c0d5cdfc Fix for passthrough VOL not passing tools tests due to incorrect
optional callback queries.
2020-04-08 16:44:19 -07:00
Vailin Choi
fcd3bce961 Merge pull request #2496 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/dtype_close_on_error to develop
* commit 'db9155c2f34bbf77a1cda01904805fe5c993b6d5':
  Fix according to PR feedback.
  Fix an error in previous merge: should use NULL instead of FAIL.
2020-04-08 18:33:00 -05:00
vchoi
db9155c2f3 Fix according to PR feedback. 2020-04-07 13:17:56 -05:00
Jacob Smith
075e74e9b2 Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into feature/vfd_splitter_mirror_a 2020-04-07 10:29:00 -05:00
Jacob Smith
d97c00013d Tidying of Mirror VFD.
* Rename server-stop utility to mirror_server_stop.
* Remove external dependency on bzero().
* Modify test/use_common to use only the public API.
* Rename internal bitswap macro to follow convention.
2020-04-07 10:20:44 -05:00
vchoi
230570b593 Fix an error in previous merge: should use NULL instead of FAIL. 2020-04-06 19:26:49 -05:00
Allen Byrne
279ea4f2a2 Update printf pointer syntax and revert fortran to f2003 2020-04-06 15:19:28 -05:00
Allen Byrne
fd18d013f1 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '4830a1796441abbb5a4fbd2cff9a651f2a0d066e':
  Updated tools dump output when dataset offset is undefined.
  Added checks for native optional call support in some of the tools.
  Misc changes for h5dump VOL changes.
2020-04-06 14:13:27 -05:00
Allen Byrne
57f5d00a43 TRILAB-192 add c++ and fortran warnings build systems one file 2020-04-05 10:50:08 -05:00
Dana Robinson
456308ff17 Added checks for native optional call support in some of the tools. 2020-04-02 02:12:19 -07:00
Dana Robinson
3cd1b46b9c Merge branch 'develop' into tools_vol_update 2020-04-01 23:27:08 -07:00
Vailin Choi
bae05235a2 Merge pull request #2461 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/dtype_close_on_error to develop
* commit 'afdcac28b85d690eebc80ab568fa5266081baaaa':
  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().
2020-04-01 22:14:42 -05:00
Dana Robinson
a267c4e5d3 Changed default dataset shared struct to initialize hid_t IDs to
H5I_INVALID_HID.
2020-04-01 18:46:07 -07:00
David Young
1547feed60 Merge pull request #2363 in HDFFV/hdf5 from ~DYOUNG/werror:thread_id to develop
* commit '63c95faf49559ea66e3066427961095b69fdb213':
  Remove tongue-in-cheek credit for Rusty Shackleford and Dale Alvin Gribble.
  Follow HDF5 conventions.
2020-04-01 15:27:51 -05:00
Dana Robinson
36e8e2be4b Misc changes for h5dump VOL changes. 2020-03-30 01:51:36 -07:00
Allen Byrne
1505fa1498 TRILAB-192 restrict extensive warnings to libraries 2020-03-24 16:45:12 -05:00
Quincey Koziol
d3ef866a29 Merge pull request #2445 in HDFFV/hdf5 from alloc_stats to develop
* commit 'b51585a9110c4322c52f9dcdc60cd26c3ea44546':
  Revise API for H5get_alloc_stats() to take a struct instead of separate values.
  Add routines to query the library's free list sizes and allocation stats.
2020-03-23 18:01:43 -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
Quincey Koziol
ae5f556415 Merge remote-tracking branch 'origin/develop' into alloc_stats 2020-03-18 16:18:09 -05:00
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
Dana Robinson
f0a687f133 Merge branch 'develop' into develop_minor 2020-03-18 13:06:15 -07:00
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
Jacob Smith
b65405439d Add Splitter VFD to library.
* "Simultaneous and equivalent" Read-Write and Write-Only channels for
  file I/O.
* Only supports drivers with the H5FD_FEAT_DEFAULT_VFD_COMPATIBLE flag for
  now, preventing issues with multi-file drivers.

Add Mirror VFD to library.

* Write-only operations over a network.
* Uses TCP/IP sockets.
* Server and auxiliary server-shutdown programs provided in a new directory,
  `utils/mirror_vfd`.
* Automated testing via loopback ("remote" of localhost).
2020-03-13 17:13:17 -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
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
Jacob Smith
2d9a81878d Fix incorrect FUNC_LEAVE macro (should match FUNC_ENTER_*_TAG). 2020-02-28 17:14:45 -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
David Young
626c60dec4 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.
2020-02-25 11:59:37 -06:00
Allen Byrne
666205a55f TRILAB-142 Change minimum CMake version to 3.12 2020-02-21 16:16:06 -06:00
Jordan Henderson
51b8c63864 Merge develop 2020-02-21 14:30:34 -06:00
David Young
158ba17be0 Replace the old H5F_DECODE_LENGTH() implementation with one that
initializes the variable it's loading on every path.
2020-02-19 13:18:48 -06:00
David Young
7b4131c2ae Merge pull request #2367 in HDFFV/hdf5 from ~DYOUNG/werror:unused to develop
* commit '50aac126d7c4082c2aeb0f3a68cad26bd1cd9783':
  Start to document the function/parameter/variable attribute macros.
  Filter all of the new _USED / _UNUSED type modifiers.
  H5_HAVE_PARALLEL, _DEBUG_API, etc.  Add attributes to some variables and parameters that are unused under some configurations.
2020-02-19 09:38:02 -06:00
David Young
47b79b7422 Merge pull request #2369 in HDFFV/hdf5 from ~DYOUNG/vs2010:develop to develop
Merged per discussion with Elena.

* commit 'b4697f969295245840350e17d75d92a0fdd7e7a9':
  Use HD prefix.
  Delete unhelpful comment per Jordan's question.
  Make sure that H5TS_thread_id() is available as either a function or a macro in all configurations.
  Provide local copies of err(3)- and errx(3)-alike functions for Visual Studio compatibility.
  Provide C99/POSIX.1 format strings PRI[doux]{8,16,32,64,MAX,PTR} on systems that are missing <inttypes.h>.
2020-02-17 10:47:29 -06:00
David Young
fa2b89c6b0 Merge pull request #2325 in HDFFV/hdf5 from ~DYOUNG/werror:h5t_copy to develop
Merged per discussion with Elena.

* commit '3f903a441ad84001ea66589728bd8b036b6fdfca':
  Take out the temporary performance tests.
  Make calls through a function pointer.  Use the same number of arguments, always.
  Increase iterations, provide a baseline for no-op, simplify the overhead case a bit.
  Temporarily add some code that measures the time to run the simplest possible H5T__copy_all()-like routine 10 million times and then measures the version with FUNC_ENTER_STATIC/_LEAVE_NOAPI and a HGOTO_ERROR() statement.
  H5T_copy() constification plus Quincey's contributions.
2020-02-17 10:46:52 -06:00
David Young
093c2c7e69 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.
2020-02-13 10:01:05 -06:00
David Young
63c95faf49 Remove tongue-in-cheek credit for Rusty Shackleford and Dale Alvin Gribble.
Delete the comment questioning whether pthread_mutex_lock is allowed
in a key destructor, since pthread_key_create(3) provides the answer:

   There  is  no  notion  of a destructor-safe function. If an application
   does not call pthread_exit() from a signal handler, or if it blocks any
   signal whose handler may call pthread_exit() while calling async-unsafe
   functions, all functions may be safely called from destructors.

Delete redundant comment.
2020-02-10 17:24:04 -06:00