* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING
file - files not in src or test.
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Small changes plus merge of tools arg parse from 1.12
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Add H5Fwait, H5Dwait, and other changes for async vol connector
* Revert temporary testing changes
* Add H5Fwait to header file
* Add H5VLreset_lib_state() routine.
* Correct VOL wrap context when retrieving library state for file open & create.
* Manage the API context's VOL connector state as part of the library state.
* Set the 'VOL connector property valid' flag when restoring the library state.
* Don't push new API context on stack when retrieving "current" one.
* Check for NULL VOL wrap context before decrementing refcount on it, when
freeing the API context state.
* Manage recount of underlying connector for VOL wrap context.
* Add H5TSmutex_acquire() and H5TSmutex_release() routines to acquire and
release the global lock on the HDF5 library.
* Update library with new functions related to library global lock
* Add asynchronous token API
* Add new lightweight FUNC_ENTER / LEAVE macros for helping to structure the
threadsafety (H5TS*) routines.
* Sync w/develop
* Initial event set code framework.
* Elaborate on the H5ES routines, starting to add API routines.
Update the "close ID" callbacks to allow asynchronous request tokens to be
passed in from an asynchronous close API call.
Refactor current asynchronous API routines (H5Fopen/H5Fclose and
H5Dread/H5Dread) to use event sets instead of directly working with request
tokens from the application.
Clean up a few other minor warnings & code style issues.
* Implement H5EScreate, H5ESget_count, and H5ESclose.
It should be possible to write a simple application that creates an event
set and uses it with H5Fopen_async, H5Dread_async, H5Dwrite_async, and
H5Fclose_async, then calls H5ESclose (which waits for all async events to
complete).
* Add source file for event set test.
* Refactor sync & async API routines to call common routine.
Move dataset API read / write routines to src/H5D.c, along with all the other
API routines.
Progress on "fake" async VOL connector, for testing.
* Modify async implementation to wrap async requests in a H5VL_object_t
struct so the VOL layer can find the connector when accessing the
request at a later point.
* Free the requests is H5ESclose. Remove comments implying that request
wait, notify, and cancel callbacks should free the request.
* Fix bug in error handling in H5Fclose.
* Fix bugs in async file routines. Rename H5VL_create_object_generic to
H5VL_create_object.
* Add explicit async version of H5Fcreate.
* Add more _async routines
* Correct typo for return value from H5Awrite changes
* Add H5EStest and H5ESwait routines
* Updated with API tracing info
* Fix NULL pointer dereference in H5ES__wait
* Add H5is_library_terminating() routine, so that VOL connectors can detect
when the library is shutting down.
* Fix typo
* Remove event from event set's linked list
* Move block of code so that vol_obj is valid
* Avoid setting properties in the DXPL when reseting the library state (and in
the test code).
* Refactor argument tracing to implement new capability for tracing arguments
of non-API routines, with the H5ARG_TRACE macro. This macro is updated
automatically with the bin/trace script that runs as part of the autogen.sh
process. Major changes were in src/H5trace.c and bin/trace, with the other
changes being cleanups to the argument lists, to improve their presentation
in the tracing output.
Also - added the "managed string" routines, which can dynamically allocate
strings, appending printf-formatted output to the string efficiently.
* Release memory for managed strings
* Fix printf() formats.
* More printf() format fixes.
* Add H5Eappend_stack routine and regression tests
* Clean up a few missed merge conflicts and update the error stacks.
* Remove unnecessary fork() operations and ten second sleep().
* Restore commented out attribute out, to better enable tracking down the previous failure
* Allow multiple H5ARG_TRACE macros within a routine to be updated
* Switch to using "new" H5ES_insert (which takes the arguments for the caller routine) for all event set operations. Renames H5ES_insert_new to H5ES_insert and removes the previous H5ES_insert.
* Merge "managed" string routines into "ref-counted" strings, and refactor code to use them.
* Add missing file.
* Add caller's name and arguments to event, for error reporting
* Refactor event set setup for "API common" internal routines
* Checkin async API routines for H5A* and H5G* modules as listed in ID-283.
Fix couple h5dump expected output files due to the changes.
* Add some of the error query routines needed for event sets.
* Refactor to make async setup / teardown and "common" routines cleaner
* (1) Add async APIs to H5L, H5F, and H5D modules
(2) Fix errors in previous checkins of async APIs in H5A and H5G modules
(3) h5dump expected output changes
* Enhance event info, for better error handling
* Change name of temporary vol_obj variable, to help reduce coding errors
* Fix oversight with vol_obj pointer
* Minor code cleanup
* Add missing \'valid\' flag for VOL wrapper context, when restoring the library\'s state
* Run source formatter
* Change H5TSmutex lock and release to include a lock count
* Update error reporting ideas
* Minor updates to improve sanity checking for retrieving / restoring library state
* Updated with feedback from h5py team members
* Refactor internal event set list and event handling, add implementation for H5ESget_err_info
* Change the VOL request subclass callbacks that switch from using "H5ES_status_t" to "H5VL_request_status_t", and also add a H5VL_request_status_t* parameter to the 'cancel' callback in the request subclass. Also more code quality cleanups to add iterator callbacks to internal event set routines.
* Update API tracing for new H5VL_request_status_t typedef
* Finish converting internal event set operations to use list iterator callbacks, instead of directly accessing the list structure
* Add H5VL_REQUEST_GET_ERR_STACK operation to request subclass, for retrieving a copy of the error stack for a failed asynchronous operation
* Remove 'canceled' event status from Java constants
* Be safer about releasing resources when inserting a newly opened/created object or file into an event set
* Remove H5EStest, add H5ES_WAIT_NONE for 0 timeout, and revise parameters to H5ESwait, to make it more "aggregate".
* Remove H5ES_STATUS_CANCELED from Java wrappers also
* (a) Add async APIs for H5O module as listed in jira issue ID-283.
(b) Remove verification of name parameter in async related routines for H55A and H5L modules
because it is checked in H5VL_setup* routine.
(c) Modify h5dump expected output due to the async changes.
* Corrections based on PR feedback.
* Further changes to make based on PR feedback.
* Fix missed merge marker, and reformatted line
* Clean up some warnings
* Correct level of indirection
* Relocate prototype (and doxygen info) for H5Aclose
* Change non-static function declarations to be static
* Ensure that H5TSpublic.h header gets installed (#129)
* Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information.
* Switch H5Aexists\*_async and H5Lexists\*_async to use flag to return status, instead of return value. Make the corresponding changes through most of the v1 and v2 B-tree code. Clean up warnings in H5public.h and cmpd_dtransform.c.
* Add H5Iregister_future routine and tests.
* Correct return value for H5Lexists_async
* Add H5_DLL macro to public H5ES API routines
* Update supported -> flags parameter for introspect_query callback
* Remove my email address. Update passthrough VOL connector ID.
* Fix comment for post_open_api_common
* Remove unused non-blocking VOL connector
* Minor cleanup in async branch in preparation for merge to develop
* Update CMake and the Autotools to use the new pass-through VOL ID
* Fix for SWMR daily test failures (#160)
The H5I_register_using_existing_id() call did not initialize the future
ID callbacks, causing the library to segfault when it tried to
resolve those function pointers.
* Added selective async APIs (#150)
* Added selective async APIs
Description:
Added the following APIs:
H5Ropen_attr_async
H5Ropen_object_async
H5Ropen_region_async
H5Mcreate_async
H5Mopen_async
H5Mput_async
H5Mget_async
H5Mclose_async
H5Tcommit_async
H5Topen_async
H5Tcopy_async
H5Tclose_async
- Updated an expected output file to include a new internal function
in the error stack for the failure case.
* Updated async APIs per reviews, including removing async version of
H5Tcopy.
* Removed statements that were added by mistake in the previous commit.
* Fix compile issues in H5M and warnings elsewhere
* Reformat code
* Brings VOL_LIST changes from develop. (#163)
Co-authored-by: Houjun Tang <htang4@lbl.gov>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: vchoi-hdfgroup <55293060+vchoi-hdfgroup@users.noreply.github.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <derobins@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
The VOL_LIST variable used in the Autotools was duplicated in many
subdirectories. It's been moved to config/conclude.am to avoid
duplication. VFD_LIST was also moved to conclude.am.
* Renames H5I_ATOM to H5I_ID, among other related changes
* Java has been updated.
* Fortran is failing on my VM, even though I don't touch that.
* Adds a RELEASE.txt note for H5E_ATOM to H5E_ID changes
* Fixes typos in comments
* Basic alignment with async branch - trivial changes to reduce clutter in overall diff.
* Update minor error code to reflect change within library
* Update the error output to match library
* Add BEGIN_FUNC / CATCH / END_FUNC to macros
* Remove incorrect trailing '{'
* Update trace script to wrap H5TRACE macros at 110 characters and improve
comments for code that performs this operation.
* Clean up printf-formatting in H5public.h and correct some oversights in the code.
* Reformat with BEGIN_FUNC / END_FUNC handled correctly by clang-format
* Run clang-format on changes.
* Correct H5_SIZEOF_HSIZE_T/H5_SIZEOF_HSSIZE_T macros to match typedef.
* And make the undef value match also.
* Update comment
* Update clang-format actions to exclude generated files.
* Post-process generated H5LTparse.h file as well as H5LTparse.c file.
* Fix formatting
* Update version of github clang-format action
* h5repacktest VFD fix and formatting changes
* Fix memory leak in H5PL__find_plugin_in_path
When encountering a directory, the current loop iteration was skipped
without freeing the memory allocated for the path.
* Refactor parser GCC diagnostic statements
* genparser on jelly with default bison/flex
Co-authored-by: Michael Kuhn <michael.kuhn@ovgu.de>
* commit 'c0fbc5c086566d5d3c1d1ef26baa81a53d59fc08': (24 commits)
Use the right format string, "%zu", for size_t.
Repair more format strings.
Fix a bunch of format string errors reported by Larry.
Fix some HDfprintf compilation errors: use the right format strings ("zu", PRIuHSIZE), avoid casting some printf arguments, pass the right number of arguments.
Test the format string "ll" before "l", "L", and "q", like the ./configure script does. This ought to fix the compilation failure in test/dt_arith.c that Allen told me about:
Cast a non-void pointer to void pointer for "%p".
Use PRIu32 and "zu" formats. Delete some casts from `size_t`.
I'm taking a guess that this code intended to point the 2-digit wide hexadecimal octet values, not 2 character-wide pointers to the bytes. The %02p format, which is a GNU-ism, disagreed with GCC 8.3.0 and the option flags we use.
%08p is not portable, it's a GNU-ism. Use %8p, instead. Squashes a GCC error.
Add format string macros PRI[doxX]HID for hid_t and use PRIdHID.
Use HDva_copy() and introduce a bunch of compatbility format-string constants for uppercase hexadecimal strings, `PRIX...`. Should fix the VS2010 errors that Allen mentioned:
Always #define HDfprintf as fprintf in this header. I believe this will fix the Windows build error that Allen reported.
Provide an HDvasprintf implementation only if it isn't #defined. This should fix the mingw compilation issue that Allen reported.
Fix va_list usage in the vasprintf(3) implementation.
Promote format-string warnings to errors.
Use the portable `-eq` operator instead of the bash-ism `==`. Fixes the tests on NetBSD, where /bin/sh != bash.
Restore a literal percent sign ("%%") that I accidentally deleted.
Fix code that made GCC complain about a NULL or `unsigned char *` arguments for "%s".
Take pains to provide UINT64_MAX in all conditions.
Correct a couple of format strings.
...
Move error_stack setup to tools library
Add structure for h5dump properties
Eliminate duplicated h5diff functions
Use properties structure in place of argument lists.
reapplication to my new warnings branch, `warnings-again`. These
changes are included:
commit 915551b7bf64e777dd2007386ec77b1d117770da
Merge: 63858c2 a8892bb
Author: David Young <dyoung@hdfgroup.org>
Date: Mon Nov 25 17:39:49 2019 -0600
Merge remote-tracking branch 'hdf5/develop' into fprintf-experiment
commit a8892bb42d
Merge: 5c911d8f907b51
Author: David Young <dyoung@hdfgroup.org>
Date: Mon Nov 25 17:33:54 2019 -0600
Merge pull request #2055 in HDFFV/hdf5 from ~DYOUNG/vchoi_fork:add-werror-and-squash-some to develop
* commit 'f907b511d06612dafc7814a7c30f2f3d2b76d52b':
Oops, remove more C99 designated initializers for VS 2010 compatibility.
commit 63858c22e168acaec0af8ced6641f26102cc6bb0
Merge: 20ae787 5c911d8
Author: David Young <dyoung@hdfgroup.org>
Date: Mon Nov 25 17:04:42 2019 -0600
Merge remote-tracking branch 'hdf5/develop' into fprintf-experiment
commit 5c911d8baf
Merge: b8a567162208b0
Author: David Young <dyoung@hdfgroup.org>
Date: Mon Nov 25 16:58:27 2019 -0600
Merge pull request #2030 in HDFFV/hdf5 from ~DYOUNG/vchoi_fork:add-werror-and-squash-some to develop
* commit '62208b056a09c01855fbac7f75146be58ad6bfe5': (44 commits)
Add an #include to get a function declaration.
Don't use C99 designated initializers, they're not compatible with Visual Studio 2010.
Quiet some more maybe-uninitialized warnings---each is a false positive, *sigh*. This is more code that may not compile with VS2010, *sigh sigh*.
Always warn on maybe-uninitialized. -Wincompatible-pointer-types was not available until GCC 5, so enable it only if that's the GCC version we're using.
Only promote maybe-uninitialized warnings to errors on GCC 8. Even on GCC 8, there may be false positives at low optimization levels? I need to check.
Only use -Werror=cast-function-type with GCC 8 and later.
Put all of the -W options back into the order I found them in so that it's easier to compare old and new config/gnu-flags.
Add new source files to CMakeLists.txt.
Mention the -Werror= flags in libhdf5.settings.in.
free -> HDfree
Promote decleration-after-statement warnings to errors.
Quiet decleration-after-statement warnings.
Move a statement under some declarations since some vintages of Visual Studio don't like declarations after statements.
Document H5D__chunk_mem_xfree_wrapper().
Undo accidental test deletion.
Oops, delete a debug printf that snuck in here.
Undo my changes to the HD macros, hadn't really intended those to be on this branch....
Make errors of some more warnings. Move disabled warnings to DEVELOPER_WARNING_CFLAGS. Put just one warning option on a line, and sort some of the options.
Cast to the parameter type, H5VL_token_t *, instead of to unsigned char *.
Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char to structs containing those arrays. Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc.
...
commit 20ae7877e33931b95e8c3502b027d6c3fe94a11f
Merge: 46f8c61 edd5297
Author: David Young <dyoung@hdfgroup.org>
Date: Fri Nov 22 15:34:09 2019 -0600
Merge remote-tracking branch 'origin/add-werror-and-squash-some' into fprintf-experiment
commit 46f8c613d5117a8be5bc8385a072daa0b4262f06
Author: David Young <dyoung@hdfgroup.org>
Date: Fri Nov 22 15:29:00 2019 -0600
GCC really wants us to use `ll` to format `long long`, so try to make that work
before any other format modifier. Seems like we're not compiling the autoconf
test program with -Werror=format ? Probably should.
commit eee35b8ef3759c391327cd48a9b3c56b6f8abc99
Author: David Young <dyoung@hdfgroup.org>
Date: Fri Nov 22 15:28:05 2019 -0600
It's hard to know just how wide an HDoff_t will be, and I don't think POSIX or
C standards provide a PRI macro for it, so cast to intmax_t and format using
PRIdMAX.
commit 86eab12df7a89b546a38e99f8178dd2adbcb3433
Author: David Young <dyoung@hdfgroup.org>
Date: Fri Nov 22 15:26:25 2019 -0600
URemove some casts.se the right format string for the argument. Here and there
stop casting a printf argument.
commit f722f7cbecbaa99449941484b014426f62f1bed5
Merge: 58e3743 6d5ec83
Author: David Young <dyoung@hdfgroup.org>
Date: Fri Nov 22 14:44:16 2019 -0600
Merge branch 'add-werror-and-squash-some' into fprintf-experiment
commit 58e3743b7faa9836606ee91798fe80dfc0040da7
Author: David Young <dyoung@hdfgroup.org>
Date: Wed Nov 20 21:07:21 2019 -0600
Remove custom HDfprintf implementation, using the standard library's,
instead. Take a swipe at repairing fprintf format strings, mainly
replacing "%Hu" with "%" PRIuHSIZE, "%a" with "%" PRIuHADDR, "%Zu" with
"%zu".
Here and there remove an awkward cast of a printf argument to `long
long` and use PRI[doux]8, PRI[doux]32, or PRI[doux]64, instead.
Change occurrences of "%t" to "%s" and perform a suitable change of
argument, `cond` -> `cond ? "TRUE" : "FALSE"`.
Some occurrences of %Hu, %a, and %t remain, they just weren't flagged by
the compiler because of #ifdef'age.
commit d4366909293fa970c23512ac80e5d865d76cddbf
Author: David Young <dyoung@hdfgroup.org>
Date: Wed Nov 20 20:54:32 2019 -0600
Promote format-string warnigns to errors.
* commit '3f3363177d5cc1efc8fcfc70e1feed7a293da2d4':
Range check # of 'extra' command-line parameters against array size.
Refactor "extra" command-line arguments, and clean up code so the tool doesn't assert when exiting.
Extend h5debug to support 3-D datasets for chunks.
* commit '785bd0975ba13c3033820d0fc809da963fcd54ca':
Fixed h5diff command-line parameters to use 1 and 2 instead of src and dst.
Added VOL command-line options to (p)h5diff, h5ls, h5dump, and h5mkgrp.
* commit 'f6514c35ea3786206a8db73e1cad8fce8fe6a715':
Updated test ddl files so CMake passes after h5dump failures.
Modifications based on PR review feedback.
Add two routines gen_ref_files() and gen_sel_files() to generate test files related to references and selections. These test files will be copied to 1.12, 1.10 and 1.8 for compatibility testing.
* 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.
* commit '5d1590079ea0061a7b86d7210cb796b6d58a17c7':
Skip testing of passthrough VOL connector in a Family File tools test
Restore previous tools library driver name behavior with passthrough VOL connector
* commit 'a5a2fb44296327787476407a249d9470b3c80427':
Skip testing of passthrough VOL connector in a Family File tools test
Restore previous tools library driver name behavior with passthrough VOL connector
* commit 'ea952b25ba0fd5c4b5f60a94e75a1b5b78e66172':
A few small tweaks to the tools from review
Replace usage of some standard library functions with HD- versions
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
* commit 'f19e06b59ee53f17465a7b5974c25c3245a40d9a':
testpar/t_2Gio.c: Fix a typo that I think was introduced by a previous warnings PR. An array element was assigned to itself---shape[2]Â =Â shape[2];---instead of being assigned to chunk[2].
previous warnings PR. An array element was assigned to
itself---shape[2]Â =Â shape[2];---instead of being assigned to
chunk[2].
fortran/src/H5Pf.c: move conditional compilation controlled by
H5_NO_DEPRECATED_SYMBOLS outside of a function for readability.
fortran/src/H5match_types.c: put a variable's declaration under the same
conditional compilation (H5_FORTRAN_HAVE_C_LONG_DOUBLE) as its
use.
For now, skip compilation of some unused debug dump routines in the JNI.
While I'm in the JNI, delete a set-but-unused variable.
src/H5Z.c: condition a variable declaration on H5_NO_DEPRECATED_SYMBOLS
so that it's not declared but unused or vice versa.
test/cache_common.h: add an #include in to get some symbols we need to
avoid implicit declaration warnings.
test/dsets.c: use a more conventional conditional-compilation syntax.
test/dt_arith.c, test/fillval.c: initialize a bunch of uninitialized
variables before use.
test/vfd.c: pass the expected type of `void **` to posix_memalign(3)
instead of `int **`.
testpar/t_bigio.c: explicitly compare with 0 instead of using ! when
"equal to 0?" is the question not "is false?" Repair some
indentation while I'm here.
testpar/testpar.h: repair misaligned line-continuation backslashes in a
macro that probably should be a function so that we don't have
to fiddle with the line continuation to begin with.
tools/src/h5repack/h5repack_main.c: fix some compiler fussing about
enums.
tools/test/perform/pio_engine.c: the compiler fusses if you cast a
function call returning double directly to off_t. It's ok if
you cast a variable that's a double to off_t, however. Write
and use a new function, sqrto(), to avoid the cast warnings.
Reduce gratuitous casts---e.g., (size_t)1.
Use the right format string for a pointer.
In the H5C sanity checks, change a "size increase" variable from ssize_t
(too narrow) to int64_t (wide enough).
Parenthesize every appearance of `storage` in the macro
`H5D_CHUNK_STORAGE_INDEX_CHK(storage)` so that you can pass in an
expression like &sc and it works properly.
Disallow re-assignment of the `dset` parameter to H5D__chunk_init()
because it helped assure me that it's safe to replace the repeating
expression `&dset->shared->layout.storage.u.chunk` with `sc` throughout.
Replace lengthy expressions such as
`&dset->shared->layout.storage.u.chunk` with `sc` throughout several
functions in H5Dchunk.c ISTR that the compiler warned that `sc` was
declared but unused in a couple of functions, and then I found that `sc`
could be used in many places. Maybe the disused `sc` appeared because a
bunch of code was copied and pasted, I don't know. Anyway, it's a lot
tighter code now that I use `sc`.
In H5D__chunk_update_old_edge_chunks() and H5D__chunk_delete()
I actually expand `sc` and another temporary variable, `pline`,
because they're used only in !defined(NDEBUG) code. This squashes
unused-variable warnings in the defined(NDEBUG) configuration.
Don't drop the `volatile` qualification with a cast in
tools/src/h5import/h5import.c.
