Commit Graph

3434 Commits

Author SHA1 Message Date
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
Allen Byrne
5abf6785cb Whitespace 2020-02-29 14:01:55 -06:00
Allen Byrne
4906d3d6a8 Fix standalone link 2020-02-25 14:57:14 -06:00
Allen Byrne
f7212df030 HDFFV-11036 add file compare test process 2020-02-24 12:45:22 -06:00
Allen Byrne
666205a55f TRILAB-142 Change minimum CMake version to 3.12 2020-02-21 16:16:06 -06:00
David Young
f9a8fd5a4c H5_HAVE_PARALLEL, _DEBUG_API, etc. Add attributes to some variables and
parameters that are unused under some configurations.
2020-02-10 14:41:20 -06:00
Muqun Yang
1b937c69f4 HDFFV-11014, fix the h5repack issue that misses a few attributes during the repacking. The flag that checks the object reference attribute is not updated properly. The fix is trivial. Just need to move the flag update line into the inner loop. Tested at Jelly. Also update the release.txt. 2020-02-07 14:43:02 -06:00
Allen Byrne
c5e2d97573 Small fixes for tools and skip autotools tests for no filter 2020-01-29 15:39:25 -06:00
David Young
43d41633a1 Merge pull request #2318 in HDFFV/hdf5 from ~DYOUNG/werror:reduce-werror-diffs-1 to develop
* commit 'fa1b2f6ef35c459c9f74ead885c119ae7f61c056':
  Reduce differences between my -Werror branch and `develop`:
2020-01-29 13:51:52 -06:00
David Young
0d6e025888 Merge pull request #2320 in HDFFV/hdf5 from ~DYOUNG/werror:reduce-werror-diffs-2 to develop
* commit 'a5f236e83bdd29e660a55c5577a69a3809605cda':
  Reduce casts of HDcalloc()/HDmalloc() that -Wc++-compat required.
2020-01-29 13:51:27 -06:00
David Young
1b49ccd7fa Merge pull request #2321 in HDFFV/hdf5 from ~DYOUNG/werror:reduce-werror-diffs-3 to develop
* 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].
2020-01-29 13:51:10 -06:00
Allen Byrne
20c09524ea Merge pull request #2319 in HDFFV/hdf5 from ~BYRN/hdf5_adb:bugfix/HDFFV-11011 to develop
* commit 'c8096118d5edd9f27ff0f6180a4dde4c10aafda7':
  HDFFV-11011 - merge include list
  HDFFV-11011 correct issues with target file extension
2020-01-29 13:12:14 -06:00
David Young
f19e06b59e 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].

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.
2020-01-29 11:44:39 -06:00
David Young
a5f236e83b Reduce casts of HDcalloc()/HDmalloc() that -Wc++-compat required.
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.
2020-01-29 10:47:30 -06:00
David Young
fa1b2f6ef3 Reduce differences between my -Werror branch and develop:
Rename index -> idx, fileno -> fnumber, fileno -> fno to avoid GCC
shadowed declaration warnings about index(3).

Convert #pragma GCC diagnostic push/pop/ignored to the HDF5 library's
H5_GCC_DIAG_OFF()/H5_GCC_DIAG_ON() macros.
2020-01-28 20:35:28 -06:00
Jordan Henderson
e41f671d2f Introduce new H5VL _by_value routines 2020-01-28 18:18:38 -06:00
Kimmy Mu
71c050f837 Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop
* commit '406330addf45529ecdd088f4d22e9aab9a03661d':
  rename macro
  change condition
  pick up from Dave's fix
  leave Wswitch-default for later fix
  fix Wredundant-decls, Wswitch-default, Wdeclaration-after-statement, Wsign-compare, Wmisleading-indentation, Wshadow
2020-01-28 13:28:26 -06:00
Allen Byrne
527aaa32b2 HDFFV-11011 correct issues with target file extension 2020-01-28 13:14:59 -06:00
Dana Robinson
15a1bce9a2 Merge pull request #2304 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:isnan_fixes to develop
* commit '8b4d774eb9bb95cb3c59f033b43ed9fba340a54a':
  Replaced my_isnan with C99 isnan in h5diff.
2020-01-28 02:44:07 -06:00
kmu
9214617e2e change condition 2020-01-27 13:41:42 -06:00
kmu
5163a7e1cf fix Wredundant-decls, Wswitch-default, Wdeclaration-after-statement, Wsign-compare, Wmisleading-indentation, Wshadow 2020-01-27 09:01:32 -06:00
Allen Byrne
87a8951fa0 Remove cmake macros from valgrind tests 2020-01-25 09:36:20 -06:00
Dana Robinson
8b4d774eb9 Replaced my_isnan with C99 isnan in h5diff. 2020-01-23 20:12:16 -08:00
Dana Robinson
9475ee5d59 Optimized the floating point comparisons a little bit. 2020-01-23 19:12:24 -08:00
Dana Robinson
a85e4a75b2 Fix for failing h5diff tests involving floating-point compares. 2020-01-23 18:58:08 -08:00
Dana Robinson
492d186a5c Revert "Revert "Moved -Wunsuffixed-float-constants to the developer warnings.""
This reverts commit 6486e06545.
2020-01-23 14:40:47 -08:00
kmu
838d4ec56b squash cast warning fix 2020-01-23 15:12:00 -06:00
Allen Byrne
ee1fa14066 Change tools debug macros to not use error stack 2020-01-23 10:20:34 -06:00
kmu
2de0ce0d8b merge and fix conflict 2020-01-22 21:30:36 -06:00
Kimmy Mu
d741405363 Merge pull request #2295 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/float to develop
* commit '9afaf94bef740f89958a1a8aae369d5f607845f4':
  not use hdf5 private header
  fix float type cmp warning
  fix float type cmp warning
2020-01-22 20:59:49 -06:00
Kimmy Mu
720ba8624a Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to develop
* commit '9f80ffa1f1908975b3100814b2529bf779521e13':
  fix missing prototype warning
2020-01-22 20:58:42 -06:00
kmu
9afaf94bef not use hdf5 private header 2020-01-22 14:15:40 -06:00
kmu
9cc63d81fb fix float type cmp warning 2020-01-22 12:55:21 -06:00
kmu
04a2d20bba fix float type cmp warning 2020-01-22 12:55:01 -06:00
kmu
9f80ffa1f1 fix missing prototype warning 2020-01-21 12:30:40 -06:00
kmu
408b9b1f3b fix uninitizlized warning 2020-01-21 12:29:48 -06:00
kmu
9be5b2842e merge and fix 2020-01-20 21:11:32 -06:00
kmu
628d267162 merge and fix conflict 2020-01-19 08:09:44 -06:00
Dana Robinson
66a94df13b Merge pull request #2269 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:stack_size_warnings to develop
* commit '44739ccd4715cc9e15595575700e945341fcdbcc':
  Tidying from code review.
  Fixed stack and frame size warnings. Not complete, but fixes most of the easier cases.
2020-01-18 13:15:39 -06:00
Allen Byrne
db65d57541 Correct standalone function attributes 2020-01-17 12:15:16 -06:00
Allen Byrne
1643f591d6 Standalone should not use import/export attributes 2020-01-17 10:08:10 -06:00
Dana Robinson
44739ccd47 Merge branch 'develop' into stack_size_warnings 2020-01-16 16:32:33 -08:00
Dana Robinson
a92c735c9b Squashed commit of the token_refactoring branch: 2020-01-16 13:29:34 -08:00
Allen Byrne
7022a3380c HDFFV-11001 need to qualify all by parallel or serial types 2020-01-15 12:28:53 -06:00
Allen Byrne
a0ae5e9b89 HDFFV-11001 Add fine control over testing 2020-01-15 11:38:06 -06:00
Dana Robinson
1f8f6f019c Fixed stack and frame size warnings. Not complete, but fixes most of
the easier cases.
2020-01-15 09:32:01 -08:00
kmu
d46ea2d08a merge and fix conflicts 2020-01-14 11:28:27 -06:00
Allen Byrne
341600b4a6 Update tools hid_t declarations with H5I_INVALID_HID 2020-01-13 17:10:09 -06:00
kmu
9712fad601 fix unused related warnings 2020-01-13 13:20:19 -06:00
Allen Byrne
2600c358a5 io_timer.c uses a parallel lib function 2020-01-10 06:49:29 -06:00
Allen Byrne
9b82f8c0ac Fix standalone compile issues 2020-01-09 16:00:13 -06:00
Kimmy Mu
8d8b9f8ae8 Merge pull request #2244 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings to develop
* commit '6b1b4b3c0bdd803835efe8c531965bb9900a5363':
  fix test assert fail error
2020-01-09 15:31:19 -06:00
kmu
6b1b4b3c0b fix test assert fail error 2020-01-09 12:06:45 -06:00
Kimmy Mu
127f07d64a Merge pull request #2071 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings to develop
* commit '0a2bb11b248df6841daabca3970df5d8504adfc7':
  address problems from comments
  fix and address comments
  change according to previous comments
  add missing piece
  remove unnecessary check macro
  fix intel compile warnings
  Revert "fix warnings from Intel compiler"
  Revert "fix warnings and some text alignment"
  Revert "let hdf5 pick up the right compiler in Intel environment"
  Revert "fix issues from previous PR comments"
  Revert "using a different MACRO"
  using a different MACRO
  fix issues from previous PR comments
  let hdf5 pick up the right compiler in Intel environment
  fix warnings and some text alignment
  fix warnings from Intel compiler
2020-01-06 12:17:10 -06:00
Quincey Koziol
0225e6d596 Small changes from the token_refactoring branch, to reduce the delta to develop 2020-01-03 22:16:38 -06:00
Jordan Henderson
9c9b9b1c7a Fix issue in h5dump where reference objects weren't being destroyed 2019-12-31 11:33:27 -06:00
Jordan Henderson
1795aa660a Clean up tools warnings introduced by H5TOOLS_ERR_INIT macro 2019-12-30 18:02:06 -06:00
Jordan Henderson
2cbf31cb3a Refactor tools library error handling macros 2019-12-28 14:08:04 -06:00
Allen Byrne
0350f4d000 Add MPI libs to standalone perf 2019-12-22 12:17:20 -06:00
Allen Byrne
b6bc749eac Grep needs to search error file 2019-12-22 10:35:05 -06:00
Allen Byrne
2fa314d8b3 Correct flaws in test scripts and files 2019-12-22 10:05:06 -06:00
Allen Byrne
a2604b1e15 grep for failure text in error stack 2019-12-21 18:04:45 -06:00
Allen Byrne
b81802b71e Add list to function arg 2019-12-21 17:36:55 -06:00
Allen Byrne
6d28cbe853 Test files for new ref types 2019-12-21 17:35:13 -06:00
Allen Byrne
9ff8fe6477 h5diff test script files 2019-12-21 14:45:12 -06:00
Allen Byrne
4be4a50fe0 Add ref changes to test script 2019-12-21 14:37:04 -06:00
Allen Byrne
de0f667076 Fix compile statement order 2019-12-20 14:18:01 -06:00
Allen Byrne
23f813026f HDFFV-10976,-10980 Init obj_type before calling H5Rget_obj_type3 2019-12-20 13:23:48 -06:00
Allen Byrne
d7c38eeee9 Add unknown define for h5dump ref objects 2019-12-20 11:08:37 -06:00
Allen Byrne
a057a82a69 Standalone doesn't use h5test implementation. 2019-12-20 09:28:02 -06:00
Allen Byrne
bc88c82308 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'b55a584fd5b3aac6f2514fba41a6182030b497ae':
  In portable shell scripts (using #!/bin/sh) we have to use single square brackets, [ ], instead of the bash-ism double square brackets, [[ ]].
  Make this script work on hosts where PERL is not installed at /usr/bin/perl.
2019-12-20 09:02:51 -06:00
Allen Byrne
628c63f125 HDFFV-10980 - h5diff uses new ref APIs 2019-12-19 16:29:43 -06:00
David Young
ec4418a757 In portable shell scripts (using #!/bin/sh) we have to use single square
brackets, [ ], instead of the bash-ism double square brackets, [[ ]].
2019-12-19 15:06:57 -06:00
Quincey Koziol
b8b6659deb Update h5debug to retrieve file pointer through VOL framework 2019-12-17 13:11:39 -06:00
Allen Byrne
a966640208 Remove duplicate instance 2019-12-16 09:47:10 -06:00
Allen Byrne
dc2cbdaf67 Revert and move declaration 2019-12-13 12:28:18 -06:00
Allen Byrne
4ab00a3d1d Correct struct access 2019-12-13 11:59:20 -06:00
Allen Byrne
f57907d22c Fix duplicate and varname 2019-12-13 11:52:38 -06:00
Allen Byrne
e3c75f6cf7 Fix compile and test issues from DT 2019-12-13 11:36:09 -06:00
kmu
0a2bb11b24 address problems from comments 2019-12-11 13:35:02 -06:00
Allen Byrne
1fc1b09bf3 Fix issues found with ONLY_SHARED_LIBS option 2019-12-11 12:28:33 -06:00
kmu
45a62b2d46 fix and address comments 2019-12-11 10:44:56 -06:00
kmu
f2614c9042 more fix and address comments 2019-12-09 14:08:47 -06:00
kmu
8b51394f38 Merge branch 'develop' into bugfix/intel_warnings 2019-12-09 09:18:56 -06:00
Allen Byrne
eed923ec70 HDFFV-10876 fix compare reference 2019-12-08 13:25:14 -06:00
Allen Byrne
972cf8e60c Add missing quotes 2019-12-07 10:30:38 -06:00
Allen Byrne
7d6d3e2956 Correct indentation 2019-12-07 08:42:19 -06:00
Allen Byrne
7225519e2a Revert declaration used in macro. 2019-12-07 08:38:06 -06:00
Allen Byrne
73c8e2f9d6 Revert declaration deletion. 2019-12-07 08:31:12 -06:00
kmu
189935ff26 remove unnecessary check macro 2019-12-06 14:12:57 -06:00
Allen Byrne
fce2a31dc5 Address compile warnings 2019-12-06 13:55:34 -06:00
Allen Byrne
cf61098fa6 Fix compile errors - mostly in jni 2019-12-06 12:57:38 -06:00
kmu
f22e258586 remove unsed var,function,macro, etc 2019-12-06 12:03:19 -06:00
Allen Byrne
e8ad5f6d1a HDFFV-10876 Update dump to match DDL spec 2019-12-05 17:21:02 -06:00
Allen Byrne
4747e2f2ad Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'c7b3d6d6a5c1d376812e17c0ddb26f55334a2c59':
  Yanked -Wc++-compat from the flags used to build the C library in both the Autotools and CMake.
2019-12-05 09:30:11 -06:00
Allen Byrne
4f74548f53 Add extra line 2019-12-04 17:00:45 -06:00
Allen Byrne
11825bc525 Adjust whitespace 2019-12-04 16:59:03 -06:00
Allen Byrne
d552e97eae Update h5ls help and rework dump_mem routines for attrs 2019-12-04 16:36:32 -06:00
Allen Byrne
8f9005570a Add debug compile option as comment 2019-12-04 12:24:53 -06:00
Allen Byrne
ba8f2f1174 Update reference calls 2019-12-04 12:24:53 -06:00