Commit Graph

982 Commits

Author SHA1 Message Date
Dana Robinson
3cd1b46b9c Merge branch 'develop' into tools_vol_update 2020-04-01 23:27:08 -07:00
Dana Robinson
b1533616f2 Minor renaming in the tools code. 2020-03-31 16:58:24 -07:00
Dana Robinson
36e8e2be4b Misc changes for h5dump VOL changes. 2020-03-30 01:51:36 -07:00
Allen Byrne
c66ce89383 Merge pull request #2473 in HDFFV/hdf5 from tools_vol_update to develop
* commit 'feb0f521b16b79485c22c86a630a1d91cb680a61':
  Fix some missing symbols issues in tools library
2020-03-27 17:06:23 -05:00
Jordan Henderson
feb0f521b1 Fix some missing symbols issues in tools library 2020-03-27 16:54:05 -05:00
Jordan Henderson
d5bbf3d408 Merge pull request #2469 in HDFFV/hdf5 from tools_vol_update to develop
* 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
2020-03-27 13:14:22 -05:00
Jordan Henderson
ea952b25ba A few small tweaks to the tools from review 2020-03-27 10:48:11 -05:00
Jordan Henderson
6d514db55a Replace usage of some standard library functions with HD- versions 2020-03-26 15:26:39 -05:00
Allen Byrne
0da6786185 unused set-variable in macro 2020-03-25 07:04:19 -05:00
Allen Byrne
2b8407a3ca Fix Werror issues in JNI and tools 2020-03-24 17:42:58 -05:00
Allen Byrne
1505fa1498 TRILAB-192 restrict extensive warnings to libraries 2020-03-24 16:45:12 -05:00
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
Allen Byrne
5abf6785cb Whitespace 2020-02-29 14:01:55 -06:00
Allen Byrne
666205a55f TRILAB-142 Change minimum CMake version to 3.12 2020-02-21 16:16:06 -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
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
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
5163a7e1cf fix Wredundant-decls, Wswitch-default, Wdeclaration-after-statement, Wsign-compare, Wmisleading-indentation, Wshadow 2020-01-27 09:01:32 -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
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
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
kmu
04a2d20bba fix float type cmp warning 2020-01-22 12:55:01 -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
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
a92c735c9b Squashed commit of the token_refactoring branch: 2020-01-16 13:29:34 -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
9b82f8c0ac Fix standalone compile issues 2020-01-09 16:00:13 -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
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
628c63f125 HDFFV-10980 - h5diff uses new ref APIs 2019-12-19 16:29:43 -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
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
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
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
d552e97eae Update h5ls help and rework dump_mem routines for attrs 2019-12-04 16:36:32 -06:00
kmu
132fa33dad fix intel compile warnings 2019-12-03 20:52:55 -06:00
Allen Byrne
7ad3d62a5c Update data output reference 2019-12-03 16:05:35 -06:00
Allen Byrne
12fd139e90 Update reference files and fix int as string 2019-12-03 14:43:05 -06:00
Allen Byrne
7e92c2e3e5 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '0772b975d1d2bfa15aedeb4b6e2c2aac78c61a2f':
  Fix missing free in H5T__ref_mem_read()
  Fix bugs in H5VL file comparison code.  Add short circuit success to H5VL_cmp_connector_cls().
  Implement file comparison VOL callback.  Other changes to allow references to work with non-native connectors.  There is a bug somewhere.
  Add support for point selections to H5S_select_project_intersection.
  Remove H5VL_NATIVE_FILE_GET_FILE_ID and add H5VL_OBJECT_GET_FILE
  Revert "Make a squash commit of 'Quiet some warnings by adjusting warnings level and fixing some code.' (commit 5c911d8baf)"
  Revert "Oops, remove more C99 designated initializers for VS 2010 compatibility."
  H5R: fix H5Tconv to check for null references
  Trivial parameter renaming in VOL API calls.
  Move checking for zero offset in selection adjust calls to the selection callbacks.  This makes the procedure for checking it consistent across selection types and between _s and _u, ensures it is always is performed even when called within the H5S package, and removes the redundant check that would occur when callins H5S_select_adjust_s() from outside the H5S package.
  Replace H5Sselect_adjust_u() and H5Shyper_adjust_s() with H5Sselect_adjust.  Implement "adjust_s" callback for all selection types.  Add range checking to H5Sselect_adjust().
2019-12-02 08:00:20 -06:00
David Young
0108072f7a Revert "Make a squash commit of 'Quiet some warnings by adjusting warnings level and fixing some code.' (commit 5c911d8baf)" 2019-11-27 11:26:02 -06:00
Allen Byrne
dcae4544a3 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'a8892bb42d6f6e4fbc30fae0eb2b957f81c938b9': (45 commits)
  Oops, remove more C99 designated initializers for VS 2010 compatibility.
  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 *.
  ...
2019-11-25 18:21:14 -06:00
Allen Byrne
5fe5caf560 Comment correction 2019-11-21 09:33:04 -06:00
David Young
77a9806ab5 Demote errors to warnings for a couple of unused-but-set variables that
I cannot untangle right now.
2019-11-13 11:26:49 -06:00
David Young
0cb24f8ad4 Mark an unused parameter H5_ATTR_UNUSED. 2019-11-13 11:25:27 -06:00
Allen Byrne
6b927a773c HDFFV-10876 Update h5dump and h5ls for new ref api. 2019-11-07 09:49:11 -06:00
Jerome Soumagne
0beba4aac2 Fix reference type comparison in h5dump 2019-10-08 14:30:24 -05:00
Jerome Soumagne
c13078a0ed Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim() 2019-10-08 14:30:24 -05:00
Allen Byrne
4394f0776b More whitespace changes 2019-10-03 12:10:24 -05:00
Allen Byrne
bc61159318 HDFFV-10919 merge synching 2019-10-02 15:13:37 -05:00
Dana Robinson
a6930a2bcf Renamed get/set_time() calls in the tools library to avoid name
clash when building static parallel HDF5 w/ static linking to OpenMPI.
2019-09-19 13:50:49 -07:00
Allen Byrne
369d17c05c HDFFV-10876 h5dump OPAQUE size should be optional 2019-08-27 15:10:37 -05:00
Dana Robinson
8c40dab59e Untangle #ifdef mess in ROS3 code. 2019-08-19 18:02:47 -07:00
Allen Byrne
64e6665b54 Add HD prefix to tests 2019-08-15 16:46:15 -05:00
Dana Robinson
d95745235a Updated h5trav.c to emit output that doesn't require ddl changes for map
support.
2019-08-13 10:55:34 -07:00
Dana Robinson
5b6bd7c922 Added the map (H5M) API 2019-08-13 01:36:42 -07:00
Larry Knox
8008294578 Squashed commit of the following:
Merge changes from update_merged_S3_HDFS branch into develop.

commit d5034315aea88629929ac0c9c59ebfafd5f21a31
Merge: 9c48823 d3fdcd8
Author: Larry Knox <lrknox@hdfgroup.org>
Date:   Thu Jul 25 08:24:53 2019 -0500

    Merge branch 'develop' into update_merged_S3_HDFS
2019-07-25 11:47:12 -05:00
Quincey Koziol
73df02f13c Merge branch 'develop' into feature/update_gcc_flags 2019-07-09 22:17:22 -05:00
Quincey Koziol
db7c43d375 Updates to warnhist script, along with a few cleanups, and add some comments
to warning cleanups that are a bit obscure.
2019-07-09 22:15:36 -05:00
Allen Byrne
ae0c16d1f2 HDFFV-10581 fix locations for static pdb files 2019-07-08 12:21:11 -05:00
Quincey Koziol
3b594992d6 Add support for GCC9, update warnhist script, and clean up warnings. 2019-07-02 23:43:45 -05:00
Quincey Koziol
d5130bb573 Updated configure & CMake compiler flags for GCC 8.x, along with corresponding
changes to warnhist script (and some extra improvements for condensing C++
and Java warnings), and fixed a bunch of warnings.
2019-06-28 09:10:43 -05:00
Quincey Koziol
1ccbdfee58 Add support for GCC 7.x warnings, update warnhist script to account for them,
clean up warnings.
2019-06-21 10:05:34 -05:00
Allen Byrne
e7f16c6f2c HDFFV-10805 Add option to only build shared targets
HDFFV-10805 Add ONLY_SHARED_LIBS option and prefer shared over static
HDFFV-10803 Update FindSZIP.cmake find module
Remove unneeded modules and update java modules
2019-06-18 07:46:25 -05:00
Binh-Minh Ribler
90d13bef33 Fixed typo
Platforms tested:
    Darwin (osx1010test)
2019-01-07 20:46:55 -06:00
Binh-Minh Ribler
78d0564c2a Refixed HDFFV-10578
Description:
    Applied Neil's fix for this issue after removing previous
    attempt.  The resources are now released in init_objs() when
    failure occurs there.
    Neil will fix HDFFV-10676 separately.
Platforms tested:
    Linux/64 (jelly)
    Linux/64 (platypus)
    Darwin (osx1010test)
2019-01-07 20:36:34 -06:00
Allen Byrne
2c48f6bd00 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '7db3ea76da5d3b5c237a707b09d1618d3206ba83':
  Makes the installed header files the same between the autotools and CMake.
2018-10-29 11:10:27 -05:00
Dana Robinson
62b92ddf40 Makes the installed header files the same between the autotools
and CMake.

* CMake will no longer install private generated headers and tools
  library headers.
* Several empty public header files (which represent internal packages)
  were removed. These were only installed by CMake.
* Autotools installs will install H5FDwindows.h.

Fixes HDFFV-10614.
2018-10-26 20:44:29 -07:00
Allen Byrne
cce1727525 TRILAB-81 check for func success before using value 2018-10-19 14:45:04 -05:00
Allen Byrne
633b7f93ce TRILAB-81 coverity fixes 2018-10-17 10:57:56 -05:00
Allen Byrne
27af9a7922 HD prefix and whitespace 2018-08-28 10:54:54 -05:00
Jordan Henderson
d075c0854d Add quotes to places where MPI_C_LIBRARIES are linked against 2018-07-27 14:58:01 -05:00
Vailin Choi
b178d80be0 Changes made based on feedback from pull request #1039. 2018-05-14 12:26:48 -05:00
Vailin Choi
ea66ac1e67 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'dcc66a4f157ace0858b788228550f3e104df3242': (35 commits)
  GGC requires attribute before function
  Correct COMPILE defs usage
  Add missing module_dir property
  Text cleanup
  Correct sentence punctuation.
  Add release note.
  Use set_property for MT flag
  Correct command usage
  Remove APPEND
  Fix typo
  Add missing test lib
  add missing folder to path
  Fix another command revert
  Missed a command revert
  Revert to old style for LINK_FLAGS gen expr not working
  LINK_FLAGS must be separate property sets
  Fix link flags syntax
  Revert refactor link flags
  refactor link flags to interface
  Refactor link flags
  ...
2018-05-14 11:20:03 -05:00
Allen Byrne
2347bffaa2 TRILABS-19 remove add_defintions and use generator expressions 2018-04-26 16:41:04 -05:00