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OESS-168: Remove clang warnings. #1309

Merged
merged 2 commits into from
Apr 15, 2022
Merged

OESS-168: Remove clang warnings. #1309

merged 2 commits into from
Apr 15, 2022

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hyoklee
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@hyoklee hyoklee commented Dec 18, 2021 

 mirror_vfd.c:2188:18: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
        HDprintf(failure_mssg);
                 ^~~~~~~~~~~~

jhendersonHDF
jhendersonHDF reviewed Jan 7, 2022
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test/mirror_vfd.c Outdated
@@ -2609,6 +2610,7 @@ main(void)
if (nerrors == 0) {
nerrors -= test_fapl_configuration();
nerrors -= test_xmit_encode_decode();
nerrors -= test_on_disk_zoo();
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Looks like test_on_disk_zoo is already tested on line 2615 originally. Should remove this.

lrknox
lrknox requested changes Jan 11, 2022
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Remove duplicated test_on_disk_zoo()

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hyoklee commented Jan 11, 2022

BTW, test fails after addressing the review on my repo

Testing File creation and immediate close                             *FAILED*
HDF5-DIAG: Error detected in HDF5 (1.13.1-1) thread 0:
  #000: H5F.c line 661 in H5Fcreate(): unable to synchronously create file
    major: File accessibility
    minor: Unable to create file
  #001: H5F.c line 615 in H5F__create_api_common(): unable to create file
    major: File accessibility
    minor: Unable to open file
  #002: H5VLcallback.c line 3428 in H5VL_file_create(): file create failed
    major: Virtual Object Layer
    minor: Unable to create file
  #003: H5VLcallback.c line 3394 in H5VL__file_create(): file create failed
    major: Virtual Object Layer
    minor: Unable to create file
  #004: H5VLnative_file.c line 94 in H5VL__native_file_create(): unable to create file
    major: File accessibility
    minor: Unable to open file
  #005: H5Fint.c line 1813 in H5F_open(): unable to open file: name = 'mirror_rw/basic_create.h5', tent_flags = 13
    major: File accessibility
    minor: Unable to open file
  #006: H5FD.c line 768 in H5FD_open(): open failed
    major: Virtual File Layer
    minor: Unable to initialize object
  #007: H5FDsplitter.c line 859 in H5FD__splitter_open(): unable to open W/O file
    major: Virtual File Layer
    minor: Unable to open file
  #008: H5FD.c line 768 in H5FD_open(): open failed
    major: Virtual File Layer
    minor: Unable to initialize object
  #009: H5FDmirror.c line 1389 in H5FD__mirror_open(): can't connect to remote server
    major: Invalid arguments to routine
    minor: Bad value
*FAILED*
   at mirror_vfd.c:1377 in test_create_and_close()...

See https://github.com/hyoklee/hdf5/runs/4778810698?check_suite_focus=true

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lrknox commented Jan 11, 2022 via email

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hyoklee commented Jan 11, 2022

All checks passed in this repo. Do you have a different test, or different code?

Different test:

https://github.com/hyoklee/hdf5/blob/develop/.github/workflows/linux-auto.yml

Please add the above action and see if it passes.

@lrknox lrknox self-assigned this Jan 14, 2022
@derobins derobins merged commit 9131d52 into HDFGroup:develop Apr 15, 2022
derobins added a commit that referenced this pull request Apr 25, 2022
@derobins @byrnHDF
@wkliao @hyoklee @gnuoyd @github-actions @qkoziol @brtnfld
Onion VFD: Sync with develop (#1685)
63197e9 
* Removes unused definitions from module headers (#1624)

* Fix these Doxygen warnings #1581 (#1589)

* Fixes a typo in H5.c (#1639)

* free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638)

* free MPI_Group/MPI_Comm/MPI_Datatype objects

* fix clang-format style

* Adds build and license shields to README.md (#1641)

* First stab at a Github status bar

* Adds a .tokeignore file for counting lines of code accurately

* Yanks lines of code calculation since it wildly overcounts

* not depend on doIO to free an MPI_Comm object (#1642)

* free MPI datatypes previously created (#1637)

* Retrieve MPI-IO hints used by MPI library after file open (#1636)

H5Pget_fapl_mpio() should return an MPI info object containing all the
MPI-IO hints used by the MPI library underneath, after the file is
opened. Some hints, such as cb_nodes (number of I/O aggregators), are
useful for HDF5 applications and I/O libraries built on top of HDF5.

* OESS-168: Remove clang warnings. (#1309)

* OESS-168: Remove clang warnings.

* OESS-168: Address @lrknox review.

* OESS-168: Remove clang warnings. (#1376)

* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)

* Do not conditionally compile code that uses a pointer dereference
and assignment to copy a potentially unaligned variable to aligned
automatic storage, or vice versa.  Instead, always use naked `memcpy(3)`s.
Disassembling the generated code reveals that the `memcpy(3)`s optimize
(`-O3`) to a single `mov` instruction for x86_64, which is not strict
about alignment.

This change reduces the size of code and scripts by 143 lines, eases
our way to cross-compilation, and avoids invoking undefined behavior.

* Committing clang-format changes

* Per discussion, use HD and add comments.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t (#1651)

* Cleans up some HL library code that inappropriately returns
htri_t values cast to herr_t

* Committing clang-format changes

* Formatted source

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Mirror vfd test fixes (#1629)

* Use the FAPL that was created earlier in the test (and delete an unused
variable).   This allows 'make check-vfd' to pass with --enable-mirror-vfd.

* Check for testing directory before creating, to avoid warning from bash.
Clean out .libs directory before re-using it (after a failed test), to
remove any files generated by libtool.

* Committing clang-format changes

* Increment error count on failed file open and skip tests for VFDs that need
modified filenames.

* Skip the mirror VFD for 'make check-vfd' - the mirror VFD requires networking
configuration parameters and can't be provided for an automated test that
is configured with an environment variable.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Removes HDF Group paths, adds shellcheck fixes (#1656)

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

* HDFFV-11306 Fixed (#1657)

* HDFFV-11306,
 * Fixed it so both h5open_f and h5close_f can be called multiple times.
 * Fixed an issue with open objects remaining after h5close_f was called.
 * Added additional tests.

* comments clean-up

* Develop clang format java (#1653)

* added HDFFV-11306 entry (#1662)

* Adds the -q flag to all swmr test programs, quieting noisy output (#1665)

* Adds paths-ignore to the Github pull request workflow (#1663)

* Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666)

So the PR action name is not the same as the one in main.yml

* Replace H5detect's build-time detection of C99 integer properties with a (#1400)

* Replace H5detect's build-time detection of C99 integer properties with a
table-driven routine, `H5T__init_native_int()`, that is run at library
initialization time.

* Improve handling of copying of dynamic libraries and clean them up after (#1681)

test finishes.

Co-authored-by: Allen Byrne <[email protected]>
Co-authored-by: Wei-keng Liao <[email protected]>
Co-authored-by: H. Joe Lee <[email protected]>
Co-authored-by: David Young <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Quincey Koziol <[email protected]>
Co-authored-by: Scot Breitenfeld <[email protected]>
derobins added a commit that referenced this pull request Apr 26, 2022
@derobins @byrnHDF
@wkliao @hyoklee @gnuoyd @github-actions @qkoziol @brtnfld @jhendersonHDF
Onion VFD: Misc cleanup (#1693)
a53f47b 
* Removes unused definitions from module headers (#1624)

* Fix these Doxygen warnings #1581 (#1589)

* Fixes a typo in H5.c (#1639)

* free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638)

* free MPI_Group/MPI_Comm/MPI_Datatype objects

* fix clang-format style

* Adds build and license shields to README.md (#1641)

* First stab at a Github status bar

* Adds a .tokeignore file for counting lines of code accurately

* Yanks lines of code calculation since it wildly overcounts

* not depend on doIO to free an MPI_Comm object (#1642)

* free MPI datatypes previously created (#1637)

* Retrieve MPI-IO hints used by MPI library after file open (#1636)

H5Pget_fapl_mpio() should return an MPI info object containing all the
MPI-IO hints used by the MPI library underneath, after the file is
opened. Some hints, such as cb_nodes (number of I/O aggregators), are
useful for HDF5 applications and I/O libraries built on top of HDF5.

* OESS-168: Remove clang warnings. (#1309)

* OESS-168: Remove clang warnings.

* OESS-168: Address @lrknox review.

* OESS-168: Remove clang warnings. (#1376)

* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)

* Do not conditionally compile code that uses a pointer dereference
and assignment to copy a potentially unaligned variable to aligned
automatic storage, or vice versa.  Instead, always use naked `memcpy(3)`s.
Disassembling the generated code reveals that the `memcpy(3)`s optimize
(`-O3`) to a single `mov` instruction for x86_64, which is not strict
about alignment.

This change reduces the size of code and scripts by 143 lines, eases
our way to cross-compilation, and avoids invoking undefined behavior.

* Committing clang-format changes

* Per discussion, use HD and add comments.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t (#1651)

* Cleans up some HL library code that inappropriately returns
htri_t values cast to herr_t

* Committing clang-format changes

* Formatted source

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Mirror vfd test fixes (#1629)

* Use the FAPL that was created earlier in the test (and delete an unused
variable).   This allows 'make check-vfd' to pass with --enable-mirror-vfd.

* Check for testing directory before creating, to avoid warning from bash.
Clean out .libs directory before re-using it (after a failed test), to
remove any files generated by libtool.

* Committing clang-format changes

* Increment error count on failed file open and skip tests for VFDs that need
modified filenames.

* Skip the mirror VFD for 'make check-vfd' - the mirror VFD requires networking
configuration parameters and can't be provided for an automated test that
is configured with an environment variable.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Removes HDF Group paths, adds shellcheck fixes (#1656)

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

* HDFFV-11306 Fixed (#1657)

* HDFFV-11306,
 * Fixed it so both h5open_f and h5close_f can be called multiple times.
 * Fixed an issue with open objects remaining after h5close_f was called.
 * Added additional tests.

* comments clean-up

* Develop clang format java (#1653)

* added HDFFV-11306 entry (#1662)

* Adds the -q flag to all swmr test programs, quieting noisy output (#1665)

* Adds paths-ignore to the Github pull request workflow (#1663)

* Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666)

So the PR action name is not the same as the one in main.yml

* Replace H5detect's build-time detection of C99 integer properties with a (#1400)

* Replace H5detect's build-time detection of C99 integer properties with a
table-driven routine, `H5T__init_native_int()`, that is run at library
initialization time.

* Improve handling of copying of dynamic libraries and clean them up after (#1681)

test finishes.

* Warnings fixes (#1680)

* Clean stack size warnings in sio_engine (#1687)

* Fixes stack size warnings in tcoords.c (#1688)

* Minor things noticed while bringing VFD SWMR in line with develop (#1691)

* Removed dead code, weird formatting, and other badness

* Fixed remaining stack size warnings in onion VFD

* Committing clang-format changes

Co-authored-by: Allen Byrne <[email protected]>
Co-authored-by: Wei-keng Liao <[email protected]>
Co-authored-by: H. Joe Lee <[email protected]>
Co-authored-by: David Young <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Quincey Koziol <[email protected]>
Co-authored-by: Scot Breitenfeld <[email protected]>
Co-authored-by: jhendersonHDF <[email protected]>
derobins added a commit that referenced this pull request May 3, 2022
@raylu-hdf @derobins
@byrnHDF @wkliao @hyoklee @github-actions
Adding a new API function to get the number of revisions for an onion…
93f65cc 
… file (#1692)

* Removes unused definitions from module headers (#1624)

* Fix these Doxygen warnings #1581 (#1589)

* Fixes a typo in H5.c (#1639)

* free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638)

* free MPI_Group/MPI_Comm/MPI_Datatype objects

* fix clang-format style

* Adds build and license shields to README.md (#1641)

* First stab at a Github status bar

* Adds a .tokeignore file for counting lines of code accurately

* Yanks lines of code calculation since it wildly overcounts

* not depend on doIO to free an MPI_Comm object (#1642)

* free MPI datatypes previously created (#1637)

* Retrieve MPI-IO hints used by MPI library after file open (#1636)

H5Pget_fapl_mpio() should return an MPI info object containing all the
MPI-IO hints used by the MPI library underneath, after the file is
opened. Some hints, such as cb_nodes (number of I/O aggregators), are
useful for HDF5 applications and I/O libraries built on top of HDF5.

* OESS-168: Remove clang warnings. (#1309)

* OESS-168: Remove clang warnings.

* OESS-168: Address @lrknox review.

* OESS-168: Remove clang warnings. (#1376)

* Adding a new API function to get the number of revisions for an onion file. This function uses H5FD_ctl().

* Committing clang-format changes

* Removed a few unused variables.

* Modified the way that the API function H5FDget_onion_revision_count is organized and added Doxygen comments for the three API functions.

* Committing clang-format changes

* Minor changes: modified some Doxygen comments.

Co-authored-by: Dana Robinson <[email protected]>
Co-authored-by: Allen Byrne <[email protected]>
Co-authored-by: Wei-keng Liao <[email protected]>
Co-authored-by: H. Joe Lee <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
derobins added a commit that referenced this pull request May 5, 2022
@raylu-hdf @derobins
@byrnHDF @wkliao @hyoklee @github-actions
Added the support to get the revision count for the onion file into t…
0566def 
…he h5dump. (#1726)

* Removes unused definitions from module headers (#1624)

* Fix these Doxygen warnings #1581 (#1589)

* Fixes a typo in H5.c (#1639)

* free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638)

* free MPI_Group/MPI_Comm/MPI_Datatype objects

* fix clang-format style

* Adds build and license shields to README.md (#1641)

* First stab at a Github status bar

* Adds a .tokeignore file for counting lines of code accurately

* Yanks lines of code calculation since it wildly overcounts

* not depend on doIO to free an MPI_Comm object (#1642)

* free MPI datatypes previously created (#1637)

* Retrieve MPI-IO hints used by MPI library after file open (#1636)

H5Pget_fapl_mpio() should return an MPI info object containing all the
MPI-IO hints used by the MPI library underneath, after the file is
opened. Some hints, such as cb_nodes (number of I/O aggregators), are
useful for HDF5 applications and I/O libraries built on top of HDF5.

* OESS-168: Remove clang warnings. (#1309)

* OESS-168: Remove clang warnings.

* OESS-168: Address @lrknox review.

* OESS-168: Remove clang warnings. (#1376)

* Added the support to get the revision count for the onion file into the h5dump.

* Committing clang-format changes

* Changed the function from H5FDget_onion_revision_count to H5FDonion_get_revision_count for better name.

* Fixed compiler warnings.

Co-authored-by: Dana Robinson <[email protected]>
Co-authored-by: Allen Byrne <[email protected]>
Co-authored-by: Wei-keng Liao <[email protected]>
Co-authored-by: H. Joe Lee <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
@hyoklee hyoklee deleted the OESS-168-mirror_vfd.c branch July 14, 2022 21:35
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Reviewers

@jhendersonHDF jhendersonHDF jhendersonHDF left review comments

@lrknox lrknox lrknox approved these changes

@derobins derobins derobins approved these changes

@fortnern fortnern Awaiting requested review from fortnern fortnern is a code owner

@jrmainzer jrmainzer Awaiting requested review from jrmainzer

@qkoziol qkoziol Awaiting requested review from qkoziol qkoziol is a code owner

@soumagne soumagne Awaiting requested review from soumagne

@vchoi-hdfgroup vchoi-hdfgroup Awaiting requested review from vchoi-hdfgroup vchoi-hdfgroup is a code owner

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@hyoklee @lrknox @derobins @jhendersonHDF