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185 Commits

Author SHA1 Message Date
Scot Breitenfeld
9d596b4a59 corrected/added note about closing creation property list identifier (#2425)
* corrected/added note about closing creation property list identifier

* removed immaterial \see APIs

* added details to H5Literate
2023-02-11 08:34:58 -06:00
Dana Robinson
2e8ea68d97 Update CODEOWNERS given personnel changes (#2453) 2023-02-11 04:50:30 -08:00
Larry Knox
48a3d92d04 Remove duplicated "help@hdfgroup.org" lines in file headers. (#2441) 2023-02-10 19:28:57 -08:00
Dana Robinson
d61fd4aba7 Add szip/libaec to GitHub CI and fix warnings (#2438)
szip (or libaec) is currently not tested in CI. This adds szip to the
the Autotools GitHub CI actions on Linux when building with the
Autotools.

This PR also cleans up a few warnings that remained in the szip-
related code so the -Werror check will pass.
2023-02-09 05:46:16 -08:00
kwryankrattiger
509fe962d4 CMake: Find MPI in HDF5 CMake config (#2400) 2023-01-18 16:26:35 -06:00
Allen Byrne
2c9de7a9ae Port VOL connector Guide to doxygen (#2333)
* Port VOL connector Guide to doxygen

* Fix spelling

* Updated VOL UG ref and added release note
2023-01-18 01:04:41 -08:00
Mark Kittisopikul
720e04e196 Include shlwapi.h explicitly on Windows (#2407)
* Include shlwapi.h explicitly

* Add shlwapi library to LINK_LIB when header is detected

Looking for StrStrIA in the shlwapi library is not reliable due
to stdcall on mingw32.
2023-01-17 07:27:25 -08:00
raylu-hdf
5543d6eb36 HDFFV-11208 (OESS-320): H5VLquery_optional had an assertion failure with a committed datatype (#2398)
* HDFFV-11208 (OESS-320): H5VLquery_optional had an assertion failure with a committed datatype.  Added a test case for the fix that Quincey checked in.

* Committing clang-format changes

* Fixed a typo in a comment.

* Fixed a typo in a comment.

* Minor change: changed H5Tcommit to H5Tcommit2.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-01-10 09:29:54 -08:00
Quincey Koziol
06c12f97cd Pass-through connector testing flexibility (#2399)
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.

* Committing clang-format changes

* Allow spaces (and tabs) in VOL connector info string from environment variable.

* Parse connector name from HDF5_PLUGIN_PATH environment variable better

* Correct H5VLquery_optional to use H5VL routine instead of H5I.  Also add an
error message to the failure return value from not finding a plugin.

* Play nice with existing plugin paths

* Use API routine to determine if native connector is terminal.

* Committing clang-format changes

* Make string size larger, to allow for connectors with longer names.

* Be more flexible about testing external pass through connectors, especially if
they have registered new optional operations.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
2023-01-09 17:18:28 -06:00
Quincey Koziol
90d20764f4 Determine if native connector is terminal (#2397)
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.

* Committing clang-format changes

* Allow spaces (and tabs) in VOL connector info string from environment variable.

* Parse connector name from HDF5_PLUGIN_PATH environment variable better

* Correct H5VLquery_optional to use H5VL routine instead of H5I.  Also add an
error message to the failure return value from not finding a plugin.

* Play nice with existing plugin paths

* Use API routine to determine if native connector is terminal.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
2023-01-09 13:49:29 -08:00
Quincey Koziol
54590f3ebd Play nice with existing plugin paths (#2394)
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.

* Committing clang-format changes

* Allow spaces (and tabs) in VOL connector info string from environment variable.

* Parse connector name from HDF5_PLUGIN_PATH environment variable better

* Correct H5VLquery_optional to use H5VL routine instead of H5I.  Also add an
error message to the failure return value from not finding a plugin.

* Play nice with existing plugin paths

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
2023-01-06 09:08:16 -08:00
Quincey Koziol
337a882af8 Update FORTRAN VOL connector test for external pass-through testing (#2393)
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.

* Committing clang-format changes

* Allow spaces (and tabs) in VOL connector info string from environment variable.

* Parse connector name from HDF5_PLUGIN_PATH environment variable better

* Correct H5VLquery_optional to use H5VL routine instead of H5I.  Also add an
error message to the failure return value from not finding a plugin.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
2023-01-05 15:42:33 -08:00
Dana Robinson
423ee69c1e Updates README.md (#2387)
* Updates release schedule for 2023

* Fixes broken build badge

* Another build badge tweak

* Even more badge tweaking

* More branch tweaking

* More badge tweaking

* More badge tweaks

* Even more badge tweaking

* Adds badges for other branches
2023-01-04 12:44:51 -08:00
Quincey Koziol
c2e3c732f0 Correct VOL connector env string parsing issue (#2350)
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.

* Committing clang-format changes

* Allow spaces (and tabs) in VOL connector info string from environment variable.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
2023-01-04 13:04:07 -06:00
Dana Robinson
83f81a6422 Adds -Warray-temporaries to the developer warnings (#2385)
These generate a LOT of noise that we are not going to address anytime
soon.
2023-01-03 06:18:48 -08:00
Dana Robinson
d326f6fae8 Adds 'make install' and 'make check-install' to the CI (Autotools only) (#2381) 2023-01-03 06:17:56 -08:00
Dana Robinson
c0b3646193 Adds RELEASE.txt notes and updates Doxygen (#2377) (#2379) 2022-12-29 12:58:54 -08:00
Dana Robinson
3da2551adb Adds Doxygen markup for H5FDdriver_query() (#2376) 2022-12-28 13:07:39 -08:00
Larry Knox
d261272ffa Restore line 264 of main.yml: "thread_safety:" (#2374) 2022-12-28 10:30:57 -08:00
Dana Robinson
23ccd7ee3b Purged references to HDF5 1.13.x from the Doxygen documentation (#2365) 2022-12-27 12:33:14 -08:00
Dana Robinson
298c7efe76 Adds missing Doxygen for H5ESpublic.h (#2364)
* Adds missing Doxygen for H5ESpublic.h

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-27 11:42:31 -08:00
Dana Robinson
1cf9ecccf5 Fix for Autotools --disable-deprecated-symbols (#2363)
* Fix for Autotools --disable-deprecated-symbols

When we added v116 as a valid option, we left the default as v114 so
using --disable-deprecated-symbols leads configure to complain that you
can't set a default API that was deprecated.

The GitHub action didn't catch this because it explicitly specifies v116

This only affects develop w/ the Autotools when
--disable-deprecated-symbols is requested.

* Added v116 & default to the --with-default-api-version help string

The Autotools --with-default-api-version help string was missing v116.
This has been added, as well as a "default" target so the CI can catch
version problems when we forget to update the defaults upon creating
a new major version.

The GitHub CI also now uses "default" as the target for the deprecated
symbols build.

* Fixes the 1.14 API GitHub CI threadsafe/build_mode

This action still had the bug we fixed where we set the build mode
and threadsafety using an array of size one instead of an object.
2022-12-24 11:36:38 -08:00
Dana Robinson
cfd5059e77 HL GIF tools changes (#2360)
* Fixes the broken Autotools option
* Removes the "build HL tools" option
2022-12-23 16:05:31 -08:00
Larry Knox
9a694db450 Update testh5cc.sh.in for new major version 1.14. (#2349)
* Update testh5cc.sh.in for new major version 1.14.

* iFix sha256sum commands in release script.
2022-12-22 13:38:51 -06:00
Dana Robinson
ab0a778593 Adds Doxygen VOL flag markup (#2340)
* Initial doxygen markup

* Committing clang-format changes

* Adds Doxygen comments to VOL flags

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-21 13:44:50 -08:00
Dana Robinson
57af2ff798 Onion VFD header cleanup (#2337)
* Partial work towards cleaning up the onion VFD code

* Committing clang-format changes

* A few minor tweaks to the onion VFD public header

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-21 10:46:05 -08:00
Allen Byrne
9f5cf0a457 H5F_LIBVER_LATEST changes for move to 1.15 (#2288)
* H5F_LIBVER_LATEST changes for move to 1.15

* Add new default api check

* Format fixes

* Fix default configure

* fix lib version tests

* Fix another version variable

* Add 1.14 doc link
2022-12-21 10:07:25 -08:00
vchoi-hdfgroup
976e8c9750 Fix up the H5Pencode2 test for virtual layout. (#2325)
* Fix up the H5Pencode2 test for virtual layout.

* Committing clang-format changes

* Remove VERIFY and use TEST_ERROR.

Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-20 16:48:56 -08:00
Allen Byrne
c1e44d32e6 Fix doxygen warnings and remove javadocs (#2324)
* Fix doxygen warnings and remove javadocs

* fix typo
2022-12-20 16:59:40 -06:00
Mark Kittisopikul
b9244a85d9 Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074)
* Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info

* Modify chunk_info test to for unsigned / hsize_t types

* Fix types in test
2022-12-19 15:13:43 -08:00
Scot Breitenfeld
70cf2c390b Removed idioms and misc. text clean-up (#2320)
* removed idioms and misc. text clean-up, Issue #2135

* removed idioms and misc. text clean-up, Issue #2135
2022-12-16 19:56:52 -08:00
Allen Byrne
149b8e9769 Disable hl tools by default (#2313)
* Disable hl tools by default

* identify the tools

* Only GIF tools are depecated

* Add new option

* Update autotools
2022-12-16 19:56:07 -08:00
Scot Breitenfeld
8102fa8c97 Only document Fortran functions (#2319)
* Only document Fortran functions

* Only document Fortran functions

* Only document Fortran functions

* Only document Fortran functions
2022-12-16 19:52:08 -08:00
Scot Breitenfeld
784061b15e moved onion VFD to FAPL group (#2321) 2022-12-16 19:51:52 -08:00
vchoi-hdfgroup
6b6bcdead6 Hdffv 11052 (#2315)
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump.
When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the
closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value"
all the way till the end of the routine.  The user-provided corrupted file has an illegal
file size causing failure when reading the image during the closing process.
At the end of this routine it sets f->shared to NULL and then frees "f".
This is done whether there is error or not in "ret_value".
Due to the failure in reading the file earlier, the routine then returns error.
The error return from H5F__dest() causes the file object "f" not being removed from the
ID node table.  When the library finally exits, it will try to close the
file objects in the table.  This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f).
Fix:
a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine.
b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before.
c) h5debug.c main(): track error return from H5Fclose().

* Committing clang-format changes

* Add test and release note info for fix to HDFFV-11052 which is merged via PR#2291.

* Committing clang-format changes

* Add the test file to Cmake.

* Skip test_misc37() for drivers that is not default compatible as it is using a pre-generated file.

* Committing clang-format changes

Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-16 13:47:29 -08:00
Dana Robinson
0e76abaf64 Removes duplicated build mode from -Werror GitHub actions (#2314) 2022-12-16 12:05:01 -08:00
Dana Robinson
4bbda3038a Converts the YAML build mode arrays to objects in special runs (#2308)
* Converts the YAML build mode arrays to objects in special runs

* Adds a dump of the matrix context for each test

This would have made it a LOT easier to debug the build_mode issues...

* Disable the mirror VFD in the -Werror checks

We can re-enable this after we fix the warnings, but I don't want to
conflate code and GitHub changes, so this is a better way to get the
CI to pass for now.
2022-12-15 23:03:02 -08:00
Gerd Heber
138daa8846 Merge pull request #2304 from gheber/develop
Update hdf5_header.html
2022-12-15 13:25:18 -06:00
Gerd Heber
10c693a04f Update hdf5_header.html
Use less awkward language.
2022-12-15 08:49:19 -06:00
vchoi-hdfgroup
0cb5808087 Hdffv 11052 (#2303)
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump.
When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the
closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value"
all the way till the end of the routine.  The user-provided corrupted file has an illegal
file size causing failure when reading the image during the closing process.
At the end of this routine it sets f->shared to NULL and then frees "f".
This is done whether there is error or not in "ret_value".
Due to the failure in reading the file earlier, the routine then returns error.
The error return from H5F__dest() causes the file object "f" not being removed from the
ID node table.  When the library finally exits, it will try to close the
file objects in the table.  This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f).
Fix:
a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine.
b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before.
c) h5debug.c main(): track error return from H5Fclose().

* Committing clang-format changes

* Add test and release note info for fix to HDFFV-11052 which is merged via PR#2291.

* Committing clang-format changes

* Add the test file to Cmake.

Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-15 05:32:23 -08:00
Dana Robinson
1b06e868fd Fixes broken CI matrix actions involving -Werror and API versions (#2302) 2022-12-14 18:05:15 -06:00
Dana Robinson
93938b3a8d Adds 'unused' hints for MDS io_info parameters (#2301)
* Adds 'unused' hints for MDS io_info parameters

* Committing clang-format changes

* Fix issue with formatter

* Committing clang-format changes

* Final fix for formatter

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-14 14:54:51 -08:00
Scot Breitenfeld
a1c81eda20 added doc. warning for H5Literate_async return value (#2295) 2022-12-14 15:22:37 -06:00
Allen Byrne
b7511c19d0 Update windows worker compilers (#2286)
* Update windows worker compilers

* Update bin and test issues

* Update script and revert java test
2022-12-14 08:58:20 -06:00
Scot Breitenfeld
502b32b0f2 Updated H5ES documenation (#2293) 2022-12-13 10:56:48 -08:00
vchoi-hdfgroup
a9036005c3 Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291)
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump.
When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the
closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value"
all the way till the end of the routine.  The user-provided corrupted file has an illegal
file size causing failure when reading the image during the closing process.
At the end of this routine it sets f->shared to NULL and then frees "f".
This is done whether there is error or not in "ret_value".
Due to the failure in reading the file earlier, the routine then returns error.
The error return from H5F__dest() causes the file object "f" not being removed from the
ID node table.  When the library finally exits, it will try to close the
file objects in the table.  This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f).
Fix:
a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine.
b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before.
c) h5debug.c main(): track error return from H5Fclose().

* Committing clang-format changes

Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-13 09:40:59 -08:00
Scot Breitenfeld
b9f4c001ad added doc. warning for H5Oflush in parallel (#2289) 2022-12-09 21:31:13 -06:00
Scot Breitenfeld
4a8be219e0 fixed unclosed objects in test (#2290) 2022-12-09 21:30:42 -06:00
Neil Fortner
ef4f1f2bd4 Check for size==0 for all datatypes read from disk, not just compound (#2287)
members
2022-12-08 10:30:29 -06:00
Egbert Eich
0b4e9cf976 Compound datatypes may not have members of size 0 (#2243)
* Compound datatypes may not have members of size 0

A member size of 0 may lead to an FPE later on as reported in
CVE-2021-46244. To avoid this, check for this as soon as the
member is decoded.
This should probably be done in H5O_dtype_decode_helper() already,
however it is not clear whether all sizes are expected to be != 0.

This fixes CVE-2021-46244 / Bug #2242.

Signed-off-by: Egbert Eich <eich@suse.com>

* Rework error recovery code in H5O__dtype_decode_helper() and
H5O__dtype_decode().

* Format changes for src/H5Odtype.c.

Signed-off-by: Egbert Eich <eich@suse.com>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2022-12-07 16:14:40 -06:00
Allen Byrne
dcccc35526 Correct requires setting for pkgconfig files (#2280)
* Correct requires setting for pkgconfig files

* Add issue number
2022-12-07 16:05:51 -06:00
Dana Robinson
64514392fb Fixes warnings in H5Opline.c error messages (#2281)
* Fixes warnings in H5Opline.c error messages

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-06 11:32:39 -08:00
Allen Byrne
0a2006d9c6 Add text about release notes (#2246) 2022-12-06 06:02:21 -08:00
Allen Byrne
2376723d4a Develop jni trans (#2266)
* Add compound and refactor out atomic types

* Add Array String tests back

* Convert Attribute version of compound example

* Update transfer atom8ic read to return object
2022-12-05 22:29:42 -06:00
V. Armando Solé
281984b3e3 H5E_ERR_CLS_g symbol missing when compiling C++ plugins (#2269)
C++ HDF5 filter plugin SZ3 fails to build under windows with failure at linking time unless that extern "C" block is added.
2022-12-05 19:19:53 -06:00
Scot Breitenfeld
c1c131260a return error message related to calling API (#2276) 2022-12-02 14:24:43 -06:00
Egbert Eich
24700e8f06 CVE 2021 46242 develop (#2255)
* When evicting driver info block, NULL the corresponding entry

Since H5C_expunge_entry() called (from H5AC_expunge_entry()) sets the  flag
H5C__FLUSH_INVALIDATE_FLAG, the driver info block will be freed. NULLing the
pointer in  f->shared->drvinfo will prevent use-after-free  when it is used in other
functions (like  H5F__dest()) - as other places will check whether the pointer is
initialized before using its value.

This fixes CVE-2021-46242 / Bug #2254

Signed-off-by: Egbert Eich <eich@suse.com>

* When evicting the superblock, NULL the corresponding entry

The call to H5AC_expunge_entry() will free the corresonding structure,
to avoid a use-after-free, the corrsponding pointer entry will be NULLed.

Signed-off-by: Egbert Eich <eich@suse.com>

Signed-off-by: Egbert Eich <eich@suse.com>
2022-12-02 14:24:14 -06:00
Allen Byrne
88b24c258b Output should only be printed if verbose. (#2273)
* Output should only be printed if verbose.

* Add note
2022-12-02 09:39:49 -08:00
Egbert Eich
4e0277c35a Report error if dimensions of chunked storage in data layout < 2 (#2241)
For Data Layout Messages version 1 & 2 the specification state
that the value stored in the data field is 1 greater than the
number of dimensions in the dataspace. For version 3 this is
not explicitly stated but the implementation suggests it to be
the case.
Thus the set value needs to be at least 2. For dimensionality
< 2 an out-of-bounds access occurs as in CVE-2021-45833.

This fixes CVE-2021-45833 / Bug #2240.

Signed-off-by: Egbert Eich <eich@suse.com>

Signed-off-by: Egbert Eich <eich@suse.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2022-12-01 23:04:42 -06:00
Allen Byrne
96a4e10102 Add aarch64 toolchain and change dump test to long opt (#2271) 2022-12-01 14:32:34 -08:00
Larry Knox
cf232a757f Develop fix ubuntu 22.04 openmpi install on github (#2268)
* Update install openmpi-bin to also install mpi-default-dev instead of
libopenmpi-dev.  This according to
https://bugs.launchpad.net/ubuntu/+source/openmpi/+bug/1870780.
2022-11-28 13:20:24 -06:00
Egbert Eich
158dff6b50 Make sure testsuite can handle multiple dependent scripts (#2256)
Commit afc54d75a1 to the test suite to eliminate a separate
shell script did not take into account that there may be
multiple dependent test scripts which resulted in the
message:
`/bin/sh: line 7: [: too many arguments`.
when running the test suite.

Beware that this new version still makes use of non-posix GNU
extensions to `test`.

Signed-off-by: Egbert Eich <eich@suse.com>

Signed-off-by: Egbert Eich <eich@suse.com>
2022-11-28 13:19:31 -06:00
Larry Knox
eac2cd54e2 Develop ubuntu 20.04 (#2267)
* Use ubuntu-20.04 for github autotools  parallel tests until parallel
configure is fixed on  ubuntu 22.04.

* Remove inactive developers from CODEOWNERS.

* Temporarily cat config.log for autotools build in github actions.

* Try ubuntu-latest.

* Attempt to cat config.log even when configure fails.

* Fix syntax.

* Try again

* Try again

* Try again.

* Back to original temporary fix.

* Install libopenmpi-dev with openmpi-bin, which was installed as a
dependency prior to ubuntu-22.04.
2022-11-23 12:00:00 -08:00
Larry Knox
3e762b07aa Use ubuntu-20.04 for github autotools parallel tests until parallel (#2264)
* Use ubuntu-20.04 for github autotools  parallel tests until parallel
configure is fixed on  ubuntu 22.04.
2022-11-18 17:30:29 -06:00
raylu-hdf
ee4d92e01b Bug Fix: Segfault in H5CX_get_vol_wrap_ctx when H5VLwrap_register is called from an application (#2248)
* Jira HDFFV-10881: Segfault in H5CX_get_vol_wrap_ctx when H5VLwrap_register is called from an application.  A quick and simple fix to make it fail with a relevant error message.

* Format changes.

* Committing clang-format changes

* Minor change: split one condition check into two for clarity.

* Adding doxygen comment for H5VLwrap_register.

* Minor change: adding a little more detail to the Doxygen comment for H5VLwrap_register.
2022-11-17 16:29:21 -06:00
Ryan Schmidt
9dd36f016a Simplify & fix check for szlib encoder (#2263)
Return the result rather than setting the exit code. "return" is a
language keyword whereas "exit" is a function for which the <stdlib.h>
header has to be included which it wasn't in this test, therefore the
test would previously fail to identify that the encoder was enabled if
"-Werror=implicit-function-declaration" was used, which it is by default
with clang from Xcode 12 and later.

Fixes #2262
2022-11-17 16:28:44 -06:00
Allen Byrne
169896aedb Remove hard-coded version text (#2260)
* Remove hard-coded version text

* Use macOS 11 until accum test is fixed see #2261
2022-11-16 15:13:46 -06:00
Allen Byrne
719d800499 Refactor JNI translate functions to a recursive switch on datatype (#2232) 2022-11-15 22:44:33 -06:00
Scot Breitenfeld
03cc221016 moved quad precision checks (#2252)
* Only check quad sizes if fortran is enabled

* fixed if struct
2022-11-12 12:53:35 -06:00
Egbert Eich
0f94940f1a H5O_dtype_decode_helper: Parent of enum needs to have same size as enum itself (#2237)
The size of the enumeration values is determined by the size of the parent.
Functions accessing the enumeration values use the size of the enumeration
to determine the size of each element and how much data to copy. Thus the
size of the enumeration and its parent need to match.
Check here to avoid unpleasant surprises later.

This fixes CVE-2018-14031 / Bug #2236.

Signed-off-by: Egbert Eich <eich@suse.com>
2022-11-11 00:05:00 -06:00
Egbert Eich
34ec3bb7bc Make sure info block for external links has at least 3 bytes (#2234)
According to the specification, the information block for external links
contains 1 byte of version/flag information and two 0 terminated strings
for the object linked to and the full path.
Although not very useful, the minimum string length for each (with
terminating 0) would be one byte.
Checking this will help to avoid SEGVs triggered by bogus files.

This fixes CVE-2018-16438 / Bug #2233.

Signed-off-by: Egbert Eich <eich@suse.com>
2022-11-10 23:41:53 -06:00
Egbert Eich
1750b4b0af Validate location (offset) of the accumulated metadata when comparing (#2231)
Initially, the accumulated metadata location is initialized to HADDR_UNDEF
- the highest available address. Bogus input files may provide a location
or size matching this value. Comparing this address against such bogus
values may provide false positives. This make sure, the value has been
initilized or fail the comparison early and let other parts of the
code deal with the bogus address/size.
Note: To avoid unnecessary checks, we have assumed that if the 'dirty'
member in the same structure is true the location is valid.

This fixes CVE-2018-13867 / Bug #2230.

Signed-off-by: Egbert Eich <eich@suse.com>
2022-11-10 23:24:56 -06:00
Egbert Eich
659bc99fd1 Make H5O__fsinfo_decode() more resilient to out-of-bound reads. (#2229)
When decoding a file space info message in H5O__fsinfo_decode() make
sure each element to be decoded is still within the message. Malformed
hdf5 files may have trunkated content which does not match the
expected size. Checking this will prevent attempting to decode
unrelated data and heap overflows. So far, only free space manager
address data was checked before decoding.

This fixes CVE-2021-45830 / Bug #2228.

Signed-off-by: Egbert Eich <eich@suse.com>

Additions

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2022-11-10 23:20:09 -06:00
Egbert Eich
99487d9e45 H5IMget_image_info(): Make sure to not exceed local array size (#2227)
Malformed hdf5 files may provide more dimensions than the array dim[] in
H5IMget_image_info() is able to hold. Check number of elements first by calling
H5Sget_simple_extent_dims() with NULL for both 'dims' and 'maxdims' arguments.
This will cause the function to return only the number of dimensions.
The fix addresse a stack overflow on write.

This fixes CVE-2018-17439 / HDFFV-10589 / Bug #2226.

Signed-off-by: Egbert Eich <eich@suse.com>

Signed-off-by: Egbert Eich <eich@suse.com>
2022-11-10 23:01:45 -06:00
Scot Breitenfeld
5985d0e0b1 removed uninterpretable line (#2249) 2022-11-10 22:56:53 -06:00
Dana Robinson
a8942c7413 Adds a release note for PR #2210 (CVE-2019-8396) (#2247)
* Adds a release note for PR #2210 (CVE-2019-8396)

* Capitalization issue fixed
2022-11-09 17:03:55 -08:00
Dana Robinson
d93c6fae43 Removes MPE instrumentation support. (#2245)
* Removes MPE instrumentation support.

The Autotools will no longer accept --with-mpe= and the logging commands
have been removed from the FUNC_ENTER macros. CMake has never supported
instrumenting for MPE.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-11-09 11:06:26 -08:00
Egbert Eich
18c438bdf0 H5O__pline_decode() Make more resilient to out-of-bounds read (#2210)
Malformed hdf5 files may have trunkated content which does not match
the expected size. When this function attempts to decode these it may
read past the end of the allocated space leading to heap overflows
as bounds checking is incomplete.
Make sure each element is within bounds before reading.

This fixes CVE-2019-8396 / HDFFV-10712 / github bug #2209.

Signed-off-by: Egbert Eich <eich@suse.com>

Signed-off-by: Egbert Eich <eich@suse.com>
2022-11-09 10:25:11 -08:00
Dana Robinson
adc467992e Moved the contributing.md document to the project root (#2244) 2022-11-09 09:58:32 -08:00
Dana Robinson
0f30852242 Removes dmalloc support (#2239)
This has not been used to debug the library in a very long time. Most
developers use valgrind, -fsanitize=address, or some other memory checker
instead of this library.

This removes:
    * dmalloc.h include from H5private.h
    * --with-dmalloc= Autotools configure option
    * HDF5_ENABLE_USING_DMALLOC CMake option
2022-11-09 09:22:14 -08:00
Gerd Heber
2025d047e2 Multidataset RFC updates (#2238) 2022-11-08 17:46:52 -08:00
raylu-hdf
81a6f6874f Bug fix: the previous checkin only supported the native connector (#2211)
* Bug fix: make sure the test case supports the pass_through connector.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-11-05 15:24:42 -07:00
Dana Robinson
018f093c09 Removes the memory allocation sanity checks feature (#2218)
* Removes the memory allocation sanity checks feature

* Committing clang-format changes

* Removes zero size checks for H5MM_(c|m)alloc()

* Explicitly return NULL when size == 0 in H5allocate_memory()

* Committing clang-format changes

* Format fix

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-11-03 16:30:08 -07:00
Scot Breitenfeld
40a0e3c7b5 correct H5Ropen_object_reference (#2212) 2022-11-03 09:56:53 -07:00
Dana Robinson
55e3f667d4 Fixed a Doxygen param in H5EScancel (#2213) 2022-11-03 09:55:59 -07:00
Larry Knox
6924d590cc Use ctest_test and APPEND to correctly report passed and failed test numbers in CDash (#2208)
* Change how HPC tests are executed

* Move ctest_test commands for serial and parallel tests into cmake files.

* Update checks for uploading Test.xml to CDash.

* Correct cmake scripots.

* Remove extraneous characters.

* Add ctest_start (APPEND).

* Add binary directories to scripts running ctest_test.

* Correct parameters for appending Test.xml.

* Set CTEST_SITE and CTEST_BUILD_NAME.

* Try to pass site and build_name to ctest_test sripts.

* Add site name and build name for ctest_test commands vi environment.

* Revert "Try to pass site and build_name to ctest_test sripts."

This reverts commit d364aaf0fa.

* Correct typo in src/CMakeLists.txt.

* Update batch scripts to run ctest_test scripts.

Co-authored-by: Allen Byrne <byrn@hdfgroup.org>
2022-11-02 09:02:47 -07:00
Larry Knox
e4fb9aa96e Update link for Software Changes in RELEASE.txt. (#2205)
* Update link for Software Changes in RELEASE.txt.
Add RELEASE.txt contents from 1.13.3 release to HISTORY-1_13.txt.

* Reverse order of entries in HISTORY-1_13.txt to match the order in previous HISTORY
files.
2022-11-01 16:14:52 -05:00
Allen Byrne
94119211a7 Correct the CMake link for MPI (#2198) 2022-11-01 16:03:13 -05:00
Larry Knox
11dfa25910 Update copyright headers (#2184)
* Updated source file copyright headers to remove "Copyright by the Board of Trustees
of the University of Illinois", which is kept in the top-level COPYING file.
2022-11-01 16:02:27 -05:00
raylu-hdf
71595e9ea3 Added a test case for H5VLget_connector_name (#2195)
* Added a test case for H5VLget_connector_name.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-10-28 13:36:49 -07:00
Scot Breitenfeld
2b8139f34c added issue with Perlmutter and subfiling (#2202)
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
2022-10-28 09:01:06 -07:00
Larry Knox
9acd203041 Update release.txt (#2201)
* Some Javadoc warning fixes

* Updated javadoc fixes

* # WARNING: head commit changed in the meantime

HDFFV-11229 Fix long double usage in tools and java

Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.

* Committing clang-format changes

* HDFFV-11229 Add release note

* HDFFV-11229 windows testfile needed

* fix typo

* Remove non supported message text

* HDFFV-11229 - change ldouble test to check both native and general

* HDFFV-11229 add second file compare

* HDFFV-11229 fix reference file

* HDFFV-11229 autotools check two refs

* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output

* Committing clang-format changes

* Update release note

* Update attribute type of ref file

* Change source of ninja for macs

* try port instead of brew

* Recommended is to use brew.

* Undo non long double changes

* remove unneeded file

* Fix perl and doxygen CMake code

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

* Add stamp files to BYPRODUCTS

* Only one copy of file exists

* Fix custom cmmand depends targets

* Fix fortran custom command DEPENDS

* Add LD_LIBRARY_PATH to tests

* Add custom target for DEPENDS

* Add h5detect conditionaly to generated target DEPENDS

* Correct DEPENDS targets

* Parallel builds need the mpi compiler for pkgconfig scripts.

* install only if MPI build

* Fortran target depends

* Remove incorrect source attribute

* doxygen adjustments

* doxygen build updates

* Correct version

* Correct function version - function has been merged to 1.12

* Correct version string for map functions

* Cleanup warnings for tools debug builds

* TRILAB-227 - fix indexing for h5diff selections

* Correct location of pos to index function call

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES because of AppleClang

* if blocks needed for build modes

* Update list of DT platforms

* VS2019 correctly displays float values

* revert VS2019 change

* Issue #669 remove version from pkgcfg filename

* remove version from h5cc script

* Java reference functions updated

enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging

* Correct BYPRODUCTS argument

* Correct more genereated files BYPRODUCTS

* BYPRODUCTS must have unique locations

* Fix typo

* Fix fortran configure checks

* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic

* Add note about fortran configure change

* Adds a quick for for some egregious chunk_info badness (#722)

* Fixes issue with ccmake that prevents building Fortran (#723)

ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations

* Fix conflicts with merge

* Move MAX_PRECISION back to HDF5UseFortran.cmake

* Use STREQUAL to test macro argument

* Move C language test to ConfigureChecks from HDF5UseFortran

* MAX_PRECISION defines must be defined

* Organize flags and align autotools and cmake

* Fix comment in no-error-general warnings files.

* Flag cleanup and fix typos

* Add comment

* Correct VAR used to find configure time file

* Set the path correctly

* Update missing release note info.

* Update code owners

* Correct JIRA note

* add known problem.

* Use only core library for testing dynamic plugins.

* Committing clang-format changes

* Update main.yml

* Update HISTORY-1_13.txt

Missing release note added for changed location of CMake configuration files.

* Update HISTORY-1_13.txt

Fix typo

* Update main.yml

revert change

* Updated version to 1.13.4-1 after creating hdf5_1_13_3 branch for 1.13.3
release.
Added new version to exceptions in lines 74-5 of src/H5.c

* Cleared RELEASE.txt entries following HDF5 1.13.3 release.

Co-authored-by: Allen Byrne <byrn@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
2022-10-28 08:10:02 -07:00
Allen Byrne
4d0501f48c Fix for documentation misunderstanding on m1 Intel builds (#2188) 2022-10-26 09:24:51 -07:00
Scot Breitenfeld
a6c1dff09a running on node-16 insteas of Node.js 12 (#2190) 2022-10-26 09:24:12 -07:00
Larry Knox
0173706826 Update develop branch version to 1.13.4-1 (#2189)
* Updated version to 1.13.4-1 after creating hdf5_1_13_3 branch for 1.13.3
release.
Added new version to exceptions in lines 74-5 of src/H5.c
2022-10-26 11:07:17 -05:00
Allen Byrne
9c61f7b1e1 JNI: Improve varlen datatype handling in H5A/H5D read/write functions (#2156)
* Improve JNI VL datatype read/write to handle complex combinations

* Implement VL of VL JNI writes and reads

* Add Java VLofVL test for attributtes

* Changes to address review issues

* Fix H5Aread vl blocks
2022-10-25 23:33:30 -05:00
Neil Fortner
ad2d77397a Add RELEASE.txt note for multi dataset feature (#2187) 2022-10-25 22:13:01 -05:00
Scot Breitenfeld
ba1fe3d1df converted from ISO-8859-1 to UTF-8 (#2185) 2022-10-25 12:29:36 -07:00
Scot Breitenfeld
7d1997ff7b Removed the file, func, line args in the _async APIs fpr doxygen (#2179)
* Removed the: file, func, line args in the _async APIs from the doxygen arguments. Documented H5ESclean.

* format fixes

* fixed DOXYGEN_PREDEFINED

* Fixed the #ifdet logic for doxygen, added missing multi-dataset va_args

* format fixes

* Use H5_DOXYGEN instead of H5_DOXYGEN_FORTRAN

* reordered multidataset declarations

* alt. for H5Aclose_async and H5Acreate_async

* made doxgyen API into seperate blocks

* updated codespell

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-10-25 10:41:38 -07:00
Allen Byrne
23e237e728 Port VOL User Guide to doxygen (#2165)
* Port VOL User Guide to doxygen

* Fix spelling

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-10-25 08:51:08 -07:00
Allen Byrne
ea902f9ace Implement option for using CMake GNUInstallDirs (#2175)
* Implement option for using CMake GNUInstallDirs

* Add release notes
2022-10-25 08:50:43 -07:00
raylu-hdf
f98c93ab19 Added a test case to verify the VOL capacity flags work correctly. (#2178)
* Added a test case to verify the VOL capacity flags work correctly.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-10-25 07:59:03 -05:00
Scot Breitenfeld
4e4c7cf66d fixed error code returned for H5Aexits (#2180) 2022-10-25 07:58:23 -05:00
Neil Fortner
7997b53589 Fix problem with variable length attributes being accessed through multiple file handles (#2181)
* Fix bug with variable length attributes being accessed through multiple
file handles.

* Committing clang-format changes

Co-authored-by: Neil Fortner <nfortne2@localhost.localdomain>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-10-25 07:46:15 -05:00
Neil Fortner
93754cae33 Multi Dataset (#2120)
* Fix bug with cross platform compatibility of references within vlens.
No testing yet.

* Merge from multi_rd_wd_coll_io to a more recent branch from develop.
Untested, probably does not work yet.

* Committing clang-format changes

* Committing clang-format changes

* Fix many bugs in multi dataset branch.  Mostly works, some issues in
SWMR tests.

* Committing clang-format changes

* Disable test in swmr.c that was failing due to bug in HDF5 unrelated to
multi dataset.

* Committing clang-format changes

* Fixed fortran multi-dataset tests

* Fixed xlf errors

* Added benchmark code for multi-datasets

* loops over datasets

* added missing error arg.

* Added gnuplot formatting

* Jonathan Kim original MD benchmarking code

* updated MD benchmarking code

* code clean-up

* Only make files in feature test mode

* misc clean-up

* removed TEST_MDSET_NO_LAST_DSET_2ND_PROC option

* Committing clang-format changes

* Change multi dataset API to use arrays of individual parameters instead
of the parameter struct.

* Committing clang-format changes

* Update to new multi dataset Fortran API and tests. (#1724)

* Update to new multi dataset Fortran API and tests.
* Sync Fortran with develop.
* skipping h5pget_mpio_actual_io_mode_f for now

* Fixed issue with dxpl_id, changed to variable size dim. (#1770)

* Remove "is_coll_broken" field from H5D_io_info_t struct

* Committing clang-format changes

* Minor cleanup in multi dataset code.

* Committing clang-format changes

* Clean up in multi dataset code.

* Committing clang-format changes

* Committing clang-format changes

* Fix speeling

* Fix bug in parallel compression. Switch base_maddr in io_info to be a
union.

* Committing clang-format changes

* Implement selection I/O support with multi dataset.  Will be broken in
parallel until PR 1803 is merged to develop then the MDS branch.

* Committing clang-format changes

* Spelling

* Fix bug in multi dataset that could cause errors when only some of the
datasets in the multi dataset I/O used type conversion.

* Committing clang-format changes

* Integrate multi dataset APIs with VOL layer.  Add async versions of
multi dataset APIs.

* Committing clang-format changes

* Spelling fixes

* Fix bug in non-parallel HDF5 compilation.

* Committing clang-format changes

* Fix potential memory/free list error. Minor performance fix. Other minor
changes.

* Committing clang-format changes

* Fix memory leak with memory dataspace for I/O.

* Committing clang-format changes

* Fix stack variables too large.  Rename H5D_dset_info_t to
H5D_dset_io_info_t.

* Committing clang-format changes

* Remove mem_space_alloc field from H5D_dset_io_info_t.  Each function is
now responsible for freeing any spaces it adds to dset_info.

* Committing clang-format changes

* fixed _multi Fortran declaration

* Refactor various things in (mostly) the serial I/O code path to make
things more maintainable.

* Committing clang-format changes

* updated to array based, doxygen, and examples

* Reinstate H5D_chunk_map_t, stored (via pointer) inside
H5D_dset_io_info_t.

* Change from calloc to malloc for H5D_dset_io_info_t and H5D_chunk_map_t.
Switch temporary dset_infos to be local stack variables.

* Committing clang-format changes

* format cleanup

* format cleanup

* added coll and ind

* Modify all parallel I/O paths to take dset_info instead of assuming
dset_info[0].

* Committing clang-format changes

* fixed output

* Rework parallel I/O code to work properly with multi dataset in more
cases.  Fix bug in parallel compression.

* Committing clang-format changes

* Prevent H5D__multi_chunk_collective_io() from messing up collective opt
property for other datasets in I/O.  Other minor cleanup.  Add new test
case to t_pmulti_dset.c for H5FD_MPIO_INDIVIDUAL_IO, disabled for now
due to failures apparently unrelated to multi dataset code.

* Fix spelling

* Committing clang-format changes

* Replace N log N algorithm for finding chunk in
H5D__multi_chunk_collective_io() with O(N) algorithm, and remove use of
io_info->sel_pieces in that function.

* Committing clang-format changes

* Replace sel_pieces skiplist in io_info with flat array of pointers, use
qsort in I/O routine only when necessary.

* Committing clang-format changes

* Add new test case to mdset.c

* Committing clang-format changes

* Fix spelling

* Very minor fix in H5VL__native_dataset_read()

* Fix bug that could affect filtered parallel multi-dataset I/O.

* Add RM entries for H5Dread_multi(), H5Dread_multi_async(),
H5Dwrite_multi(), and H5Dwrite_multi_async()

* Unskip test in swmr.c

* Committing clang-format changes

* Eliminate H5D__pre_read and H5D__pre_write

* Remove examples/ph5mdsettest.c. Will fix and re-add as a test.

* Enable hyperslab combinations in mdset test

* Committing clang-format changes

* Clarify H5Dread/write_multi documentation.

* Fix bugs in multi-dataset I/O.  Expand serial multi dataset test.
Update macro in parallel multi dataset test.

* Committing clang-format changes

* Spelling

* Remove obsolete entry in bin/trace

* Rework type conversion buffer allocation. Only one buffer is shared
between datasets in mdset mode, and it is malloced instead of calloced.

* Committing clang-format changes

* Fix bug in error handling in H5D__read/write

* added multi-dataset fortran check with optional dataset creation id (#2150)

* removed dup. dll entry

* Address comments from code review.

* Remove spurious changes in H5Fmpi.c

* Fix issue with reading unallocated datasets in multi-dataset mode.
Address other comments from code review.

* Committing clang-format changes

* Delay chunk index lookup from io_init to mdio_init so it doesn't add
overhead to single dataset I/O.

* Committing clang-format changes

* Fix inappropriate use of piece_count

* updated copyright on new file, removed benchmark from testing dir.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: M. Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
2022-10-19 09:13:15 -07:00
Pierce Brooks
a898cef6c2 make sure to match the debug library postfix with external cmake projects and allow for zlib link name to be manually overridden (#2166) 2022-10-19 09:06:51 -05:00
Scot Breitenfeld
889dc1e9a7 address test failing when default real and integers are 8 bytes (#2173) 2022-10-19 08:55:06 -05:00
Scot Breitenfeld
0fd867390a changed to referencing C APIs by empty brackets (Fortran) (#2167) 2022-10-17 15:37:19 -05:00
Scot Breitenfeld
afb92a3e22 Fix H5Dfill_f test (#2162)
* change to integer for legacy H5Dfill_f testing

* fixed H5Dfill testing issues with promoted real and integer

* updated build fortran dependencies
2022-10-14 11:35:52 -07:00
vchoi-hdfgroup
5021fd9d4d Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion (#2153)
* Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion
if it is large enough, a buffer is allocated regardless so that the element
in fill->buf can later be reclaimed.
Valgrind is run on test/set_extent.c and there is no memory leak.

* Add information of this fix to release notes.

Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
2022-10-14 11:05:14 -07:00
Dana Robinson
80f80d61db Cleans final production mode warnings from H5Shyper.c (#2163)
* H5S__hyper_free_span_info() returns herr_t (not checked)

* Set up H5S__hyper_free_span_info() error handling

* Set up H5S__hyper_free_span() error handling

* Added error handling to H5S_HYPER_ADVANCE_SPAN

* Handled errors in H5S__hyper_iter_get_seq_list_gen()

* Added a production mode build target for -Werror

* Committing clang-format changes

* Updated names for -Werror checks

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-10-14 06:15:33 -07:00
Scot Breitenfeld
edc3790f5c renamed H5_FORTRAN_C_LONG_DOUBLE_IS_UNIQUE DLL (#2158)
* changed DLL define to a unique name
2022-10-13 11:41:33 -05:00
Scot Breitenfeld
cffaf47c15 Fix for missing h5dfill_c_long_double in dll (#2155)
* added conditionally include h5dfill_c_long_double in dll
2022-10-12 07:38:27 -05:00
Scot Breitenfeld
64e69d9291 Implemented C matching (and general) H5Dfill Fortran wrappers (#2152) 2022-10-11 07:25:05 -05:00
Scot Breitenfeld
306db409d4 Avoid calling H5FD_subfiling_init from h5open_f. (#2149)
* Only call H5FD_SUBFILING if subfiling conditions are met

* clang format
2022-10-07 09:01:42 -07:00
Scot Breitenfeld
e80079fd21 Subfiling Fortran wrapper work. (#2143)
* added C ref. for Fortran constants

* added C ref. for Fortran constants

* move constant paramters to H5* module listing

* added back comment

* Fortran subfiling and ioc FD with tests. H5Pset/get_mpi_params wrappers with tests, misc.. parallel test clean-up.

* misc. fixes

* fixed CMake testpar issues, formatted, misc. updates

* updated tests
2022-10-06 09:08:56 -07:00
Allen Byrne
a322eb6147 Fix static-cast format (#2141)
* Fix static-cast format

* clang format fix
2022-10-04 08:31:46 -05:00
Allen Byrne
c114bd64b0 Fix mostly java warnings, and cpp cast (#2134) 2022-10-03 13:31:32 -05:00
Scot Breitenfeld
1fb83da215 Grouped the Fortran constants in Doxygen (#2136) 2022-10-03 11:13:00 -05:00
Dana Robinson
ce67e4eb05 Adds a first cut at a "getting started with HDF5 development" guide (#2137)
* Added empty "getting started" markdown file

* Added title and brief tour of source code

* Moved platform-independence text to markdown

* Added anatomy of a function documentation

* Adds information on public/private/package calls and macros

* Adds much getting started guide text

* Fixed typos

* Fixed codespell issues
2022-09-30 21:44:39 -07:00
jhendersonHDF
79bdc6183e Subfiling testing fix and documentation (#2132)
* Fix a sporadic failure in Subfiling VFD tests

* Subfiling VFD - add note to H5Pget_fapl_subfiling documentation

Adds note about how H5Pget_fapl_subfiling only returns the original
settings on a FAPL and those settings could have been modified by the
Subfiling VFD's environment variables
2022-09-29 21:06:17 -05:00
Scot Breitenfeld
1bec0ce2d7 Misc. Fortran Doxygen updates (#2129) 2022-09-28 10:52:19 -05:00
Neil Fortner
4184bac2ec Fixed an issue that could occur when combining hyperslab selections (#2122) 2022-09-26 22:51:52 -05:00
Scot Breitenfeld
1c26386c38 Added C references to Fortran constants. (#2126)
* added C references for Fortran APIs
2022-09-26 22:50:09 -05:00
Allen Byrne
dcd332d231 Restructure ref manual presentation (#2123) 2022-09-26 22:49:29 -05:00
Allen Byrne
853a592d2d Add missing windows include/lib configure for StrStrIA (#2114) 2022-09-22 13:52:31 -05:00
Frank Berghaus
100b22e6c2 Use case-insensitive comparison for headers fix #2100 (#2101)
* Use case-inseneitive comparison for headers

HTTP headers should be case-insensitive. Use case-insensitive string
comparisons when working with HTTP header responses to ensure
compatibility.

* Revert "Use case-inseneitive comparison for headers"

This reverts commit a02f591723506b62b7208449be6eef7122120398

* Ignore case when searching HTTP header responses

Looking up the Content-Length in the header returned by S3 storage
endpoints should ignore case. To guarantee portability implement a
function for case-insensitive string search, because it is non-standard.

* Add an _ after H5 for the strcasestr implementation

It is a private function and should sport that underscore.

* Remove author comment from the doc comment

* Use search function defined by system if available

Check whether the system provides a function implementing case
insensitive string searches. Only use the custom implementation if the
system does not provide the functionality.

* Add tests for case-insensitive search

Basic tests:
  - Search for empty string
  - Search with exact match
  - Search with case-insensitive match
  - search with no match

* Enforce clang-format style

Some variable definitions in the th5_system tests did not conform to
clang-format's expectations. Updated the offending lines.

* Correct comment describing test case

* Added some spaces to please clang-format

* Ignore discarding const

Ask the compiler to ignore discarding the const when retunring a match from H5_strcasestr

Co-authored-by: Frank Berghaus <frank.berghaus@mpcdf.mpg.de>
2022-09-21 11:50:17 -05:00
Allen Byrne
d491c33a72 Update examples reference to single-source version 2.0.1 (#2107) 2022-09-20 17:21:15 -05:00
Dana Robinson
6d89634445 Updates VOL capabilities flags (#2105)
* Added feature/vol_cap_flags branch to GitHub actions

* Convert unsigned cap flag field to uint64_t and add flags

* Committing clang-format changes

* Convert unsigned cap flag field to uint64_t and add flags

* Committing clang-format changes

* Updates the VOL struct version number

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-09-17 09:49:38 -07:00
Allen Byrne
a9d8b469f4 Use doxygen snippets for common tables (#2104) 2022-09-16 12:45:06 -05:00
jhendersonHDF
16aa2dbaa0 Subfiling VFD updates (#2106) 2022-09-16 11:17:30 -05:00
Allen Byrne
45178c87a3 develop Merge doxygen from 1.12 branch (#2095) 2022-09-14 15:44:24 -05:00
Scot Breitenfeld
dcf3b54b6e removed H5R interface definition (#2090) 2022-09-14 15:43:27 -05:00
Neil Fortner
b5598575bb Fix memory bug in selection I/O (#2096)
* Fix memory bug in selection I/O

* Change error messages for calls to H5I_remove() in
H5FD_read/write_selection()
2022-09-14 11:10:05 -05:00
Dana Robinson
fe9c07fd90 Adds file locking documentation (#2084)
* Added initial (partial) file locking document

* Almost done with file locking document

* Fix intro

* Cleaned up text

* Updated environment variable verion info

* Fix typo

* Fix typos
2022-09-14 05:53:35 -07:00
Allen Byrne
05a0411140 Remove bitbucket.hdfgroup.org dependency. #2082 (#2086)
*
2022-09-07 17:12:55 -05:00
H. Joe Lee
2d4a96b32c Change test to example. (#2087)
* Remove the commented line.
2022-09-07 17:12:19 -05:00
H. Joe Lee
ecc687c4ff Fix grammar and spelling in comment block. (#2089) 2022-09-07 17:11:40 -05:00
Scot Breitenfeld
99f17c7271 Doxygen Fortran (#2062) 2022-09-07 17:11:20 -05:00
Dana Robinson
1804e0e0c4 Updates release schedule for 2023 (#2085)
* Updates release schedule for 2023

* Updates figure to put 1.13 and 1.14 on the same line
2022-09-04 04:42:25 -07:00
Allen Byrne
c8fdd92cd4 Update CMake code to 3.18 minimum version (#2080)
* Update CMake code to 3.18 minimum version

* Updated release note
2022-09-02 17:31:29 -07:00
Dana Robinson
6e8aaab1b4 Minor changes to CMake comments, etc. (#2078) 2022-08-31 11:03:37 -05:00
Dana Robinson
ccdcec273a Updates onion VFD major error codes (#2076) 2022-08-31 11:01:52 -05:00
Neil Fortner
5de9d63ff4 Address review comments from downstream merge of #2016 (#2073) 2022-08-31 11:01:05 -05:00
jhendersonHDF
5719187a34 Fix Java tests for Developer build modes (#2079) 2022-08-29 09:00:42 -07:00
Dana Robinson
5097ff016f Tidying of configure check C code (#2077)
* Tidying of configure check C code

* Fixed missing endif removal
2022-08-29 08:59:15 -07:00
Dana Robinson
08aebb6d1a Adds documentation for config directory (#2065)
* Adds documentation for config directory

* Fix spelling error
2022-08-24 23:05:28 -07:00
Gerd Heber
e1d6157c5d Added VOL connector feature flag RFC. (#2064) 2022-08-24 10:30:15 -05:00
Dana Robinson
ee55dd777b Fortran module directory improvements (#2060)
* Removes the module directory from the Automake flags as this
  generated a large number of "missing include directory" warnings
  and is unecessary
* Adds the module path to libhdf5.settings
2022-08-23 12:25:07 -07:00
Scot Breitenfeld
88ed5b69d4 removed h5rget_object_type_f module interface (#2057) 2022-08-23 09:09:08 -07:00
Dana Robinson
f020d129b2 Corrects more Fortran warnings (#2059)
* Moves -Wunused-dummy-arguments to the developer warnings since this
  generates a lot of spurious, unfixable noise due to things like
  callback wrappers
* Changes the return cast in h5fget_fileno_c, fixes a comment, and comment
  on potential badness
* Initializes a variable in tH5L_F03.F90 to quiet a 'maybe
  uninitialized' warning
2022-08-23 08:48:14 -07:00
Neil Fortner
21ec337855 Fix inappropriate use of HGOTO_ERROR (#2055) 2022-08-22 11:39:49 -05:00
Dana Robinson
801edb4f52 Quiets Fortran warnings about large arrays (#2053) 2022-08-22 08:28:48 -07:00
Dana Robinson
ec3737ab69 GitHub workflow cleanup (#2047)
* Cleans up main GitHub workflow(s)

* Combines main.yml and pr-check.yml, which differed trivially
* Reduces config redundancy via proper use of the matrix scheme
* Adds build-only configs for:
    - Version 1.6 default API
    - No deprecated symbols
    - Parallel HDF5
* The -Werror config was converted to build-only
* Makes the naming scheme more uniform
* Spaces out the code and adds comments

* Typo fix

* Fix mirror VFD CMake configure typo

* Debugging hack

* Undo debug hack and fix CMake build mode

* Set CC=mpicc for parallel builds

* Another attempt to fix parallel builds

* Updates comments in main.yml

* Fixes a v16 API bug in the mirror VFD test code

* Committing clang-format changes

* Added checks for v1.8 - 1.12 APIs

* Manually specify Windows configs

Java debug builds time out when running tests on Windows. We'll disable
them in debub mode while we investigate.

* Revert "Manually specify Windows configs"

This reverts commit d710d8d219.

* Skip Debug Windows configs while we investigate Java H5L timeouts

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-22 08:21:27 -07:00
Dana Robinson
f24dff5157 Quiets Fortran Autotools builds (#2052) 2022-08-22 08:21:06 -07:00
Dana Robinson
3015e3d7ab Quiets Automake rules in src directory (#2051)
* Quiets Automake rules in src directory

* Fix whitespace
2022-08-22 06:25:17 -07:00
Dana Robinson
10eb43d0c2 Removes ST from the list of debug packages (Autotools only) (#2045)
* Removes ST from the list of debug packages

The ST package (ternary search trees) was removed from the library a while ago

* Replaced B2 package

I did some crude timing with and without the B2 debug code enabled
and it doesn't seem to make much of a difference.
2022-08-22 04:12:12 -07:00
Dana Robinson
3e38a001a1 Simplify the CODEOWNERS file (#2049)
Simplify the CODEOWNERS file
2022-08-22 03:01:00 -07:00
jhendersonHDF
2b786ffe5a [WIP] Add Developer build mode to CMake (#1659)
* Add Developer build mode to CMake

* Set a few CMake variables for Developer build modes

* Refactor enabling of debug and developer-level compile definitions

* Convert cache debugging macros to normal ifdef style

Normal ifdef-style instead of if-style allows build system to define macros
without warning about redefining macros with different values (0 vs. 1)

* Add HDF5 Developer compile definitions to testing files

* Temporarily disable -fanalyzer flag for GCC 12+ Developer builds
2022-08-19 17:18:30 -07:00
jhendersonHDF
281db5876e Cleanup some warnings in Java JNI code (#2034) 2022-08-19 09:05:43 -07:00
Dana Robinson
7f6261a677 Removes cmake_ext_mod (files moved to cmake) (#2041)
At one time this content was a git submodule shared between several
projects but that time has long passed.
2022-08-19 07:54:42 -07:00
Dana Robinson
de46019a86 Removes bin/deploy, which just calls h5redeploy under the hood (#2027) 2022-08-19 09:11:22 -05:00
Dana Robinson
8cd97c4793 Updates the warnist script to report gfortran generic warnings (#2040)
These are not associated with a file and line number, like specifying
a non-existant include directory on the compile line.
2022-08-19 09:09:59 -05:00
Larry Knox
9dfcca0bbb Release updates (#2033)
* Update HISTORy-1_13.txt and clean RELEASE.txt entries after 1.13.2 release.
2022-08-18 08:35:21 -05:00
Neil Fortner
a3fd350483 Add note to RELEASE.txt for GitHub #2016 (#2030)
* Fix bug in attribute type conversion where the background buffer would
not be initialized with the destination contents when necessary.  Other
minor simplification.

* Committing clang-format changes

* Fix warnings.

* Address review comments.

* Add RELEASE.txt note for PR #2016

* Add GitHub number to release note

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-17 22:08:43 -05:00
Dana Robinson
e6f16c0ec2 Fixes codespell issues (#2032)
* Fixes codespell issues

* Fixed another typo
2022-08-17 16:31:54 -07:00
Neil Fortner
9304f277e8 Add note to RELEASE.txt for HDFFV-11308 (#2029)
* Add note to RELEASE.txt for HDFFV-11308

* Fix formatting error in RELEASE.txt
2022-08-17 13:35:48 -07:00
Dana Robinson
cf482563cc Remove unused dependency files (#2025) 2022-08-17 11:21:03 -07:00
Dana Robinson
d201907a4b Update bin/README.md
Correct missing space after # and ##
2022-08-17 10:46:21 -07:00
Dana Robinson
e4de06057a Adds a TODO section to bin/README.md (#2028)
Mainly to address the semi-broken state of chkcopyright
2022-08-17 10:45:05 -07:00
jhendersonHDF
07efecd9f4 Adjustments to t_bigio.c for >2GiB I/O test (#1992) 2022-08-17 10:44:00 -07:00
Dana Robinson
ecc9bbe4b6 Adds a README.md file to bin that indicates script usage (#2024)
* Adds a README.md file to bin that indicates script usage

* Forgot header row
2022-08-17 09:34:45 -07:00
Dana Robinson
b54d01fcb5 Removes bin/chkconfigure (#2023)
We check autoconf in configure.ac and can check for anything else in
autogen.sh
2022-08-17 09:22:39 -07:00
Dana Robinson
1483eeef34 Removes bin/format_source_patch (#2022)
This differs only trivially from bin/format_source
2022-08-17 09:22:13 -07:00
Dana Robinson
dc9562ee77 Removes the bin/gcov_script file (#2021)
We don't need fragile scripts to run basic profiling programs
2022-08-17 09:21:38 -07:00
Dana Robinson
afc54d75a1 Replaces bin/newer with -nt comparison in Makefiles (#2020) 2022-08-17 09:21:24 -07:00
Dana Robinson
2bba853375 Removes the bin/yodconfigure script which appears unused (#2019) 2022-08-17 08:03:14 -07:00
Dana Robinson
d6927e49c0 Replaced bin/mkdirs w/ mkdir -p -m 755, which is POSIX (#2018) 2022-08-17 08:02:39 -07:00
Dana Robinson
191c27c0a9 Removes the broken bin/errors script (#2017) 2022-08-16 15:42:55 -07:00
bmribler
951566a4ad Fix cpp comment (#2011)
* Fix test failure

Description:
    - Added two H5File constructors to open file with non-default fapl
    - Added non-default fapl to test functions
    - Commented certain renaming attribute tests because of the unexpected
      behavior in renaming an attribute (HDFFV-11327)

Platform tested:
    Linux/64 (jelly)

* Committing clang-format changes

* Update H5File.cpp

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-16 14:06:55 -07:00
Neil Fortner
75f4d9b042 Fix bug in attribute type conversion wiith compound types (#2016)
* Fix bug in attribute type conversion where the background buffer would
not be initialized with the destination contents when necessary.  Other
minor simplification.

* Committing clang-format changes

* Fix warnings.

* Address review comments.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-16 14:04:48 -07:00
bmribler
10e4dd4ef1 Fix c++ test failure (#2005)
* Fix test failure

Description:
    - Added two H5File constructors to open file with non-default fapl
    - Added non-default fapl to test functions
    - Commented certain renaming attribute tests because of the unexpected
      behavior in renaming an attribute (HDFFV-11327)

Platform tested:
    Linux/64 (jelly)

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-12 13:33:30 -05:00
Larry Knox
25ef534039 Update version to 1.13.3-1 after creating hdf5_1_13_2 branch for 1.13.2 (#2004)
release.
Added new version to exceptions in line 75 of src/H5.c.
2022-08-12 08:17:25 -05:00
Larry Knox
029cde6111 Revert "Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for release"
This reverts commit c58558e872.

H5TEST-tcheck_version-release failed.
2022-08-11 22:45:43 -05:00
Larry Knox
c58558e872 Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for release
of HDF5 1.13.2.
2022-08-11 22:15:46 -05:00
1787 changed files with 81650 additions and 46360 deletions

View File

@@ -1,5 +1,4 @@
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

37
.github/CODEOWNERS vendored
View File

@@ -2,41 +2,10 @@
# Each line is a file pattern followed by one or more owners.
# These owners will be the default owners for everything in the repo.
* @lrknox
* @lrknox @derobins @byrnHDF @fortnern @jhendersonHDF @qkoziol @vchoi-hdfgroup @bmribler @raylu-hdf @mattjala @brtnfld
# Order is important. The last matching pattern has the most precedence.
# So if a pull request only touches javascript files, only these owners
# will be requested to review.
*.cmake @byrnHDF @ChristopherHogan @gnuoyd @derobins
CMakeLists.txt @byrnHDF @ChristopherHogan @gnuoyd @derobins
CMakeTests.* @byrnHDF @ChristopherHogan @gnuoyd @derobins
/bin/ @lrknox @ChristopherHogan @gnuoyd @derobins @qkoziol
/c++/ @bmribler @byrnHDF @ChristopherHogan @gnuoyd @derobins
/config/ @lrknox @byrnHDF @ChristopherHogan @gnuoyd @derobins @qkoziol
/doc/ @ChristopherHogan @gnuoyd @jrmainzer
/examples/ @lrknox @bmribler @ChristopherHogan @gnuoyd @derobins
/fortran/ @brtnfld @epourmal
/hl/ @bmribler @byrnHDF @ChristopherHogan @gnuoyd @derobins
/java/ @jhendersonHDF @byrnHDF
/m4/ @lrknox @ChristopherHogan @gnuoyd @derobins
/release_docs/ @lrknox @bmribler @byrnHDF
/src/ @jhendersonHDF @fortnern @soumagne @vchoi-hdfgroup @ChristopherHogan @gnuoyd @derobins @jrmainzer @qkoziol
/test/ @jhendersonHDF @fortnern @soumagne @vchoi-hdfgroup @ChristopherHogan @gnuoyd @derobins @jrmainzer @qkoziol
/testpar/ @jhendersonHDF @ChristopherHogan @gnuoyd @jrmainzer @qkoziol
/tools/ @byrnHDF @bmribler @ChristopherHogan @gnuoyd @derobins
/utils/ @lrknox @byrnHDF @ChristopherHogan @gnuoyd @derobins
/fortran/ @brtnfld @derobins
/java/ @jhendersonHDF @byrnHDF @derobins

View File

@@ -7,7 +7,7 @@ jobs:
runs-on: ubuntu-latest
if: "!contains(github.event.head_commit.message, 'skip-ci')"
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Run clang-format style check for C and Java programs.
uses: DoozyX/clang-format-lint-action@v0.13
with:

View File

@@ -8,7 +8,7 @@ jobs:
runs-on: ubuntu-latest
if: "!contains(github.event.head_commit.message, 'skip-ci')"
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Run clang-format style check for C and Java programs.
uses: DoozyX/clang-format-lint-action@v0.13
with:

View File

@@ -8,8 +8,8 @@ jobs:
name: Check for spelling errors
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- uses: codespell-project/actions-codespell@master
with:
skip: ./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c
skip: ./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c,./config/sanitizer/LICENSE,./tools/test/h5repack/testfiles/*.dat
ignore_words_list: isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,minnum,ake,gord,numer,ro,oce

View File

@@ -4,279 +4,493 @@ name: hdf5 dev CI
on:
workflow_dispatch:
push:
branches: [ develop, hdf5_1_12, hdf5_1_10, hdf5_1_8 ]
pull_request:
branches: [ develop, hdf5_1_14, hdf5_1_12, hdf5_1_10, hdf5_1_8 ]
paths-ignore:
- '.github/CODEOWNERS'
- '.github/FUNDING.yml'
- 'doc/**'
- 'release_docs/**'
- 'ACKNOWLEDGEMENTS'
- 'COPYING**'
- '**.md'
- '.github/CODEOWNERS'
- '.github/FUNDING.yml'
- 'doc/**'
- 'release_docs/**'
- 'ACKNOWLEDGEMENTS'
- 'COPYING**'
- '**.md'
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
# A workflow run is made up of one or more jobs that can run sequentially or
# in parallel. We just have one job, but the matrix items defined below will
# run in parallel.
jobs:
# This workflow contains a single job called "build"
build:
# A workflow that builds the library and runs all the tests
build_and_test:
strategy:
# fail-fast: false
# The current matrix has three dimensions:
#
# * config name
# * thread-safety on/off
# * release vs. debug build
#
# Most configuration information is added via the 'include' mechanism,
# which will append the key-value pairs in the configuration where the
# names match.
matrix:
name: ["Windows Latest MSVC", "Ubuntu Latest GCC", "Ubuntu Debug GCC", "macOS Latest Clang", "Ubuntu Autotools GCC", "Ubuntu Debug Autotools GCC", "-Werror Ubuntu Debug Autotools GCC", "Windows TS MSVC", "Ubuntu TS GCC", "TS Debug GCC", "macOS TS Clang", "TS Autotools GCC"]
name:
- "Windows MSVC CMake"
- "Ubuntu gcc CMake"
- "Ubuntu gcc Autotools"
- "Ubuntu gcc Autotools parallel (build only)"
- "MacOS Clang CMake"
thread_safety:
- enabled: true
text: " TS"
- enabled: false
text: ""
build_mode:
- text: " REL"
cmake: "Release"
autotools: "production"
- text: " DBG"
cmake: "Debug"
autotools: "debug"
# This is where we list the bulk of the options for each configuration.
# The key-value pair values are usually appropriate for being CMake or
# Autotools configure values, so be aware of that.
include:
- name: "Windows Latest MSVC"
artifact: "Windows-MSVC.tar.xz"
# Windows w/ MSVC + CMake
#
# No Fortran, parallel, or VFDs that rely on POSIX things
- name: "Windows MSVC CMake"
os: windows-2022
build_type: "Release"
toolchain: ""
cpp: ON
fortran: OFF
java: ON
ts: OFF
hl: ON
parallel: OFF
mirror_vfd: OFF
direct_vfd: OFF
generator: "-G \"Visual Studio 17 2022\" -A x64"
flags: ""
- name: "Ubuntu Latest GCC"
artifact: "Linux.tar.xz"
run_tests: true
# Linux (Ubuntu) w/ gcc + CMake
#
# We might think about adding Clang, but MacOS already tests that
# so it's not critical
- name: "Ubuntu gcc CMake"
os: ubuntu-latest
build_type: "Release"
cpp: ON
fortran: ON
java: ON
ts: OFF
hl: ON
parallel: OFF
mirror_vfd: ON
direct_vfd: ON
toolchain: "config/toolchain/GCC.cmake"
generator: "-G Ninja"
run_tests: true
# Linux (Ubuntu) w/ gcc + Autotools
#
# Keep this identical to the CMake configs. Note the difference in
# the values.
- name: "Ubuntu gcc Autotools"
os: ubuntu-latest
cpp: enable
fortran: enable
java: enable
parallel: disable
mirror_vfd: enable
direct_vfd: enable
deprec_sym: enable
default_api: v114
szip: yes
toolchain: ""
generator: "autogen"
flags: ""
- name: "macOS Latest Clang"
artifact: "macOS.tar.xz"
os: macos-latest
build_type: "Release"
run_tests: true
# Parallel Linux (Ubuntu) w/ gcc + Autotools
#
# The GitHub runners are inadequate for running parallel HDF5 tests,
# so we catch most issues in daily testing. What we have here is just
# a compile check to make sure nothing obvious is broken.
- name: "Ubuntu gcc Autotools parallel (build only)"
os: ubuntu-latest
cpp: disable
fortran: enable
java: disable
parallel: enable
mirror_vfd: disable
direct_vfd: disable
deprec_sym: enable
default_api: v114
szip: yes
toolchain: ""
generator: "autogen"
flags: "CC=mpicc"
run_tests: false
# MacOS w/ Clang + CMake
#
# We could also build with the Autotools via brew installing them,
# but that seems unnecessary
- name: "MacOS Clang CMake"
os: macos-11
cpp: ON
fortran: OFF
java: ON
ts: OFF
hl: ON
parallel: OFF
mirror_vfd: ON
direct_vfd: OFF
toolchain: "config/toolchain/clang.cmake"
generator: "-G Ninja"
flags: ""
- name: "Ubuntu Debug GCC"
artifact: "LinuxDBG.tar.xz"
run_tests: true
#
# SPECIAL AUTOTOOLS BUILDS
#
# These do not run tests and are not built into the matrix and instead
# become NEW configs as their name would clobber one of the matrix
# names (so make sure the names are UNIQUE).
#
- name: "Ubuntu gcc Autotools v1.6 default API (build only)"
os: ubuntu-latest
build_type: "Debug"
cpp: ON
fortran: OFF
java: OFF
ts: OFF
hl: ON
parallel: OFF
mirror_vfd: ON
direct_vfd: ON
toolchain: "config/toolchain/GCC.cmake"
generator: "-G Ninja"
flags: ""
- name: "Ubuntu Autotools GCC"
artifact: "LinuxA.tar.xz"
os: ubuntu-latest
build_type: "production"
cpp: enable
fortran: enable
java: enable
ts: disable
hl: enable
parallel: disable
mirror_vfd: enable
direct_vfd: enable
deprec_sym: enable
default_api: v16
szip: yes
toolchain: ""
generator: "autogen"
flags: ""
- name: "Ubuntu Debug Autotools GCC"
artifact: "LinuxA.tar.xz"
run_tests: false
thread_safety:
enabled: false
text: ""
build_mode:
text: " DBG"
cmake: "Debug"
autotools: "debug"
- name: "Ubuntu gcc Autotools v1.8 default API (build only)"
os: ubuntu-latest
build_type: "debug"
cpp: enable
fortran: enable
java: enable
ts: disable
hl: enable
parallel: disable
mirror_vfd: enable
direct_vfd: enable
deprec_sym: enable
default_api: v18
szip: yes
toolchain: ""
generator: "autogen"
flags: ""
# Build that ensures no new warnings sneak into the library.
- name: "-Werror Ubuntu Debug Autotools GCC"
artifact: "LinuxA.tar.xz"
run_tests: false
thread_safety:
enabled: false
text: ""
build_mode:
text: " DBG"
cmake: "Debug"
autotools: "debug"
- name: "Ubuntu gcc Autotools v1.10 default API (build only)"
os: ubuntu-latest
cpp: enable
fortran: enable
java: enable
parallel: disable
mirror_vfd: enable
direct_vfd: enable
deprec_sym: enable
default_api: v110
szip: yes
toolchain: ""
generator: "autogen"
flags: ""
run_tests: false
thread_safety:
enabled: false
text: ""
build_mode:
text: " DBG"
cmake: "Debug"
autotools: "debug"
- name: "Ubuntu gcc Autotools v1.12 default API (build only)"
os: ubuntu-latest
cpp: enable
fortran: enable
java: enable
parallel: disable
mirror_vfd: enable
direct_vfd: enable
deprec_sym: enable
default_api: v112
szip: yes
toolchain: ""
generator: "autogen"
flags: ""
run_tests: false
thread_safety:
enabled: false
text: ""
build_mode:
text: " DBG"
cmake: "Debug"
autotools: "debug"
- name: "Ubuntu gcc Autotools v1.14 default API (build only)"
os: ubuntu-latest
cpp: enable
fortran: enable
java: enable
parallel: disable
mirror_vfd: enable
direct_vfd: enable
deprec_sym: enable
default_api: v114
szip: yes
toolchain: ""
generator: "autogen"
flags: ""
run_tests: false
thread_safety:
enabled: false
text: ""
build_mode:
text: " DBG"
cmake: "Debug"
autotools: "debug"
- name: "Ubuntu gcc Autotools no deprecated symbols (build only)"
os: ubuntu-latest
cpp: enable
fortran: enable
java: enable
parallel: disable
mirror_vfd: enable
direct_vfd: enable
deprec_sym: disable
default_api: default
szip: yes
toolchain: ""
generator: "autogen"
flags: ""
run_tests: false
thread_safety:
enabled: false
text: ""
build_mode:
text: " DBG"
cmake: "Debug"
autotools: "debug"
- name: "Ubuntu gcc Autotools -Werror (build only)"
os: ubuntu-latest
build_type: "debug"
cpp: enable
fortran: disable
java: disable
ts: disable
hl: enable
parallel: disable
mirror_vfd: disable
direct_vfd: enable
deprec_sym: enable
default_api: v114
szip: yes
toolchain: ""
generator: "autogen"
flags: "CFLAGS=-Werror"
# Threadsafe runs
- name: "Windows TS MSVC"
artifact: "Windows-MSVCTS.tar.xz"
os: windows-2019
build_type: "Release"
toolchain: ""
cpp: OFF
fortran: OFF
java: OFF
ts: ON
hl: OFF
parallel: OFF
mirror_vfd: OFF
direct_vfd: OFF
generator: "-G \"Visual Studio 16 2019\" -A x64"
flags: ""
- name: "Ubuntu TS GCC"
artifact: "LinuxTS.tar.xz"
run_tests: false
thread_safety:
enabled: false
text: ""
build_mode:
text: " DBG"
cmake: "Debug"
autotools: "debug"
- name: "Ubuntu gcc Autotools -Werror (build only)"
os: ubuntu-latest
build_type: "Release"
cpp: OFF
fortran: OFF
java: OFF
ts: ON
hl: OFF
parallel: OFF
mirror_vfd: ON
direct_vfd: ON
toolchain: "config/toolchain/GCC.cmake"
generator: "-G Ninja"
flags: ""
- name: "macOS TS Clang"
artifact: "macOSTS.tar.xz"
os: macos-latest
build_type: "Release"
cpp: OFF
fortran: OFF
java: OFF
ts: ON
hl: OFF
parallel: OFF
mirror_vfd: ON
direct_vfd: OFF
toolchain: "config/toolchain/clang.cmake"
generator: "-G Ninja"
flags: ""
- name: "TS Debug GCC"
artifact: "LinuxTSDBG.tar.xz"
os: ubuntu-latest
build_type: "Debug"
cpp: OFF
fortran: OFF
java: OFF
ts: ON
hl: OFF
parallel: OFF
mirror_vfd: ON
direct_vfd: ON
toolchain: "config/toolchain/GCC.cmake"
generator: "-G Ninja"
flags: ""
- name: "TS Autotools GCC"
artifact: "LinuxATS.tar.xz"
os: ubuntu-latest
build_type: "production"
cpp: disable
cpp: enable
fortran: disable
java: disable
ts: enable
hl: disable
parallel: disable
mirror_vfd: enable
mirror_vfd: disable
direct_vfd: enable
deprec_sym: enable
default_api: v114
szip: yes
toolchain: ""
generator: "autogen"
flags: ""
flags: "CFLAGS=-Werror"
run_tests: false
thread_safety:
enabled: false
text: ""
build_mode:
text: " REL"
cmake: "Release"
autotools: "production"
# Sets the job's name from the properties
name: "${{ matrix.name }}${{ matrix.build_mode.text }}${{ matrix.thread_safety.text }}"
# Don't run the action if the commit message says to skip CI
if: "!contains(github.event.head_commit.message, 'skip-ci')"
name: ${{ matrix.name }}
# The type of runner that the job will run on
runs-on: ${{ matrix.os }}
if: "!contains(github.event.head_commit.message, 'skip-ci')"
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
- name: Install Dependencies (Linux)
run: sudo apt-get install ninja-build
if: matrix.os == 'ubuntu-latest'
- name: Install Autotools Dependencies (Linux)
run: |
#
# SETUP
#
#Useful for debugging
- name: Dump matrix context
run: echo '${{ toJSON(matrix) }}'
- name: Install CMake Dependencies (Linux)
run: sudo apt-get install ninja-build
if: matrix.os == 'ubuntu-latest'
- name: Install Autotools Dependencies (Linux, serial)
run: |
sudo apt update
sudo apt install automake autoconf libtool libtool-bin
sudo apt install gcc-11 g++-11 gfortran-11
sudo apt install openmpi-bin openmpi-common
if: matrix.generator == 'autogen'
- name: Install Dependencies (Windows)
run: choco install ninja
if: matrix.os == 'windows-latest'
- name: Install Dependencies (macOS)
run: brew install ninja
if: matrix.os == 'macos-latest'
- name: Set environment for MSVC (Windows)
if: matrix.os == 'windows-latest'
run: |
# Set these env vars so cmake picks the correct compiler
echo "CXX=cl.exe" >> $GITHUB_ENV
echo "CC=cl.exe" >> $GITHUB_ENV
echo "CC=gcc-11" >> $GITHUB_ENV
echo "CXX=g++-11" >> $GITHUB_ENV
echo "FC=gfortran-11" >> $GITHUB_ENV
sudo apt install libaec0 libaec-dev
if: (matrix.generator == 'autogen') && (matrix.parallel != 'enable')
- name: Install Autotools Dependencies (Linux, parallel)
run: |
sudo apt update
sudo apt install automake autoconf libtool libtool-bin
sudo apt install openmpi-bin openmpi-common mpi-default-dev
echo "CC=mpicc" >> $GITHUB_ENV
echo "FC=mpif90" >> $GITHUB_ENV
sudo apt install libaec0 libaec-dev
if: (matrix.generator == 'autogen') && (matrix.parallel == 'enable')
- name: Install Dependencies (Windows)
run: choco install ninja
if: matrix.os == 'windows-latest'
- name: Install Dependencies (macOS)
run: brew install ninja
if: matrix.os == 'macos-11'
- name: Set environment for MSVC (Windows)
run: |
# Set these environment variables so CMake picks the correct compiler
echo "CXX=cl.exe" >> $GITHUB_ENV
echo "CC=cl.exe" >> $GITHUB_ENV
if: matrix.os == 'windows-latest'
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- name: Get Sources
uses: actions/checkout@v2
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- name: Get Sources
uses: actions/checkout@v3
- name: Autotools Configure
if: matrix.generator == 'autogen'
run: |
sh ./autogen.sh
mkdir "${{ runner.workspace }}/build"
cd "${{ runner.workspace }}/build"
${{ matrix.flags }} $GITHUB_WORKSPACE/configure --enable-build-mode=${{ matrix.build_type }} --enable-shared --${{ matrix.ts }}-threadsafe --${{ matrix.hl }}-hl --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --${{ matrix.java }}-java --${{ matrix.mirror_vfd }}-mirror-vfd --${{ matrix.direct_vfd }}-direct-vfd
shell: bash
env:
CC: gcc-11
CXX: g++-11
FC: gfortran-11
#
# AUTOTOOLS CONFIGURE
#
- name: Configure
if: matrix.generator != 'autogen'
run: |
mkdir "${{ runner.workspace }}/build"
cd "${{ runner.workspace }}/build"
cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_THREADSAFE:BOOL=${{ matrix.ts }} -DHDF5_BUILD_HL_LIB:BOOL=${{ matrix.hl }} -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=${{ matrix.java }} -DHDF5_ENABLE_MIRROR_VFD:BOOL={{ matrix.mirror_vfd }} -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} $GITHUB_WORKSPACE
shell: bash
- name: Autotools Configure
run: |
sh ./autogen.sh
mkdir "${{ runner.workspace }}/build"
cd "${{ runner.workspace }}/build"
${{ matrix.flags }} $GITHUB_WORKSPACE/configure --enable-build-mode=${{ matrix.build_mode.autotools }} --${{ matrix.deprec_sym }}-deprecated-symbols --with-default-api-version=${{ matrix.default_api }} --enable-shared --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --${{ matrix.java }}-java --${{ matrix.mirror_vfd }}-mirror-vfd --${{ matrix.direct_vfd }}-direct-vfd --with-szlib=${{ matrix.szip }}
shell: bash
if: (matrix.generator == 'autogen') && (! matrix.thread_safe.enabled)
- name: Autotools Build
if: matrix.generator == 'autogen'
run: make
working-directory: ${{ runner.workspace }}/build
- name: Autotools Configure (Thread-Safe)
run: |
sh ./autogen.sh
mkdir "${{ runner.workspace }}/build"
cd "${{ runner.workspace }}/build"
${{ matrix.flags }} $GITHUB_WORKSPACE/configure --enable-build-mode=${{ matrix.build_mode.autotools }} --enable-shared --enable-threadsafe --disable-hl --${{ matrix.parallel }}-parallel --${{ matrix.mirror_vfd }}-mirror-vfd --${{ matrix.direct_vfd }}-direct-vfd --with-szlib=${{ matrix.szip }}
shell: bash
if: (matrix.generator == 'autogen') && (matrix.thread_safe.enabled)
- name: Build
if: matrix.generator != 'autogen'
run: cmake --build . --config ${{ matrix.build_type }}
working-directory: ${{ runner.workspace }}/build
#
# CMAKE CONFIGURE
#
- name: Autotools Test
if: matrix.generator == 'autogen'
run: make check
working-directory: ${{ runner.workspace }}/build
- name: CMake Configure
run: |
mkdir "${{ runner.workspace }}/build"
cd "${{ runner.workspace }}/build"
cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_mode.cmake }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=${{ matrix.java }} -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} $GITHUB_WORKSPACE
shell: bash
if: (matrix.generator != 'autogen') && (! matrix.thread_safe.enabled)
- name: Test
if: matrix.generator != 'autogen'
run: ctest --build . -C ${{ matrix.build_type }} -V
working-directory: ${{ runner.workspace }}/build
- name: CMake Configure (Thread-Safe)
run: |
mkdir "${{ runner.workspace }}/build"
cd "${{ runner.workspace }}/build"
cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_mode.cmake }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_THREADSAFE:BOOL=ON -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_HL_LIB:BOOL=OFF -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} $GITHUB_WORKSPACE
shell: bash
if: (matrix.generator != 'autogen') && (matrix.thread_safe.enabled)
#
# BUILD
#
- name: Autotools Build
run: make
working-directory: ${{ runner.workspace }}/build
if: matrix.generator == 'autogen'
- name: CMake Build
run: cmake --build . --config ${{ matrix.build_mode.cmake }}
working-directory: ${{ runner.workspace }}/build
if: matrix.generator != 'autogen'
#
# RUN TESTS
#
- name: Autotools Run Tests
run: make check
working-directory: ${{ runner.workspace }}/build
if: (matrix.generator == 'autogen') && (matrix.run_tests)
- name: CMake Run Tests
run: ctest --build . -C ${{ matrix.build_mode.cmake }} -V
working-directory: ${{ runner.workspace }}/build
# Skip Debug MSVC while we investigate H5L Java test timeouts
if: (matrix.generator != 'autogen') && (matrix.run_tests) && ! ((matrix.name == 'Windows MSVC CMake') && (matrix.build_mode.cmake == 'Debug'))
#
# INSTALL (note that this runs even when we don't run the tests)
#
- name: Autotools Install
run: make install
working-directory: ${{ runner.workspace }}/build
if: (matrix.generator == 'autogen')
- name: Autotools Verify Install
run: make check-install
working-directory: ${{ runner.workspace }}/build
if: (matrix.generator == 'autogen')

View File

@@ -1,281 +0,0 @@
name: PR hdf5 dev CI
# Controls when the action will run. Triggers the workflow on push or pull request
on:
pull_request:
branches: [ develop, hdf5_1_12, hdf5_1_10, hdf5_1_8 ]
paths-ignore:
- '.github/CODEOWNERS'
- '.github/FUNDING.yml'
- 'doc/**'
- 'release_docs/**'
- 'ACKNOWLEDGEMENTS'
- 'COPYING**'
- '**.md'
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
# This workflow contains a single job called "build"
build:
strategy:
# fail-fast: false
matrix:
name: ["Windows Latest MSVC", "Ubuntu Latest GCC", "Ubuntu Debug GCC", "macOS Latest Clang", "Ubuntu Autotools GCC", "Ubuntu Debug Autotools GCC", "-Werror Ubuntu Debug Autotools GCC", "Windows TS MSVC", "Ubuntu TS GCC", "TS Debug GCC", "macOS TS Clang", "TS Autotools GCC"]
include:
- name: "Windows Latest MSVC"
artifact: "Windows-MSVC.tar.xz"
os: windows-2022
build_type: "Release"
toolchain: ""
cpp: ON
fortran: OFF
java: ON
ts: OFF
hl: ON
parallel: OFF
mirror_vfd: OFF
direct_vfd: OFF
generator: "-G \"Visual Studio 17 2022\" -A x64"
flags: ""
- name: "Ubuntu Latest GCC"
artifact: "Linux.tar.xz"
os: ubuntu-latest
build_type: "Release"
cpp: ON
fortran: ON
java: ON
ts: OFF
hl: ON
parallel: OFF
mirror_vfd: ON
direct_vfd: ON
toolchain: "config/toolchain/GCC.cmake"
generator: "-G Ninja"
flags: ""
- name: "macOS Latest Clang"
artifact: "macOS.tar.xz"
os: macos-latest
build_type: "Release"
cpp: ON
fortran: OFF
java: ON
ts: OFF
hl: ON
parallel: OFF
mirror_vfd: ON
direct_vfd: OFF
toolchain: "config/toolchain/clang.cmake"
generator: "-G Ninja"
flags: ""
- name: "Ubuntu Debug GCC"
artifact: "LinuxDBG.tar.xz"
os: ubuntu-latest
build_type: "Debug"
cpp: ON
fortran: OFF
java: OFF
ts: OFF
hl: ON
parallel: OFF
mirror_vfd: ON
direct_vfd: ON
toolchain: "config/toolchain/GCC.cmake"
generator: "-G Ninja"
flags: ""
- name: "Ubuntu Autotools GCC"
artifact: "LinuxA.tar.xz"
os: ubuntu-latest
build_type: "production"
cpp: enable
fortran: enable
java: enable
ts: disable
hl: enable
parallel: disable
mirror_vfd: enable
direct_vfd: enable
toolchain: ""
generator: "autogen"
flags: ""
- name: "Ubuntu Debug Autotools GCC"
artifact: "LinuxA.tar.xz"
os: ubuntu-latest
build_type: "debug"
cpp: enable
fortran: enable
java: enable
ts: disable
hl: enable
parallel: disable
mirror_vfd: enable
direct_vfd: enable
toolchain: ""
generator: "autogen"
flags: ""
# Build that ensures no new warnings sneak into the library.
- name: "-Werror Ubuntu Debug Autotools GCC"
artifact: "LinuxDBG.tar.xz"
os: ubuntu-latest
build_type: "debug"
cpp: enable
fortran: disable
java: disable
ts: disable
hl: enable
parallel: disable
mirror_vfd: disable
direct_vfd: enable
toolchain: ""
generator: "autogen"
flags: "CFLAGS=-Werror"
# Threadsafe runs
- name: "Windows TS MSVC"
artifact: "Windows-MSVCTS.tar.xz"
os: windows-2019
build_type: "Release"
toolchain: ""
cpp: OFF
fortran: OFF
java: OFF
ts: ON
hl: OFF
parallel: OFF
mirror_vfd: OFF
direct_vfd: OFF
generator: "-G \"Visual Studio 16 2019\" -A x64"
flags: ""
- name: "Ubuntu TS GCC"
artifact: "LinuxTS.tar.xz"
os: ubuntu-latest
build_type: "Release"
cpp: OFF
fortran: OFF
java: OFF
ts: ON
hl: OFF
parallel: OFF
mirror_vfd: ON
direct_vfd: ON
toolchain: "config/toolchain/GCC.cmake"
generator: "-G Ninja"
flags: ""
- name: "macOS TS Clang"
artifact: "macOSTS.tar.xz"
os: macos-latest
build_type: "Release"
cpp: OFF
fortran: OFF
java: OFF
ts: ON
hl: OFF
parallel: OFF
mirror_vfd: ON
direct_vfd: OFF
toolchain: "config/toolchain/clang.cmake"
generator: "-G Ninja"
flags: ""
- name: "TS Debug GCC"
artifact: "LinuxTSDBG.tar.xz"
os: ubuntu-latest
build_type: "Debug"
cpp: OFF
fortran: OFF
java: OFF
ts: ON
hl: OFF
parallel: OFF
mirror_vfd: ON
direct_vfd: ON
toolchain: "config/toolchain/GCC.cmake"
generator: "-G Ninja"
flags: ""
- name: "TS Autotools GCC"
artifact: "LinuxATS.tar.xz"
os: ubuntu-latest
build_type: "production"
cpp: disable
fortran: disable
java: disable
ts: enable
hl: disable
parallel: disable
mirror_vfd: enable
direct_vfd: enable
toolchain: ""
generator: "autogen"
flags: ""
name: ${{ matrix.name }}
# The type of runner that the job will run on
runs-on: ${{ matrix.os }}
if: "!contains(github.event.head_commit.message, 'skip-ci')"
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
- name: Install Dependencies (Linux)
run: sudo apt-get install ninja-build
if: matrix.os == 'ubuntu-latest'
- name: Install Autotools Dependencies (Linux)
run: |
sudo apt update
sudo apt install automake autoconf libtool libtool-bin
sudo apt install gcc-11 g++-11 gfortran-11
sudo apt install openmpi-bin openmpi-common
if: matrix.generator == 'autogen'
- name: Install Dependencies (Windows)
run: choco install ninja
if: matrix.os == 'windows-latest'
- name: Install Dependencies (macOS)
run: brew install ninja
if: matrix.os == 'macos-latest'
- name: Set environment for MSVC (Windows)
if: matrix.os == 'windows-latest'
run: |
# Set these env vars so cmake picks the correct compiler
echo "CXX=cl.exe" >> $GITHUB_ENV
echo "CC=cl.exe" >> $GITHUB_ENV
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- name: Get Sources
uses: actions/checkout@v2
- name: Autotools Configure
if: matrix.generator == 'autogen'
run: |
sh ./autogen.sh
mkdir "${{ runner.workspace }}/build"
cd "${{ runner.workspace }}/build"
${{ matrix.flags }} $GITHUB_WORKSPACE/configure --enable-build-mode=${{ matrix.build_type }} --enable-shared --${{ matrix.ts }}-threadsafe --${{ matrix.hl }}-hl --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --${{ matrix.java }}-java --${{ matrix.mirror_vfd }}-mirror-vfd --${{ matrix.direct_vfd }}-direct-vfd
shell: bash
env:
CC: gcc-11
CXX: g++-11
FC: gfortran-11
- name: Configure
if: matrix.generator != 'autogen'
run: |
mkdir "${{ runner.workspace }}/build"
cd "${{ runner.workspace }}/build"
cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_THREADSAFE:BOOL=${{ matrix.ts }} -DHDF5_BUILD_HL_LIB:BOOL=${{ matrix.hl }} -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=${{ matrix.java }} -DHDF5_ENABLE_MIRROR_VFD:BOOL={{ matrix.mirror_vfd }} -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} $GITHUB_WORKSPACE
shell: bash
- name: Autotools Build
if: matrix.generator == 'autogen'
run: make
working-directory: ${{ runner.workspace }}/build
- name: Build
if: matrix.generator != 'autogen'
run: cmake --build . --config ${{ matrix.build_type }}
working-directory: ${{ runner.workspace }}/build
- name: Autotools Test
if: matrix.generator == 'autogen'
run: make check
working-directory: ${{ runner.workspace }}/build
- name: Test
if: matrix.generator != 'autogen'
run: ctest --build . -C ${{ matrix.build_type }} -V
working-directory: ${{ runner.workspace }}/build

View File

@@ -1,5 +1,4 @@
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -33,9 +33,7 @@ if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MAT
set (ZLIB_URL ${TGZPATH}/${ZLIB_TGZ_NAME})
if (NOT EXISTS "${ZLIB_URL}")
set (HDF5_ENABLE_Z_LIB_SUPPORT OFF CACHE BOOL "" FORCE)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter ZLIB file ${ZLIB_URL} not found")
endif ()
message (VERBOSE "Filter ZLIB file ${ZLIB_URL} not found")
endif ()
set (SZIP_URL ${TGZPATH}/${SZIP_TGZ_NAME})
if (USE_LIBAEC)
@@ -43,9 +41,7 @@ if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MAT
endif ()
if (NOT EXISTS "${SZIP_URL}")
set (HDF5_ENABLE_SZIP_SUPPORT OFF CACHE BOOL "" FORCE)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter SZIP file ${SZIP_URL} not found")
endif ()
message (VERBOSE "Filter SZIP file ${SZIP_URL} not found")
endif ()
else ()
set (ZLIB_USE_EXTERNAL 0)
@@ -81,9 +77,7 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT)
set (H5_HAVE_FILTER_DEFLATE 1)
set (H5_HAVE_ZLIB_H 1)
set (H5_HAVE_LIBZ 1)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter HDF5_ZLIB is built")
endif ()
message (VERBOSE "Filter HDF5_ZLIB is built")
else ()
message (FATAL_ERROR " ZLib is Required for ZLib support in HDF5")
endif ()
@@ -99,9 +93,7 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT)
endif ()
set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_STATIC_LIBRARY})
INCLUDE_DIRECTORIES (${ZLIB_INCLUDE_DIRS})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter HDF5_ZLIB is ON")
endif ()
message (VERBOSE "Filter HDF5_ZLIB is ON")
endif ()
#-----------------------------------------------------------------------------
@@ -142,13 +134,9 @@ if (HDF5_ENABLE_SZIP_SUPPORT)
set (H5_HAVE_FILTER_SZIP 1)
set (H5_HAVE_SZLIB_H 1)
set (H5_HAVE_LIBSZ 1)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter SZIP is built")
endif ()
message (VERBOSE "Filter SZIP is built")
if (USE_LIBAEC)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "... with library AEC")
endif ()
message (VERBOSE "... with library AEC")
set (SZIP_PACKAGE_NAME ${LIBAEC_PACKAGE_NAME})
else ()
set (SZIP_PACKAGE_NAME ${SZIP_PACKAGE_NAME})
@@ -159,9 +147,7 @@ if (HDF5_ENABLE_SZIP_SUPPORT)
endif ()
set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_STATIC_LIBRARY})
INCLUDE_DIRECTORIES (${SZIP_INCLUDE_DIRS})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter SZIP is ON")
endif ()
message (VERBOSE "Filter SZIP is ON")
if (H5_HAVE_FILTER_SZIP)
set (EXTERNAL_FILTERS "${EXTERNAL_FILTERS} DECODE")
endif ()

View File

@@ -242,7 +242,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED)
endif ()
install (
FILES ${release_files}
DESTINATION ${HDF5_INSTALL_DATA_DIR}
DESTINATION ${HDF5_INSTALL_DOC_DIR}
COMPONENT hdfdocuments
)
endif ()
@@ -273,7 +273,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
else ()
set (CPACK_PACKAGE_INSTALL_DIRECTORY "${CPACK_PACKAGE_VENDOR}/${CPACK_PACKAGE_NAME}/${CPACK_PACKAGE_VERSION}")
endif ()
set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_EXT_DIR}/hdf.bmp")
set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_DIR}/hdf.bmp")
set (CPACK_GENERATOR "TGZ")
if (WIN32)
@@ -296,10 +296,10 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
endif ()
# set the install/unistall icon used for the installer itself
# There is a bug in NSI that does not handle full unix paths properly.
set (CPACK_NSIS_MUI_ICON "${HDF_RESOURCES_EXT_DIR}\\\\hdf.ico")
set (CPACK_NSIS_MUI_UNIICON "${HDF_RESOURCES_EXT_DIR}\\\\hdf.ico")
set (CPACK_NSIS_MUI_ICON "${HDF_RESOURCES_DIR}\\\\hdf.ico")
set (CPACK_NSIS_MUI_UNIICON "${HDF_RESOURCES_DIR}\\\\hdf.ico")
# set the package header icon for MUI
set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_EXT_DIR}\\\\hdf.bmp")
set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_DIR}\\\\hdf.bmp")
set (CPACK_NSIS_DISPLAY_NAME "${CPACK_NSIS_PACKAGE_NAME}")
if (OVERRIDE_INSTALL_VERSION)
set (CPACK_PACKAGE_INSTALL_DIRECTORY "${CPACK_PACKAGE_VENDOR}\\\\${CPACK_PACKAGE_NAME}\\\\${OVERRIDE_INSTALL_VERSION}")
@@ -329,7 +329,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
set (CPACK_RESOURCE_FILE_LICENSE "${HDF5_BINARY_DIR}/COPYING.txt")
# .. variable:: CPACK_WIX_PRODUCT_ICON
# The Icon shown next to the program name in Add/Remove programs.
set(CPACK_WIX_PRODUCT_ICON "${HDF_RESOURCES_EXT_DIR}\\\\hdf.ico")
set(CPACK_WIX_PRODUCT_ICON "${HDF_RESOURCES_DIR}\\\\hdf.ico")
#
# .. variable:: CPACK_WIX_UI_BANNER
#
@@ -360,14 +360,14 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
list (APPEND CPACK_GENERATOR "DragNDrop")
set (CPACK_COMPONENTS_ALL_IN_ONE_PACKAGE ON)
set (CPACK_PACKAGING_INSTALL_PREFIX "/${CPACK_PACKAGE_INSTALL_DIRECTORY}")
set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_EXT_DIR}/hdf.icns")
set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_DIR}/hdf.icns")
option (HDF5_PACK_MACOSX_FRAMEWORK "Package the HDF5 Library in a Frameworks" OFF)
if (HDF5_PACK_MACOSX_FRAMEWORK AND HDF5_BUILD_FRAMEWORKS)
set (CPACK_BUNDLE_NAME "${HDF5_PACKAGE_STRING}")
set (CPACK_BUNDLE_LOCATION "/") # make sure CMAKE_INSTALL_PREFIX ends in /
set (CMAKE_INSTALL_PREFIX "/${CPACK_BUNDLE_NAME}.framework/Versions/${CPACK_PACKAGE_VERSION}/${CPACK_PACKAGE_NAME}/")
set (CPACK_BUNDLE_ICON "${HDF_RESOURCES_EXT_DIR}/hdf.icns")
set (CPACK_BUNDLE_ICON "${HDF_RESOURCES_DIR}/hdf.icns")
set (CPACK_BUNDLE_PLIST "${HDF5_BINARY_DIR}/CMakeFiles/Info.plist")
set (CPACK_SHORT_VERSION_STRING "${CPACK_PACKAGE_VERSION}")
#-----------------------------------------------------------------------------
@@ -382,7 +382,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
${HDF5_BINARY_DIR}/CMakeFiles/PkgInfo @ONLY
)
configure_file (
${HDF_RESOURCES_EXT_DIR}/version.plist.in
${HDF_RESOURCES_DIR}/version.plist.in
${HDF5_BINARY_DIR}/CMakeFiles/version.plist @ONLY
)
install (

View File

@@ -1,4 +1,4 @@
cmake_minimum_required (VERSION 3.12)
cmake_minimum_required (VERSION 3.18)
project (HDF5 C)
if (POLICY CMP0074)
@@ -12,6 +12,11 @@ if (POLICY CMP0083)
cmake_policy (SET CMP0083 NEW)
endif ()
# Avoid warning about DOWNLOAD_EXTRACT_TIMESTAMP in CMake 3.24:
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.24.0")
cmake_policy(SET CMP0135 NEW)
endif()
#-----------------------------------------------------------------------------
# Instructions for use : Normal Build
#
@@ -39,16 +44,6 @@ if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
)
endif ()
# CMake version 3.14 added option --ignore-eol to compare files
# cmake -E compare_files --ignore-eol file1 file2
set (CMAKE_IGNORE_EOL "--ignore-eol")
if (CMAKE_VERSION VERSION_LESS "3.14.0")
set (CMAKE_IGNORE_EOL "")
if (WIN32)
message (FATAL_ERROR "Windows builds require a minimum of CMake 3.14")
endif()
endif ()
#-----------------------------------------------------------------------------
# Instructions for use : Sub-Project Build
#
@@ -215,7 +210,6 @@ set (HDF5_HL_F90_C_LIBSH_TARGET "${HDF5_HL_F90_C_LIB_CORENAME}-shared")
#-----------------------------------------------------------------------------
set (HDF_CONFIG_DIR ${HDF5_SOURCE_DIR}/config)
set (HDF_RESOURCES_DIR ${HDF5_SOURCE_DIR}/config/cmake)
set (HDF_RESOURCES_EXT_DIR ${HDF5_SOURCE_DIR}/config/cmake_ext_mod)
set (HDF5_SRC_DIR ${HDF5_SOURCE_DIR}/src)
set (HDF5_TEST_SRC_DIR ${HDF5_SOURCE_DIR}/test)
set (HDF5_CPP_SRC_DIR ${HDF5_SOURCE_DIR}/c++)
@@ -251,9 +245,7 @@ string (REGEX REPLACE ".*#define[ \t]+H5_VERS_RELEASE[ \t]+([0-9]*).*$"
"\\1" H5_VERS_RELEASE ${_h5public_h_contents})
string (REGEX REPLACE ".*#define[ \t]+H5_VERS_SUBRELEASE[ \t]+\"([0-9A-Za-z._-]*)\".*$"
"\\1" H5_VERS_SUBRELEASE ${_h5public_h_contents})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (TRACE "VERSION: ${H5_VERS_MAJOR}.${H5_VERS_MINOR}.${H5_VERS_RELEASE}-${H5_VERS_SUBRELEASE}")
endif ()
message (TRACE "VERSION: ${H5_VERS_MAJOR}.${H5_VERS_MINOR}.${H5_VERS_RELEASE}-${H5_VERS_SUBRELEASE}")
#-----------------------------------------------------------------------------
# parse the full soversion number from config/lt_vers.am and include in H5_SOVERS_INFO
@@ -266,9 +258,7 @@ string (REGEX REPLACE ".*LT_VERS_REVISION[ \t]+=[ \t]+([0-9]*).*$"
string (REGEX REPLACE ".*LT_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
"\\1" H5_LIB_SOVERS_RELEASE ${_lt_vers_am_contents})
math (EXPR H5_LIB_SOVERS_MAJOR ${H5_LIB_SOVERS_INTERFACE}-${H5_LIB_SOVERS_RELEASE})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "SOVERSION: ${H5_LIB_SOVERS_MAJOR}.${H5_LIB_SOVERS_RELEASE}.${H5_LIB_SOVERS_MINOR}")
endif ()
message (VERBOSE "SOVERSION: ${H5_LIB_SOVERS_MAJOR}.${H5_LIB_SOVERS_RELEASE}.${H5_LIB_SOVERS_MINOR}")
string (REGEX MATCH ".*LT_TOOLS_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_TOOLS_SOVERS_EXISTS ${_lt_vers_am_contents})
if (H5_TOOLS_SOVERS_EXISTS)
string (REGEX REPLACE ".*LT_TOOLS_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$"
@@ -278,9 +268,7 @@ if (H5_TOOLS_SOVERS_EXISTS)
string (REGEX REPLACE ".*LT_TOOLS_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
"\\1" H5_TOOLS_SOVERS_RELEASE ${_lt_vers_am_contents})
math (EXPR H5_TOOLS_SOVERS_MAJOR ${H5_TOOLS_SOVERS_INTERFACE}-${H5_TOOLS_SOVERS_RELEASE})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "SOVERSION_TOOLS: ${H5_TOOLS_SOVERS_MAJOR}.${H5_TOOLS_SOVERS_RELEASE}.${H5_TOOLS_SOVERS_MINOR}")
endif ()
message (VERBOSE "SOVERSION_TOOLS: ${H5_TOOLS_SOVERS_MAJOR}.${H5_TOOLS_SOVERS_RELEASE}.${H5_TOOLS_SOVERS_MINOR}")
endif ()
string (REGEX MATCH ".*LT_CXX_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_CXX_SOVERS_EXISTS ${_lt_vers_am_contents})
if (H5_CXX_SOVERS_EXISTS)
@@ -291,9 +279,7 @@ if (H5_CXX_SOVERS_EXISTS)
string (REGEX REPLACE ".*LT_CXX_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
"\\1" H5_CXX_SOVERS_RELEASE ${_lt_vers_am_contents})
math (EXPR H5_CXX_SOVERS_MAJOR ${H5_CXX_SOVERS_INTERFACE}-${H5_CXX_SOVERS_RELEASE})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "SOVERSION_CXX: ${H5_CXX_SOVERS_MAJOR}.${H5_CXX_SOVERS_RELEASE}.${H5_CXX_SOVERS_MINOR}")
endif ()
message (VERBOSE "SOVERSION_CXX: ${H5_CXX_SOVERS_MAJOR}.${H5_CXX_SOVERS_RELEASE}.${H5_CXX_SOVERS_MINOR}")
endif ()
string (REGEX MATCH ".*LT_F_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_F_SOVERS_EXISTS ${_lt_vers_am_contents})
if (H5_F_SOVERS_EXISTS)
@@ -304,9 +290,7 @@ if (H5_F_SOVERS_EXISTS)
string (REGEX REPLACE ".*LT_F_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
"\\1" H5_F_SOVERS_RELEASE ${_lt_vers_am_contents})
math (EXPR H5_F_SOVERS_MAJOR ${H5_F_SOVERS_INTERFACE}-${H5_F_SOVERS_RELEASE})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "SOVERSION_F: ${H5_F_SOVERS_MAJOR}.${H5_F_SOVERS_RELEASE}.${H5_F_SOVERS_MINOR}")
endif ()
message (VERBOSE "SOVERSION_F: ${H5_F_SOVERS_MAJOR}.${H5_F_SOVERS_RELEASE}.${H5_F_SOVERS_MINOR}")
endif ()
string (REGEX MATCH ".*LT_HL_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_HL_SOVERS_EXISTS ${_lt_vers_am_contents})
if (H5_HL_SOVERS_EXISTS)
@@ -317,9 +301,7 @@ if (H5_HL_SOVERS_EXISTS)
string (REGEX REPLACE ".*LT_HL_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
"\\1" H5_HL_SOVERS_RELEASE ${_lt_vers_am_contents})
math (EXPR H5_HL_SOVERS_MAJOR ${H5_HL_SOVERS_INTERFACE}-${H5_HL_SOVERS_RELEASE})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "SOVERSION_HL: ${H5_HL_SOVERS_MAJOR}.${H5_HL_SOVERS_RELEASE}.${H5_HL_SOVERS_MINOR}")
endif ()
message (VERBOSE "SOVERSION_HL: ${H5_HL_SOVERS_MAJOR}.${H5_HL_SOVERS_RELEASE}.${H5_HL_SOVERS_MINOR}")
endif ()
string (REGEX MATCH ".*LT_HL_CXX_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_HL_CXX_SOVERS_EXISTS ${_lt_vers_am_contents})
if (H5_HL_CXX_SOVERS_EXISTS)
@@ -330,9 +312,7 @@ if (H5_HL_CXX_SOVERS_EXISTS)
string (REGEX REPLACE ".*LT_HL_CXX_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
"\\1" H5_HL_CXX_SOVERS_RELEASE ${_lt_vers_am_contents})
math (EXPR H5_HL_CXX_SOVERS_MAJOR ${H5_HL_CXX_SOVERS_INTERFACE}-${H5_HL_CXX_SOVERS_RELEASE})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "SOVERSION_HL_CXX: ${H5_HL_CXX_SOVERS_MAJOR}.${H5_HL_CXX_SOVERS_RELEASE}.${H5_HL_CXX_SOVERS_MINOR}")
endif ()
message (VERBOSE "SOVERSION_HL_CXX: ${H5_HL_CXX_SOVERS_MAJOR}.${H5_HL_CXX_SOVERS_RELEASE}.${H5_HL_CXX_SOVERS_MINOR}")
endif ()
string (REGEX MATCH ".*LT_HL_F_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_HL_F_SOVERS_EXISTS ${_lt_vers_am_contents})
if (H5_HL_F_SOVERS_EXISTS)
@@ -343,9 +323,7 @@ if (H5_HL_F_SOVERS_EXISTS)
string (REGEX REPLACE ".*LT_HL_F_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
"\\1" H5_HL_F_SOVERS_RELEASE ${_lt_vers_am_contents})
math (EXPR H5_HL_F_SOVERS_MAJOR ${H5_HL_F_SOVERS_INTERFACE}-${H5_HL_F_SOVERS_RELEASE})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "SOVERSION_HL_F: ${H5_HL_F_SOVERS_MAJOR}.${H5_HL_F_SOVERS_RELEASE}.${H5_HL_F_SOVERS_MINOR}")
endif ()
message (VERBOSE "SOVERSION_HL_F: ${H5_HL_F_SOVERS_MAJOR}.${H5_HL_F_SOVERS_RELEASE}.${H5_HL_F_SOVERS_MINOR}")
endif ()
string (REGEX MATCH ".*LT_JAVA_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_JAVA_SOVERS_EXISTS ${_lt_vers_am_contents})
if(H5_JAVA_SOVERS_EXISTS)
@@ -356,9 +334,7 @@ if(H5_JAVA_SOVERS_EXISTS)
string (REGEX REPLACE ".*LT_JAVA_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
"\\1" H5_JAVA_SOVERS_RELEASE ${_lt_vers_am_contents})
math (EXPR H5_JAVA_SOVERS_MAJOR ${H5_JAVA_SOVERS_INTERFACE}-${H5_JAVA_SOVERS_RELEASE})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "SOVERSION_JAVA: ${H5_JAVA_SOVERS_MAJOR}.${H5_JAVA_SOVERS_RELEASE}.${H5_JAVA_SOVERS_MINOR}")
endif ()
message (VERBOSE "SOVERSION_JAVA: ${H5_JAVA_SOVERS_MAJOR}.${H5_JAVA_SOVERS_RELEASE}.${H5_JAVA_SOVERS_MINOR}")
endif ()
#-----------------------------------------------------------------------------
@@ -435,11 +411,11 @@ set (HDF5_PACKAGE_BUGREPORT "help@hdfgroup.org")
#-----------------------------------------------------------------------------
# Include some macros for reusable code
#-----------------------------------------------------------------------------
include (${HDF_RESOURCES_EXT_DIR}/HDFMacros.cmake)
include (${HDF_RESOURCES_DIR}/HDFMacros.cmake)
HDF_DIR_PATHS(${HDF5_PACKAGE_NAME})
include (${HDF_RESOURCES_EXT_DIR}/HDFLibMacros.cmake)
include (${HDF_RESOURCES_DIR}/HDFLibMacros.cmake)
include (${HDF_RESOURCES_DIR}/HDF5PluginMacros.cmake)
include (${HDF_RESOURCES_DIR}/HDF5Macros.cmake)
@@ -567,15 +543,6 @@ if (HDF5_ENABLE_COVERAGE)
endif ()
endif ()
#-----------------------------------------------------------------------------
# Option to indicate using dmalloc
#-----------------------------------------------------------------------------
# option (HDF5_ENABLE_USING_DMALLOC "Indicate that dmalloc is used" OFF)
# if (HDF5_ENABLE_USING_DMALLOC)
# find_package (DMALLOC)
# set (H5_HAVE_DMALLOC DMALLOC_FOUND)
# endif ()
#-----------------------------------------------------------------------------
# Option to indicate using a memory checker
#-----------------------------------------------------------------------------
@@ -584,14 +551,6 @@ if (HDF5_ENABLE_USING_MEMCHECKER)
set (H5_USING_MEMCHECKER 1)
endif ()
#-----------------------------------------------------------------------------
# Option to indicate internal memory allocation sanity checks are enabled
#-----------------------------------------------------------------------------
option (HDF5_MEMORY_ALLOC_SANITY_CHECK "Indicate that internal memory allocation sanity checks are enabled" OFF)
if (HDF5_MEMORY_ALLOC_SANITY_CHECK)
set (H5_MEMORY_ALLOC_SANITY_CHECK 1)
endif ()
#-----------------------------------------------------------------------------
# Option to enable/disable using pread/pwrite for VFDs
#-----------------------------------------------------------------------------
@@ -659,6 +618,13 @@ if (${HDF_CFG_NAME} MATCHES "Debug")
mark_as_advanced (HDF5_ENABLE_INSTRUMENT)
endif ()
#-----------------------------------------------------------------------------
# Add some definitions for Developer Builds
#-----------------------------------------------------------------------------
if (${HDF_CFG_NAME} MATCHES "Developer")
include (${HDF_RESOURCES_DIR}/HDF5DeveloperBuild.cmake)
endif ()
#-----------------------------------------------------------------------------
# Option to embed library info into executables
#-----------------------------------------------------------------------------
@@ -672,7 +638,7 @@ else ()
endif ()
include (${HDF_RESOURCES_DIR}/HDFCompilerFlags.cmake)
set (CMAKE_MODULE_PATH ${HDF_RESOURCES_DIR} ${HDF_RESOURCES_EXT_DIR} ${CMAKE_MODULE_PATH})
set (CMAKE_MODULE_PATH ${HDF_RESOURCES_DIR} ${HDF_RESOURCES_DIR} ${CMAKE_MODULE_PATH})
#-----------------------------------------------------------------------------
# Option to Enable HDFS
@@ -757,6 +723,12 @@ option (HDF5_ENABLE_SUBFILING_VFD "Build Parallel HDF5 Subfiling VFD" OFF)
if (HDF5_ENABLE_SUBFILING_VFD)
if (NOT HDF5_ENABLE_PARALLEL)
message (FATAL_ERROR "Subfiling VFD requires a parallel HDF5 build")
else ()
# Check for MPI_Comm_split_type
CHECK_SYMBOL_EXISTS (MPI_Comm_split_type "mpi.h" H5_HAVE_MPI_Comm_split_type)
if (NOT H5_HAVE_MPI_Comm_split_type)
message (FATAL_ERROR "Subfiling VFD requires MPI-3 support for MPI_Comm_split_type")
endif ()
endif()
if (NOT DEFINED Threads_FOUND)
@@ -840,6 +812,17 @@ if (DEFAULT_API_VERSION MATCHES "v114")
set (H5_USE_114_API_DEFAULT 1)
endif ()
#-----------------------------------------------------------------------------
# Option to use 1.16.x API
#-----------------------------------------------------------------------------
if (NOT DEFAULT_API_VERSION)
set (DEFAULT_API_VERSION "v116")
endif ()
set (H5_USE_116_API_DEFAULT 0)
if (DEFAULT_API_VERSION MATCHES "v116")
set (H5_USE_116_API_DEFAULT 1)
endif ()
#-----------------------------------------------------------------------------
# Include user macros
#-----------------------------------------------------------------------------
@@ -874,42 +857,32 @@ option (HDF5_ENABLE_THREADSAFE "Enable thread-safety" OFF)
if (HDF5_ENABLE_THREADSAFE)
# check for unsupported options
if (WIN32)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE " **** thread-safety option not supported with static library **** ")
message (VERBOSE " **** thread-safety option will not be used building static library **** ")
endif ()
message (VERBOSE " **** thread-safety option not supported with static library **** ")
message (VERBOSE " **** thread-safety option will not be used building static library **** ")
endif ()
if (HDF5_BUILD_FORTRAN)
if (NOT ALLOW_UNSUPPORTED)
message (FATAL_ERROR " **** Fortran and thread-safety options are not supported, override with ALLOW_UNSUPPORTED option **** ")
else ()
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE " **** Allowing unsupported Fortran and thread-safety options **** ")
endif ()
message (VERBOSE " **** Allowing unsupported Fortran and thread-safety options **** ")
endif ()
endif ()
if (HDF5_BUILD_CPP_LIB)
if (NOT ALLOW_UNSUPPORTED)
message (FATAL_ERROR " **** C++ and thread-safety options are not supported, override with ALLOW_UNSUPPORTED option **** ")
else ()
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE " **** Allowing unsupported C++ and thread-safety options **** ")
endif ()
message (VERBOSE " **** Allowing unsupported C++ and thread-safety options **** ")
endif ()
endif ()
if (HDF5_BUILD_HL_LIB)
if (NOT ALLOW_UNSUPPORTED)
message (FATAL_ERROR " **** HL and thread-safety options are not supported, override with ALLOW_UNSUPPORTED option **** ")
else ()
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE " **** Allowing unsupported HL and thread-safety options **** ")
endif ()
message (VERBOSE " **** Allowing unsupported HL and thread-safety options **** ")
endif ()
endif ()
if (H5_HAVE_IOEO)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE " **** Win32 threads requires WINVER>=0x600 (Windows Vista/7/8) **** ")
endif ()
message (VERBOSE " **** Win32 threads requires WINVER>=0x600 (Windows Vista/7/8) **** ")
set (H5_HAVE_WIN_THREADS 1)
else ()
if (NOT H5_HAVE_PTHREAD_H)
@@ -1141,11 +1114,9 @@ set (H5_FC_FUNC_ "H5_FC_FUNC_(name,NAME) name ## _")
if (EXISTS "${HDF5_SOURCE_DIR}/fortran" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/fortran")
option (HDF5_BUILD_FORTRAN "Build FORTRAN support" OFF)
if (HDF5_BUILD_FORTRAN)
include (${HDF_RESOURCES_EXT_DIR}/HDFUseFortran.cmake)
include (${HDF_RESOURCES_DIR}/HDFUseFortran.cmake)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Fortran compiler ID is ${CMAKE_Fortran_COMPILER_ID}")
endif ()
message (VERBOSE "Fortran compiler ID is ${CMAKE_Fortran_COMPILER_ID}")
include (${HDF_RESOURCES_DIR}/HDFFortranCompilerFlags.cmake)
include (${HDF_RESOURCES_DIR}/HDF5UseFortran.cmake)
set (LINK_Fortran_LIBS ${LINK_LIBS})
@@ -1156,6 +1127,7 @@ if (EXISTS "${HDF5_SOURCE_DIR}/fortran" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/for
# Parallel IO usage requires MPI to be Linked and Included
if (H5_HAVE_PARALLEL)
find_package(MPI REQUIRED COMPONENTS Fortran)
set (LINK_Fortran_LIBS ${LINK_Fortran_LIBS} ${MPI_Fortran_LIBRARIES})
if (MPI_Fortran_LINK_FLAGS)
set (CMAKE_Fortran_EXE_LINKER_FLAGS "${MPI_Fortran_LINK_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
@@ -1194,9 +1166,7 @@ if (EXISTS "${HDF5_SOURCE_DIR}/c++" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/c++")
if (NOT ALLOW_UNSUPPORTED)
message (FATAL_ERROR " **** Parallel and C++ options are mutually exclusive, override with ALLOW_UNSUPPORTED option **** ")
else ()
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE " **** Allowing unsupported Parallel and C++ options **** ")
endif ()
message (VERBOSE " **** Allowing unsupported Parallel and C++ options **** ")
endif ()
endif ()

142
CONTRIBUTING.md Normal file
View File

@@ -0,0 +1,142 @@
# How to contribute to HDF5
The HDF Group encourages community members to contribute to the HDF5 project. We accept and are very grateful for any contributions,
from minor typos and bug fixes to new features. The HDF Group is committed to work with the code contributors and make contribution
process enjoyable and straightforward.
This document describes guiding principles for the HDF5 code contributors and does not pretend to address any possible
contribution. If in doubt, please do not hesitate to ask us for guidance.
***Note that no contribution may be accepted unless the donor agrees with the HDF Group software license terms
found in the COPYING file in every branch's top source directory.***
> We will assume that you are familiar with `git` and `GitHub`. If not, you may go through the GitHub tutorial found at
[https://guides.github.com/activities/hello-world/](https://guides.github.com/activities/hello-world/). This tutorial should only take
around 10 minutes.
## Table of Contents
* [Workflow](#workflow)
* [Acceptance criteria for a pull request](#criteria)
* [Release Note](#releasenote)
* [Check List](#checklist)
# Workflow <A NAME="workflow"></A>
The process for contributing code to HDF5 is as follows:
* Open an issue on [HDF5 GitHub](https://github.com/HDFGroup/hdf5/issues).
> This step is ***required*** unless the change is minor (e.g., typo fix).
* Fork the [HDF5](https://github.com/HDFGroup/hdf5) repository.
* Make the desired changes to the HDF5 software.
* New features should always go to _develop_ branch first and later should be merged to the appropriate maintenance branches.
* Bug fixes should go to all appropriate branches (_develop_ and maintenance).
* Build and test your changes. Detailed instructions on building and testing HDF5 can be found in the `INSTALL*` files in the `release_docs` directory.
* Push your changes to GitHub.
* Issue a pull request and address any code formatting and testing issues reported.
Once a pull request is correctly formatted and passes **ALL** CI tests, it will be reviewed and evaluated by The HDF Group developers and HDF5
community members who can approve pull requests. The HDF Group developers will work with you to ensure that the pull request satisfies the acceptance
criteria described in the next section.
# Acceptance criteria for a pull request <A NAME="criteria"></A>
We appreciate every contribution we receive, but we may not accept them all. Those that we *do* satisfy the following criteria:
* **The pull request has a clear purpose** - What does the pull request address? How does it benefit the HDF5 community?
If the pull request does not have a clear purpose and benefits, it will not be accepted.
* **The pull request is documented** - The HDF5 developers must understand not only *what* a change is doing, but *how* it is doing it.
Documenting the code makes it easier for us to understand your patch and maintain the code in the future.
* **The pull request passes HDF5 regression testing** - Any issue fixed or functionality added should be accompanied by the corresponding
tests and pass HDF5 regression testing run by The HDF Group. We do not expect you to perform comprehensive testing across multiple platforms
before we accept the pull request. If the pull request does not pass regression testing after the merge, The HDF Group developers will work
with you on the fixes.
* **The pull request does not compromise the principles behind HDF5** - HDF5 has a 100% commitment to backward compatibility.
* Any file ever created with HDF5 must be readable by any future version of HDF5.
If your patch's purpose is to modify the HDF5 data model or file format,
**please** discuss this with us first. File format changes and features required by those changes can be introduced only in a new major release.
* HDF5 has a commitment to remaining *machine-independent*; data created on one platform/environment/architecture **must** remain readable by HDF5 on any other.
* For binary compatibility, no changes are allowed to public APIs and data structures in the maintenance releases; new APIs can be added.
* **New features are documented** - Any new features should have proper documentation; talk to us if you have any questions.
* **When to Write a Release Note** - Generally, a release note must be written for every change that is made to the code for which
users might see a change in the way the software works. In other words, if a user might see a difference in the way the software works,
a note should be written. By code we mean the text that will be compiled into one of the company's software products. The code includes
configuration changes and changes to tools users might work with to configure and build our software.
* Notes should be added for known problems. Known problems are issues that we know about and have not yet been able to fix.
* Any change made to address a user-reported problem should be described in a release note.
* A release note does not need to be written for changes to the code that users will not see. Here are some examples. If you add a
comment, you do not need to write a release note describing the comment you added. If you rewrite some code to make it read more
clearly and if there is no change in functionality or performance, then you do not need to write a release note. If you change the
process by which user software is made, you may not need to write a release note since the change was not made to the code.
* Users. We have different kinds of users. A release note may be written to be helpful to
application developers and not system administrators. Users who may find the RELEASE.txt file helpful include the following:
application developers, library developers, and system administrators.
# Release Note <A NAME="releasenote"></A>
* **Entry Syntax**
The release note entry syntax is shown below.
```
- Title/Problem
Problem/Solution
Signature
```
* **Entry Elements** - The elements of the entry - title, problem, solution, and signature - are described in more detail in the table
below. Descriptions of the problem and the solution should be clear without any ambiguities and should be short without losing clarity or specifics.
* **Title** - The title or tag should identify one or more categories that will help readers decide if the entry is something they need to study. Can be combined with the `Problem` element
* **Problem** - Describe the problem and how users might see the problem in a paragraph.
You might also consider the following as you describe the problem:
* Under what specific conditions does this issue arise?
* Under what specific conditions are we sure this issue will not arise?
* For a performance issue, instead of saying something is a performance issue, describe what the performance impact of issue is?
* **Solution** - Describe the solution in another paragraph.
You might also consider the following as you describe the solution:
* What was done to resolve the issue?
* What is the functional impact?
* Is there a workaround a way for users design their software so as not to encounter the issue? If so, what is the workaround?
* For a performance fix, how has the performance improved? Links to published documentation would be good.
* **Signature** - Each entry must be signed with the initials of the author, the date in YYYY/MM/DD format, and the JIRA ticket number. The
following is an example entry written by developer Xavier Zolo on April 16, 2014 about JIRA ticket HDFFV-5555: (XYZ - 2014/04/16, HDFFV-5555). The
signature is enclosed in parentheses. JIRA or Github numbers should not be used in the description of the problem or the solution. They are like
abbreviations that customers and external users will not be able to interpret.
# Checklist <A NAME="checklist"></A>
Please make sure that you check the items applicable to your pull request:
* Code
* [ ] Does the pull request have a corresponding GitHub issue and clear purpose?
* [ ] Does the pull request follow HDF5 best practices (naming conventions, code portability, code structure, etc.)? <<TODO: link to the document>>
* [ ] If changes were done to Autotools build, were they added to CMake and vice versa?
* [ ] Is the pull request applicable to any other branches? If yes, which ones? Please document it in the GitHub issue.
* [ ] Is the new code sufficiently documented for future maintenance?
* [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://portal.hdfgroup.org/display/HDF5/API+Compatibility+Macros)
* Documentation
* [ ] Was the change described in the release_docs/RELEASE.txt file?
* [ ] Was MANIFEST updated if new files had been added to the source?
* [ ] Was the new function documented in the corresponding public header file using [Doxygen](https://docs.hdfgroup.org/hdf5/develop/_r_m_t.html)?
* [ ] Was new functionality documented for the HDF5 community (the level of documentation depends on the feature; ask us what would be appropriate)
* Testing
* [ ] Does the pull request have tests?
* [ ] Does the pull request affect HDF5 library performance?
We want as many contributions as we can get, and we are here to help. Feel free to reach out to us if you have any questions
Thank you for your contribution!

View File

@@ -12,7 +12,7 @@
## This file should be placed in the root directory of your project.
## Then modify the CMakeLists.txt file in the root directory of your
## project to incorporate the testing dashboard.
## # The following are required to uses Dart and the Cdash dashboard
## # The following are required to use Dart and the CDash dashboard
## ENABLE_TESTING()
## INCLUDE(CTest)
set (CTEST_PROJECT_NAME "HDF5")

View File

@@ -1,6 +1,5 @@
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,7 +1,6 @@
# Top-level distributed Makefile -*- makefile -*-
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,8 +1,12 @@
HDF5 version 1.13.2-1 currently under development
HDF5 version 1.15.0 currently under development
![HDF5 Logo](doxygen/img/HDF5.png)
[![Build](https://img.shields.io/github/workflow/status/HDFGroup/hdf5/hdf5%20dev%20CI/develop)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Adevelop)
[![develop build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=develop&label=develop)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Adevelop)
[![1.14 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_14&label=1.14)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Ahdf5_1_14)
[![1.12 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_12&label=1.12)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Ahdf5_1_12)
[![1.10 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_10&label=1.10)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Ahdf5_1_10)
[![1.8 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_8&label=1.8)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Ahdf5_1_8)
[![BSD](https://img.shields.io/badge/License-BSD-blue.svg)](https://github.com/HDFGroup/hdf5/blob/develop/COPYING)
*Please refer to the release_docs/INSTALL file for installation instructions.*
@@ -79,12 +83,19 @@ RELEASE SCHEDULE
HDF5 does not release on a regular schedule. Instead, releases are driven by
new features and bug fixes, though we try to have at least one release of each
maintenance branch per year. Future HDF5 releases indicated on this schedule
are tentative.
are tentative.
**NOTE**: HDF5 1.12 is being retired early due to its incomplete and incompatible VOL
layer.
| Release | New Features |
| ------- | ------------ |
| 1.13.2 | Onion VFD, Selection I/O, Subfiling |
| 1.13.3 | VFD SWMR, Multi-Dataset I/O |
| 1.8.23 | last HDF5 1.8 release |
| 1.10.10 | CVE fixes, performance improvements, H5Dchunk\_iter() |
| 1.12.3 | CVE fixes, performance improvements, H5Dchunk\_iter(), last HDF5 1.12 release |
| 1.14.1 | selection I/O with datatype conversion |
| 2.0.0 | TBD |
| TBD | VFD SWMR |
This list of feature release versions is also tentative, and the specific release
in which a feature is introduced may change.

View File

@@ -2,7 +2,6 @@ dnl -------------------------------------------------------------------------
dnl -------------------------------------------------------------------------
dnl
dnl Copyright by The HDF Group.
dnl Copyright by the Board of Trustees of the University of Illinois.
dnl All rights reserved.
dnl
dnl This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,10 +1,10 @@
#!/bin/sh
#
# Copyright by The HDF Group.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# Copyright by The HDF Group.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from

View File

@@ -1,6 +1,5 @@
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

31
bin/README.md Normal file
View File

@@ -0,0 +1,31 @@
# Scripts in `bin` and their purpose
Programs run via `autogen.sh` (or the equivalent in CMake) are indicated.
|Program|Purpose|
|-------|-------|
|`buildhdf5`|Convenience script to build HDF5 using the Autotools|
|`checkapi`|Checks if public API calls are used in internal functions|
|`checkposix`|Checks if C/POSIX calls are prefixed with `HD`|
|`chkcopyright`|Checks if files have appropriate copyright statements|
|`cmakehdf5`|Convenience script to build HDF5 using CMake|
|`debug-ohdr`|Examines debug output from `H5O_open/close` to look for open objects|
|`format_source`|Runs `clang-format` over the source files, applying our rules|
|`genparser`|Creates the flex/bison-based parser files in the high-level library|
|`h5cc.in`|Input file from which h5cc is created|
|`h5redeploy.in`|Input file from which h5redeploy is created|
|`h5vers`|Updates the library version number|
|`make_err`|Generates the H5E header files (called in `autogen.sh`)|
|`make_vers`|Generates H5version.h (called in `autogen.sh`)|
|`make_overflow`|Generates H5overflow.h (called in `autogen.sh`)|
|`output_filter`|Used in the tools test code to strip extraneous output before we diff files|
|`restore.sh`|Removes files generated by `autogen.sh`|
|`runbkprog`|Used by CMake to run test programs in the background|
|`switch_maint_mode`|Switches maintainer mode on/off in `configure.ac`|
|`trace`|Adds `TRACE` macros to HDF5 C library source files (run by `autogen.sh`)|
|`warnhist`|Generates compiler warning statistics for gcc/clang when fed output of make|
## TODO
* chkcopyright is currently semi-broken as it doesn't handle the full variety of copyright headers we need. We're leaving it in place, though, in the hopes that someone will update it in the future.
* Extending warnhist to better understand the output of additional compilers/languages would be nice.

View File

@@ -11,11 +11,13 @@ CTEST_CMD=`which ctest`
cd @HDF5_BINARY_DIR@
if [[ $SUMMARY_FILE == *"ctestS"* ]]; then
CMD="${CTEST_CMD} . -E MPI_TEST_ -C Release -j 32 -T test"
CMD="${CTEST_CMD} -S ctest_serial.cmake"
qsub -t 60 -n 1 -q debug-flat-quad -A ${ACCOUNT_ID} ${CMD} >& ${SUMMARY_FILE}
echo "Done running ctest serial command."
touch ctestS.done
else
CMD="${CTEST_CMD} . -R MPI_TEST_ ${SKIP_TESTS} -C Release -T test"
CMD="${CTEST_CMD} -S ctest_parallel.cmake"
qsub -t 60 -n 1 -q debug-flat-quad -A ${ACCOUNT_ID} ${CMD} >& ${SUMMARY_FILE}
echo "Done running ctest parallel command."
touch ctestP.done
fi
qsub -t 60 -n 1 -q debug-flat-quad -A ${ACCOUNT_ID} ${CMD} >& ${SUMMARY_FILE}
echo "Done running ctest parallel command."

View File

@@ -14,6 +14,7 @@
cd @HDF5_BINARY_DIR@
echo "Run parallel test command. Test output will be in build/ctestP.out"
ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
ctest -S ctest_parallel.cmake >& ctestP.out
echo "Done running ctest parallel command."
touch ctestP.done

View File

@@ -8,7 +8,8 @@
#SBATCH --job-name=h5_ctestP
cd @HDF5_BINARY_DIR@
ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
echo "Done running ctestP.sl"
echo "Run parallel test command. Test output will be in build/ctestP.out"
ctest -S ctest_parallel.cmake >& ctestP.out
echo "Done running ctest parallel command."
touch ctestP.done

View File

@@ -11,8 +11,7 @@
cd @HDF5_BINARY_DIR@
echo "Run command. Test output will be in build/ctestS.out"
ctest . -E MPI_TEST_ -C Release -j 32 -T test >& ctestS.out
ctest -S ctest_serial.cmake >& ctestS.out
##$CMD >& ctestS.out
echo "Done running command."
touch ctestS.done

View File

@@ -8,8 +8,8 @@
#SBATCH --job-name=h5_ctestS
cd @HDF5_BINARY_DIR@
CMD="ctest . -E MPI_TEST_ -C Release -j 32 -T test"
echo "Run command. Test output will be in build/ctestS.out"
ctest -S ctest_serial.cmake >& ctestS.out
echo "Run $CMD. Test output will be in build/ctestS.out"
$CMD >& ctestS.out
echo "Done running $CMD"
echo "Done running command."
touch ctestS.done

View File

@@ -0,0 +1,12 @@
if(NOT "$ENV{CI_SITE_NAME}" STREQUAL "")
set(CTEST_SITE "$ENV{CI_SITE_NAME}")
endif()
if(NOT "$ENV{CI_BUILD_NAME}" STREQUAL "")
set(CTEST_BUILD_NAME "$ENV{CI_BUILD_NAME}")
endif()
ctest_start ("$ENV{CI_MODEL}" "@HDF5_SOURCE_DIR@" "@HDF5_BINARY_DIR@" APPEND)
ctest_test (BUILD "@HDF5_BINARY_DIR@" APPEND INCLUDE MPI_TEST_ RETURN_VALUE res)
if (${res} LESS 0 OR ${res} GREATER 0)
file (APPEND ${CTEST_SCRIPT_DIRECTORY}/FailedCTest.txt "Failed Tests: ${res}\n")
endif ()

View File

@@ -0,0 +1,12 @@
if(NOT "$ENV{CI_SITE_NAME}" STREQUAL "")
set(CTEST_SITE "$ENV{CI_SITE_NAME}")
endif()
if(NOT "$ENV{CI_BUILD_NAME}" STREQUAL "")
set(CTEST_BUILD_NAME "$ENV{CI_BUILD_NAME}")
endif()
ctest_start ("$ENV{CI_MODEL}" "@HDF5_SOURCE_DIR@" "@HDF5_BINARY_DIR@" APPEND)
ctest_test (BUILD "@HDF5_BINARY_DIR@" APPEND EXCLUDE MPI_TEST_ PARALLEL_LEVEL 32 RETURN_VALUE res)
if (${res} LESS 0 OR ${res} GREATER 0)
file (APPEND ${CTEST_SCRIPT_DIRECTORY}/FailedCTest.txt "Failed Tests: ${res}\n")
endif ()

View File

@@ -9,8 +9,8 @@
#SBATCH --job-name=h5_ctestP
cd @HDF5_BINARY_DIR@
#run parallel tests except t_cache_image test
ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
echo "Done running $CMD"
echo "Run parallel test command. Test output will be in build/ctestP.out"
ctest -S ctest_parallel.cmake >& ctestP.out
echo "Done running ctest parallel command."
touch ctestP.done

View File

@@ -9,9 +9,8 @@
#SBATCH --job-name=h5_ctestS
cd @HDF5_BINARY_DIR@
CMD="ctest . -E MPI_TEST_ -C Release -j 32 -T test"
echo "Run $CMD. Test output will be in build/ctestS.out"
$CMD >& ctestS.out
echo "Done running $CMD"
echo "Run command. Test output will be in build/ctestS.out"
ctest -S ctest_serial.cmake >& ctestS.out
echo "Done running command."
touch ctestS.done

View File

@@ -15,6 +15,8 @@
cd @HDF5_BINARY_DIR@
echo "Run parallel test command. Test output will be in build/ctestP.out"
ctest . -R 'MPI_TEST_' -C Release -T test >& ctestP.out
ctest -S ctest_parallel.cmake >& ctestP.out
echo "Done running ctest parallel command."
touch ctestP.done
~

View File

@@ -11,8 +11,7 @@
cd @HDF5_BINARY_DIR@
echo "Run command. Test output will be in build/ctestS.out"
ctest . -E 'MPI_TEST_' -C Release -j 32 -T test >& ctestS.out
ctest -S ctest_serial.cmake >& ctestS.out
##$CMD >& ctestS.out
echo "Done running command."
touch ctestS.done

View File

@@ -1,7 +1,6 @@
#!/bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,7 +1,6 @@
#!/bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,7 +1,6 @@
#!/usr/bin/env perl
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -4,7 +4,6 @@ use warnings;
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
@@ -144,7 +143,7 @@ foreach $arg (@ARGV) {
next if $name =~ /^(_beginthread|(Initialize|Enter|Leave)CriticalSection|TlsAlloc)$/;
# These are MPI function calls. Ignore them.
next if $name =~ /^(MPI_|MPE_)/;
next if $name =~ /^(MPI_)/;
# These are POSIX threads function calls. Ignore them.
next if $name =~ /^pthread_/;

View File

@@ -1,82 +0,0 @@
#!/bin/sh
##
## Copyright by the Board of Trustees of the University of Illinois.
## All rights reserved.
##
## This file is part of HDF5. The full HDF5 copyright notice, including
## terms governing use, modification, and redistribution, is contained in
## the COPYING file, which can be found at the root of the source code
## distribution tree, or in https://www.hdfgroup.org/licenses.
## If you do not have access to either file, you may request a copy from
## help@hdfgroup.org.
##
# Check that all the configure files are properly generated.
#
# Programmer: Albert Cheng
# Created Date: 2004/12/07
#
# Configure: should be generated by autoconf version 2.69.
# autoconf: should be of version 2.69.
# variable initialization
nerrors=0
AUTOCONFVERSION=2.69
AUTOCONFVERSIONLEAD='Generated by GNU Autoconf'
CONFIGUREFILES="configure"
# Function definitions
#
# PRINTMSG
# Print a one line message left justified in a field of 70 characters
# without newline. More output for this line later.
#
PRINTMSG() {
SPACES=" "
echo "$* $SPACES" | cut -c1-70 | tr -d '\012'
}
# print result passed.
PASSED() {
echo " PASSED"
}
# print result failed.
FAILED() {
echo "*FAILED*"
}
# Main body
# Check configure files
# The autoconf version should be among the first 5 lines.
echo "Check autoconf version. Should be version $AUTOCONFVERSION"
for xf in $CONFIGUREFILES; do
PRINTMSG $xf
if [ ! -f $xf ]; then
FAILED
echo File not found
nerrors=`expr $nerrors + 1`
continue
fi
autoconf_version=`head -5 $xf | grep "$AUTOCONFVERSIONLEAD"`
echo $autoconf_version | grep "$AUTOCONFVERSIONLEAD $AUTOCONFVERSION" > /dev/null 2>&1
if [ $? -eq 0 ]; then
PASSED
else
FAILED
echo "Expected: $AUTOCONFVERSIONLEAD $AUTOCONFVERSION"
echo "Got: $autoconf_version"
nerrors=`expr $nerrors + 1`
fi
done
# Summary
echo $0 found $nerrors errors
if [ $nerrors != 0 ]; then
exit 1
fi
exit 0

View File

@@ -1,7 +1,6 @@
#! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
@@ -10,7 +9,6 @@
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
# Check Copyright notice.
# Check that all the files have the proper copyright notice.
@@ -39,8 +37,8 @@ NFIXEDFILES=0 # Number of files fixed.
NFIXFAILEDFILES=0 # Number of files fix failed.
NUMBEGINLINES=60 # Copyright notice should be located within the
# this number of lines at the beginning of the file.
UICOPYRIGHTSTR="Copyright by the Board of Trustees of the University of Illinois"
THGCOPYRIGHTSTR="Copyright by The HDF Group."
UICOPYRIGHTSTR="Copyright by the Board of Trustees of the University of Illinois"
PASSEDLOG=/tmp/h5chkright_passed.$$
SKIPPEDLOG=/tmp/h5chkright_skipped.$$
@@ -111,113 +109,92 @@ BUILDCOPYRIGHT()
# C and C++ source Copyright notice
cat > ${C_COPYRIGHT} << \EOF
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
EOF
# Fortran9X source Copyright notice
cat > ${FTN_COPYRIGHT} << \EOF
! Copyright by The HDF Group. *
! Copyright by the Board of Trustees of the University of Illinois. *
! All rights reserved. *
! *
! This file is part of HDF5. The full HDF5 copyright notice, including *
! terms governing use, modification, and redistribution, is contained in *
! the files COPYING and Copyright.html. COPYING can be found at the root *
! of the source code distribution tree; Copyright.html can be found at the *
! root level of an installed copy of the electronic HDF5 document set and *
! is linked from the top-level documents page. It can also be found at *
! http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
! access to either file, you may request a copy from help@hdfgroup.org. *
! the COPYING file, which can be found at the root of the source code *
! distribution tree, or in https://www.hdfgroup.org/licenses. *
! If you do not have access to either file, you may request a copy from *
! help@hdfgroup.org. *
EOF
# HTML file Copyright notice
cat > ${HTM_COPYRIGHT} << \EOF
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
EOF
# Shell style Copyright notice
cat > ${SH_COPYRIGHT} << \EOF
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the files COPYING and Copyright.html. COPYING can be found at the root
# of the source code distribution tree; Copyright.html can be found at the
# root level of an installed copy of the electronic HDF5 document set and
# is linked from the top-level documents page. It can also be found at
# http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have
# access to either file, you may request a copy from help@hdfgroup.org.
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
EOF
# Shell style Copyright notice (2nd type)
cat > ${SH_COPYRIGHT2} << \EOF
## Copyright by The HDF Group.
## Copyright by the Board of Trustees of the University of Illinois.
## All rights reserved.
##
## This file is part of HDF5. The full HDF5 copyright notice, including
## terms governing use, modification, and redistribution, is contained in
## the files COPYING and Copyright.html. COPYING can be found at the root
## of the source code distribution tree; Copyright.html can be found at the
## root level of an installed copy of the electronic HDF5 document set and
## is linked from the top-level documents page. It can also be found at
## http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have
## access to either file, you may request a copy from help@hdfgroup.org.
## the COPYING file, which can be found at the root of the source code
## distribution tree, or in https://www.hdfgroup.org/licenses.
## If you do not have access to either file, you may request a copy from
## help@hdfgroup.org.
EOF
# Windows Batch file Copyright notice
cat > ${WINBAT_COPYRIGHT} << \EOF
@REM Copyright by The HDF Group.
@REM Copyright by the Board of Trustees of the University of Illinois.
@REM All rights reserved.
@REM
@REM This file is part of HDF5. The full HDF5 copyright notice, including
@REM terms governing use, modification, and redistribution, is contained in
@REM the files COPYING and Copyright.html. COPYING can be found at the root
@REM of the source code distribution tree; Copyright.html can be found at the
@REM root level of an installed copy of the electronic HDF5 document set and
@REM is linked from the top-level documents page. It can also be found at
@REM http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have
@REM access to either file, you may request a copy from help@hdfgroup.org.
@REM the COPYING file, which can be found at the root of the source code
@REM distribution tree, or in https://www.hdfgroup.org/licenses.
@REM If you do not have access to either file, you may request a copy from
@REM help@hdfgroup.org.
EOF
# configure.ac file Copyright notice
cat > ${CONFIGURE_AC_COPYRIGHT} << \EOF
dnl Copyright by The HDF Group.
dnl Copyright by the Board of Trustees of the University of Illinois.
dnl All rights reserved.
dnl
dnl This file is part of HDF5. The full HDF5 copyright notice, including
dnl terms governing use, modification, and redistribution, is contained in
dnl the files COPYING and Copyright.html. COPYING can be found at the root
dnl of the source code distribution tree; Copyright.html can be found at the
dnl root level of an installed copy of the electronic HDF5 document set and
dnl is linked from the top-level documents page. It can also be found at
dnl http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have
dnl access to either file, you may request a copy from help@hdfgroup.org.
dnl the COPYING file, which can be found at the root of the source code
dnl distribution tree, or in https://www.hdfgroup.org/licenses.
dnl If you do not have access to either file, you may request a copy from
dnl help@hdfgroup.org.
EOF
}
@@ -364,7 +341,7 @@ FindLineInFile()
# $1 file which contains the expected copyright notice.
# $2 file in which to look for the copyright notice.
# Copyright notice must be found within the beginning $NUMBEGINLINES of lines.
# Hunt for the particular string $UICOPYRIGHTSTR which signifies the beginning
# Hunt for the particular string $THGCOPYRIGHTSTR which signifies the beginning
# of the copyright notice.
#
MATCH_COPYRIGHT()
@@ -379,7 +356,7 @@ MATCH_COPYRIGHT()
nlines=`wc -l ${COPYRIGHTFILE} | cut -f1 -d' '`
# Find a line that contains the copyright string and its line number in
# the file.
begin=`FindLineInFile "${UICOPYRIGHTSTR}" $f`
begin=`FindLineInFile "${THGCOPYRIGHTSTR}" $f`
if [ "$begin" -le 0 ] ; then
# Not found, generate an empty dummy file
cp /dev/null ${EXTRACTEDFILE}
@@ -404,7 +381,7 @@ MATCH_COPYRIGHT()
# $1 file which contains the expected copyright notice.
# $2 file in which to look for the copyright notice.
# Copyright notice must be found within the beginning $NUMBEGINLINES of lines.
# Hunt for the particular string $UICOPYRIGHTSTR which signifies the beginning
# Hunt for the particular string $THGCOPYRIGHTSTR which signifies the beginning
# of the copyright notice.
#
FIX_COPYRIGHT()
@@ -427,7 +404,12 @@ FIX_COPYRIGHT()
# the file.
insertbegin=`FindLineInFile "${THGCOPYRIGHTSTR}" $f`
if [ $insertbegin -gt 0 ]; then
insertend=`expr $insertbegin + $nlines` # no need to -1. See below.
insertUIbegin=`FindLineInFile "${UICOPYRIGHTSTR}" $f`
if [ $insertUIbegin -gt 0 ]; then
insertend=`expr $insertbegin + $nlines + 1`
else
insertend=`expr $insertbegin + $nlines`
fi
else
insertbegin=`FindLineInFile "${UICOPYRIGHTSTR}" $f`
if [ $insertbegin -gt 0 ]; then

View File

@@ -1,7 +1,6 @@
#!/usr/bin/env perl
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,51 +0,0 @@
#!/usr/bin/env perl
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
use warnings;
my $depend_file;
my $new_depend_file;
my $srcdir;
my $top_srcdir;
my $top_builddir;
while ($_ = shift @ARGV) {
if (/^--top_srcdir=([^ \t\n]*)/) {
$top_srcdir = $1;
$top_srcdir =~ s/\+/\\\+/g;
$top_srcdir =~ s/\./\\\./g;
} elsif (/^--top_builddir=([^ \t\n]*)/) {
$top_builddir = $1;
$top_builddir =~ s/\+/\\\+/g;
$top_builddir =~ s/\./\\\./g;
} else {
$depend_file = $_;
$new_depend_file = "$_.new";
last;
}
}
open(DEPEND, "<$depend_file") || die "cannot open file $depend_file: $!\n";
open(NEW, ">$new_depend_file") || die "cannot open file $new_depend_file: $!\n";
while (<DEPEND>) {
s/\.o(\b)/\.lo$1/g;
s/ $top_srcdir/ \$\(top_srcdir\)/g;
s/ $top_builddir/ \$\(top_builddir\)/g;
print NEW $_;
}
close(DEPEND);
close(NEW);
`mv $new_depend_file $depend_file`;

View File

@@ -1,58 +0,0 @@
#!/bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
# Deploy the HDF5 binary.
#
# Programmer: Albert Cheng
# Created Date: 2004/12/15
#
# Modifications
# Function definitions
#
# Print Usage page
USAGE()
{
cat << EOF
Usage: $0 <dir>
Install the binary to directory <dir>
Examples:
$ bin/deploy /usr/local/hdf5
....
EOF
}
# Variables
if [ $# != 1 ]; then
USAGE
exit 1
fi
installdir=$1
# create installdir if it does not exist yet.
if [ -d $installdir ] || mkdir $installdir ; then
${MAKE:-gmake} install prefix=$installdir && \
( cd $installdir/bin; ./h5redeploy -force)
exit $?
else
echo $installdir is not a valid directory
USAGE
exit 1
fi

View File

@@ -1,27 +0,0 @@
#!/bin/sh
#! -*-perl-*-
eval 'exec perl -p -x -S $0 ${1+"$@"}'
if 0;
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
# Usage: $0 [<].depend
# Takes dependency info and generates on stdout dependencies suitable for
# distribution by removing all the system include files from the list and
# removing all but the base name of other include files (since the Makefiles
# contain the logic for searching).
($h,$_)=/\s*\\/?$h.$`:("",$h.$_);
s|( +/\S*)*( *)|$2?" \\\n ":""|eg;
#s|(([-\w\.]+)/)+([-\w\.]+)|\3|g;

View File

@@ -1,139 +0,0 @@
#!/usr/bin/env perl
require 5.003;
use warnings;
use Text::Tabs;
# NOTE: THE FORMAT OF HRETURN_ERROR AND HGOTO_ERROR MACROS HAS
# CHANGED. THIS SCRIPT NO LONGER WORKS! --rpm
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
# Robb Matzke
# 30 Aug 1997
#
# Purpose: This script will read standard input which should be a
# function prologue followed by a C function and will emit
# on standard output the same source code with the function
# prologue containing documentation for the various errors
# that occur in the function.
#
# Errors are raised by calling HGOTO_ERROR() or
# HRETURN_ERROR(). The reason for the error message is a
# comment which appears immediately after the error macro
# call and is contained entirely on one line:
#
# HRETURN_ERROR (...); /*entry not found*/
#
# If such a comment doesn't exist, then the previous comment
# is used, subject to the constraint that raising an error
# clears the previous comment.
#
# /* Entry not found */
# HGOTO_ERROR (...);
#
# Emacs users can use this script interactively with the
# c-mark-function and shell-command-on-region functions which
# are normally bound to M-C-h and M-|.
# Split STDIN into the prolog and the function body. Preserve leading
# white space.
$_ = join "", <STDIN>;
my ($head, $prolog, $body) = (/^(\s*)(\/\*(.*?)\*\/)?(.*)/s)[0,2,3];
$prolog = "" unless $prolog;
# Find each error and the comment that goes with it.
for ($_=$body,$comment=""; /\/\*|H(RETURN|GOTO)_ERROR/s;) {
$_ = $&.$';
if (/^H(RETURN|GOTO)_ERROR\s*\(\s*H5E_(\w+)\s*,\s*H5E_(\w+)\s*,/s) {
($major, $minor, $_) = ($2, $3, $');
$comment=$1 if /^.*?\)\s*;\s*\/\*\s*(.*?)\s*\*\//;
$comment =~ s/^\s*\*+\s*/ /mg; # leading asterisks.
$comment =~ s/^\s+//s; # leading white space.
$comment =~ s/\s+$//s; # trailing white space.
$comment =~ s/(\w)$/$1./s; # punctuation.
$comment ||= "***NO COMMENT***";
$errors{"$major\000$minor\000\u$comment"} = 1;
$comment = "";
} else {
($comment) = /^\/\*\s*(.*?)\s*\*\//s;
$_ = $';
}
}
# Format an error so it isn't too wide.
sub fmt_error ($) {
local ($_) = @_;
my ($prefix,$space,$err) = /^((.*?)([A-Z_0-9]+\s+[A-Z_0-9]+\s+))/;
$_ = $';
tr/\n / /s;
my $w = 70 - length expand $prefix;
s/(.{$w}\S+)\s+(\S)/$1."\n".$space.' 'x(length $err).$2/eg;
return $prefix . $_."\n";
}
# Sort the errors by major, then minor, then comment. Duplicate
# triplets have already been removed.
sub by_triplet {
my ($a_maj, $a_min, $a_com) = split /\000/, $a;
my ($b_maj, $b_min, $b_com) = split /\000/, $b;
$a_maj cmp $b_maj || $a_min cmp $b_min || $a_com cmp $b_com;
}
@errors = map {sprintf "%-9s %-13s %s\n", split /\000/}
sort by_triplet keys %errors;
# Add the list of errors to the prologue depending on the type of
# prolog.
if (($front, $back) = $prolog=~/^(.*?Errors:\s*?(?=\n)).*?\n\s*\*\s*\n(.*)/s) {
#| * Errors: |#
#| * __list_of_error_messages__ (zero or more lines) |#
#| * |#
print $head, "/*", $front, "\n";
map {print fmt_error " *\t\t".$_} @errors;
print " *\n", $back, "*/", $body;
} elsif (($front,$back) = $prolog =~
/(.*?\n\s*ERRORS:?\s*?(?=\n)).*?\n\s*\n(.*)/s) {
#| ERRORS |#
#| __list_of_error_messages__ (zero or more lines) |#
#| |#
print $head, "/*", $front, "\n";
map {print fmt_error " ".$_} @errors;
print "\n", $back, "*/", $body;
} elsif ($prolog eq "") {
# No prolog present.
print $head;
print " \n/*", "-"x73, "\n * Function:\t\n *\n * Purpose:\t\n *\n";
print " * Errors:\n";
map {print fmt_error " *\t\t".$_} @errors;
print " *\n * Return:\tSuccess:\t\n *\n *\t\tFailure:\t\n *\n";
print " * Programmer:\t\n *\n * Modifications:\n *\n *", '-'x73, "\n";
print " */\n", $body;
} else {
# Prolog format not recognized.
print $head, "/*", $prolog, "*/\n\n";
print "/*\n * Errors returned by this function...\n";
map {print fmt_error " *\t".$_} @errors;
print " */\n", $body;
}

View File

@@ -1,34 +0,0 @@
#!/bin/bash
#
# Recursively format all C & C++ sources and header files, except those in the
# 'config' directory and generated files, such as H5LTanalyze.c, etc.
#
# Note that any files or directories that are excluded here should also be
# added to the 'exclude' list in .github/workflows/clang-format-check.yml
#
# (Remember to update both bin/format_source and bin/format_source_patch)
find . \( -type d -path ./config -prune -and -not -path ./config \) \
-or \( \( \! \( \
-name H5LTanalyze.c \
-or -name H5LTparse.c \
-or -name H5LTparse.h \
-or -name H5Epubgen.h \
-or -name H5Einit.h \
-or -name H5Eterm.h \
-or -name H5Edefin.h \
-or -name H5version.h \
-or -name H5overflow.h \
\) \) \
-and \( -iname *.h -or -iname *.c -or -iname *.cpp -or -iname *.hpp -or -iname *.java \) \) \
| xargs clang-format -style=file -i -fallback-style=none
git diff > clang_format.patch
# Delete if 0 size
if [ ! -s clang_format.patch ]
then
rm clang_format.patch
fi
exit 0

View File

@@ -1,51 +0,0 @@
#! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
# A script to generate coverage files for HDF5 using gcov.
# Configures, builds, and runs tests in-place; the output files will be placed
# in a directory called gcov_logs.
# Must be invoked from the root hdf5 directory.
# This script has been tested on kagiso.
CFLAGS="$CFLAGS -ftest-coverage -fprofile-arcs"
export CFLAGS
LDFLAGS="$LDFLAGS -lgcov"
export LDFLAGS
CC=gcc
export CC
./configure
make
make check
mkdir gcov_logs
cd src
for j in *.h *.c
do
ln -s ../$j .libs/$j
done
cd .libs
for j in *.gcda
do
gcov -b $j >> gcov.log 2>&1
done
for j in *.gcov
do
mv $j ../../gcov_logs
done
mv gcov.log ../../gcov_logs
for j in *.c *.h
do
rm $j
done
cd ../..

View File

@@ -3,7 +3,7 @@
# Copyright by The HDF Group.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.

View File

@@ -1,7 +1,6 @@
#! /bin/sh
##
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,7 +1,6 @@
#! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -7,7 +7,6 @@ require 5.003;
use strict;
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
@@ -377,7 +376,7 @@ if ($H5_JAVA) {
my $version_string2 = sprintf("%d, %d, %d", @newver[0,1,2]);
$data =~ s/\@version HDF5 .* <BR>/\@version HDF5 $version_string1 <BR>/;
$data =~ s/ public final static int LIB_VERSION\[\] = \{ \d*, \d*, \d* \};/ public final static int LIB_VERSION[] = \{ $version_string2 \};/;
$data =~ s/ public final static int LIB_VERSION\[\] = \{\d*,.\d*,.\d*\};/ public final static int LIB_VERSION[] = \{$version_string2\};/;
write_file($H5_JAVA, $data);
}
@@ -394,7 +393,7 @@ if ($TESTH5_JAVA) {
my $version_string1 = sprintf("%d, %d, %d", @newver[0,1,2]);
my $version_string2 = sprintf("int majnum = %d, minnum = %d, relnum = %d", @newver[0,1,2]);
$data =~ s/ int libversion\[\] = \{ .* \};/ int libversion\[\] = \{ $version_string1 \};/;
$data =~ s/ int libversion\[\] = \{.*\};/ int libversion\[\] = \{$version_string1\};/;
$data =~ s/ int majnum = \d*, minnum = \d*, relnum = \d*;/ $version_string2;/;
write_file($TESTH5_JAVA, $data);

View File

@@ -1,7 +1,6 @@
#!/usr/bin/env perl
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -5,7 +5,6 @@ use warnings;
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
@@ -32,7 +31,6 @@ sub print_copyright ($) {
print $fh "/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n";
print $fh " * Copyright by The HDF Group. *\n";
print $fh " * Copyright by the Board of Trustees of the University of Illinois. *\n";
print $fh " * All rights reserved. *\n";
print $fh " * *\n";
print $fh " * This file is part of HDF5. The full HDF5 copyright notice, including *\n";

View File

@@ -10,7 +10,6 @@ my @ctypes = ( () );
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
@@ -61,7 +60,6 @@ sub print_copyright ($) {
print $fh "/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n";
print $fh " * Copyright by The HDF Group. *\n";
print $fh " * Copyright by the Board of Trustees of the University of Illinois. *\n";
print $fh " * All rights reserved. *\n";
print $fh " * *\n";
print $fh " * This file is part of HDF5. The full HDF5 copyright notice, including *\n";

View File

@@ -8,8 +8,8 @@ use warnings;
# is added (like support for 1.4, etc), the min_sup_idx parameter will
# need to be decremented.)
# Max. library "index" (0 = v1.0, 1 = 1.2, 2 = 1.4, 3 = 1.6, 4 = 1.8, 5 = 1.10, 6 = 1.12, 7 = 1.14, etc)
$max_idx = 7;
# Max. library "index" (0 = v1.0, 1 = 1.2, 2 = 1.4, 3 = 1.6, 4 = 1.8, 5 = 1.10, 6 = 1.12, 7 = 1.14, 8 = 1.16, etc)
$max_idx = 8;
# Min. supported previous library version "index" (0 = v1.0, 1 = 1.2, etc)
$min_sup_idx = 3;
@@ -19,7 +19,6 @@ $indent = 2;
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
@@ -46,7 +45,6 @@ sub print_copyright ($) {
print $fh "/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n";
print $fh " * Copyright by The HDF Group. *\n";
print $fh " * Copyright by the Board of Trustees of the University of Illinois. *\n";
print $fh " * All rights reserved. *\n";
print $fh " * *\n";
print $fh " * This file is part of HDF5. The full HDF5 copyright notice, including *\n";

View File

@@ -1,33 +0,0 @@
#! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
# This is a small program which will create directories n-levels deep.
# You just call it with something like:
#
# mkdirs /tmp/foo/bar/baz
#
# and it will create all the directories from /tmp down to baz which
# don't exist.
#
chmodprog="${CHMODPROG-chmod}"
mkdirprog="${MKDIRPROG-mkdir}"
make_dir () {
if test ! -d $1; then
make_dir `echo $1 | sed -e 's#/[^/]*$##'`
$mkdirprog $1
$chmodprog 755 $1
fi
}
make_dir `echo $1 | sed -e 's#/$##'`

View File

@@ -1,43 +0,0 @@
#!/bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
# Compare the modification time of file argument 1 against other file arguments.
# Return true (0) if argument 1 is newer than all others, otherwise return
# false (1). If any of the argument is not a file, return false (1).
#
# Programmer: Albert Cheng
# Created Date: 2005/07/06
# Modification:
# Albert Cheng 2005/8/30
# Changed from two arguments to multiple arguments.
if test $# -lt 2; then
exit 1
fi
if test ! -f $1; then
exit 1
fi
f1=$1
shift
for f in $*; do
if test ! -f $f; then
exit 1
fi
if test X = X`find $f1 -newer $f -print`; then
exit 1
fi
done
# passed all tests. Must be a file newer than all others.
exit 0

View File

@@ -61,26 +61,21 @@ STDOUT_FILTER() {
# Remove them from the stderr result file.
# $1 is the file name of the file to be filtered.
# Cases of filter needed:
# 1. MPE:
# In parallel mode and if MPE library is used, it prints the following
# two message lines whether the MPE tracing is used or not.
# Writing logfile.
# Finished writing logfile.
# 2. LANL MPI:
# * LANL MPI:
# The LANL MPI will print some messages like the following,
# LA-MPI: *** mpirun (1.5.10)
# LA-MPI: *** 3 process(es) on 2 host(s): 2*fln21 1*fln22
# LA-MPI: *** libmpi (1.5.10)
# LA-MPI: *** Copyright 2001-2004, ACL, Los Alamos National Laboratory
# 3. h5diff debug output:
# * h5diff debug output:
# Debug output all have prefix "h5diff debug: ".
# 4. AIX system prints messages like these when it is aborting:
# * AIX system prints messages like these when it is aborting:
# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0
# ERROR: 0031-250 task 4: Terminated
# ERROR: 0031-250 task 3: Terminated
# ERROR: 0031-250 task 2: Terminated
# ERROR: 0031-250 task 1: Terminated
# 5. LLNL Blue-Gene mpirun prints messages like there when it exit non-zero:
# * LLNL Blue-Gene mpirun prints messages like there when it exit non-zero:
# <Apr 12 15:01:49.075658> BE_MPI (ERROR): The error message in the job record is as follows:
# <Apr 12 15:01:49.075736> BE_MPI (ERROR): "killed by exit(1) on node 0"
STDERR_FILTER() {
@@ -91,12 +86,6 @@ STDERR_FILTER() {
cp $result_file $tmp_file
sed -e '/ BE_MPI (ERROR): /d' \
< $tmp_file > $result_file
# Filter MPE messages
if test -n "$pmode"; then
cp $result_file $tmp_file
sed -e '/^Writing logfile./d' -e '/^Finished writing logfile./d' \
< $tmp_file > $result_file
fi
# Filter LANL MPI messages
# and LLNL srun messages
# and AIX error messages

View File

@@ -1,7 +1,6 @@
#! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -2,7 +2,6 @@
# makeTarFiles.pl
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,215 +0,0 @@
#!/usr/bin/perl
# makeInternalREADME.pl
#
# Copyright by The HDF Group.
# All rights reserved.
#
# This file is part of HDF4. The full HDF4 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the files COPYING and Copyright.html. COPYING can be found at the root
# of the source code distribution tree; Copyright.html can be found at the
# root level of an installed copy of the electronic HDF4 document set and
# is linked from the top-level documents page. It can also be found at
# http://hdfgroup.org/HDF4/doc/Copyright.html. If you do not have
# access to either file, you may request a copy from help@hdfgroup.org.
#
use warnings;
use strict;
my $section2="For information on compilers and settings used to build these HDF5
libraries, please refer to:
./lib/libhdf5.settings
The contents of this directory are:
COPYING - Copyright notice
README - This file
RELEASE.txt - Detailed information regarding this release
bin/ - Directory containing HDF5 pre-compiled utilities
include/ - Directory containing HDF5 include files
lib/ - Directory containing HDF5 libraries and settings
share/ - Directory containing example code in C, C++, and
Fortran using HDF5 and HDF5 HL library APIs. The
shell scripts provided with these examples will
compile and run them, and will also test the
h5cc, h5c++, and h5fc compile scripts found
in the installed bin directory.
These binaries were built with the ZLIB and SZIP (version 2.1, Encoder
ENABLED) external libraries which are included in the lib directory for
convenience.
We also provide the ZLIB and SZIP source code on our ftp server at:
ftp://ftp.hdfgroup.org/lib-external/
The official ZLIB and SZIP pages are at:
ZLIB: http://www.zlib.net/
SZIP: http://hdfgroup.org/doc_resource/SZIP/
";
my $section3 = "If using the shared libraries, you must add the HDF5 library path
to the LD_LIBRARY_PATH variable.
";
my $section4 = "We provide scripts for compiling applications with the HDF5 libraries:
bin/h5cc - for C
bin/h5fc - for F90 (if Fortran 90 library is included with the binaries)
bin/h5c++ - for C++ (if C++ library is included with the binaries)
After you have installed the binaries to their final destination, you can use
these scripts (h5cc, h5fc, h5c++) to compile. However, you must first run
./h5redeploy in the bin directory to change site specific paths in the scripts.
You may also need to change other variables in the scripts, depending
on how things are set up on your system. Here are some of the variables
to check:
prefix - Path to the HDF5 top level installation directory
CCBASE - Name of the C compiler
CLINKERBASE - Name of the linker
LIBS - Libraries your application will link with
For further details refer to the INSTALL files in
ftp://ftp.hdfgroup.org/HDF5/current/src/unpacked/release_docs/
or in the ./release_docs/ directory of the HDF5 source code, which can be found
on the HDF Group ftp server at ftp://ftp.hdfgroup.org/HDF5/current/src/.
Please send questions, comments, and suggestions to the appropriate
contact address from http://www.hdfgroup.org/about/contact.html
";
my $indirectory = ".";
$indirectory = shift;
my $linktype = "shared";
if ($indirectory =~ /static/) {
$linktype = "static";
}
my $modestring="";
if ($indirectory =~ /32/) {
$modestring = "in 32 bit mode ";
}
my $version;
my $outfile = "$indirectory/README";
open OUTFILE, ">$outfile" or die "$!Couldn't open $outfile - check permissions for $indirectory\n";
my $hostname;
my $cmd = "grep \"HDF5 Version\" $indirectory/lib/libhdf5.settings";
$_ = `$cmd`;
#print OUTFILE $_, "\n";
s/HDF5 Version://;
s/^\s+//;
chomp;
$version = $_;
#print OUTFILE $_, "\n";
my $versionstring= "This directory contains the $linktype binary distribution of HDF5-".$version;
$cmd = "grep \"Uname information:\" $indirectory/lib/libhdf5.settings";
$_ = `$cmd`;
s/Uname information://;
s/^\s+//;
#print OUTFILE $_;
chomp;
#s/(^\w+)(\s)(\S+)/$1/;
#s/(^.*)(-)(.*)(200[7-8])(.*)(\s)(\S+)/$1 $5/;
#my $platformstring = "\nthat was compiled on:" . $_ . " ";
my $platformstring = "";
my $hostnamestring = $_;
my @hostnamestring = split / /, $hostnamestring;
#print OUTFILE "Size of hostnamestring is ", scalar @hostnamestring, "\n";
#print OUTFILE $hostnamestring[0] . "\t" . $hostnamestring[2]."\t".$hostnamestring[19]."\n";
$hostname = $hostnamestring[1];
#my $size = scalar @hostnamestring;
if ($hostname =~ /loyalty/) {
$platformstring = "\nthat was compiled " . $modestring . "on: " . $hostnamestring[0]." " . $hostnamestring[2]." " . $hostnamestring[-1] . " ";
}
elsif ($hostname =~ /freedom/) {
$platformstring = "\nthat was compiled " . $modestring . "on: " . $hostnamestring[0]." " . $hostnamestring[2]." " . $hostnamestring[-1] . " ";
} elsif ($hostname =~ /emu/) {
$platformstring = "\nthat was compiled " . $modestring . "on: " . $hostnamestring[0]." " . $hostnamestring[2] . " " . $hostnamestring[-2] . " ";
} elsif ($hostname =~ /fred/) {
$platformstring = "\nthat was compiled " . $modestring . "on: " . $hostnamestring[0]." " . $hostnamestring[2] . " " . $hostnamestring[-1] . " ";
} else {
$_ = $hostnamestring[2];
my $pos = index $_, '-';
my $os = substr $_, 0, $pos;
$platformstring = "\nthat was compiled " . $modestring . "on: " . $hostnamestring[0] . " " . $os . " " . $hostnamestring[-2] . " ";
}
my $mappingstring = "";
#no mappingstring for 1.6. Put it back for 1.8.
#$cmd = "grep \"Default API Mapping:\" $indirectory/lib/libhdf5.settings";
#$_ = `$cmd`;
#s/Default API Mapping://;
#s/^\s+//;
#chomp;
#if (/v\d+/) {
# s/v//;
# s/(\d)(\d)/$1\.$2/g;
# $mappingstring = "using the default\nAPI mapping for VERSION ".$_.".";
#
#}
print OUTFILE $versionstring;
print OUTFILE $platformstring."\n\n";
#print OUTFILE $mappingstring;
#if ($hostname eq "loyalty.hdfgroup.uiuc.edu" || $hostname eq "freedom.hdfgroup.uiuc.edu") {
# print OUTFILE " It includes the C APIs,\nbuilt using the following ";
# print OUTFILE "compilers:\n\n";
#}
#else {
if ($linktype eq "shared" && !($hostname =~ /32/)) {
print OUTFILE "\n\nIt includes the C, C++, F90 and Java APIs, built using the following\n";
} else {
print OUTFILE "\n\nIt includes the C, C++, and F90 APIs, built using the following\n";
}
print OUTFILE "compilers:\n\n";
#}
# Only the gcc compiler version is in libhdf5.settings, so for now I looked
# up the versions and hardcoded them here. We will put them in libhdf5.settings
# for the next release.
if ($indirectory =~ /gnu484/) {
print OUTFILE "\tgcc, g++, and gfortran 4.8.4\n\n";
} elsif ($hostname =~ /jam/ || $hostname =~ /koala/) {
print OUTFILE "\tgcc, g++, and gfortran 4.1.2\n\n";
} elsif ($hostname =~ /platypus/) {
print OUTFILE "\tgcc, g++, and gfortran 4.4.7\n\n";
if ($linktype eq "shared" && !($hostname =~ /32/)) {
print OUTFILE "\tjava 1.8.0_51\n\n";
}
} elsif ($hostname =~ /moohan/) {
print OUTFILE "\tgcc, g++, and gfortran 4.8.5\n\n";
if ($linktype eq "shared" && !($hostname =~ /32/)) {
print OUTFILE "\tjava 1.8.0_51\n\n";
}
} elsif ($hostname =~ /emu/) {
print OUTFILE "\tSun C and C++ 5.12, Sun Fortran 95 8.6\n\n";
} elsif ($hostname =~ /loyalty/ || $hostname =~ /freedom/) {
print OUTFILE "\tgcc, g++, and gfortran 4.6.1\n\n";
} elsif ($hostname =~ /duck/) {
print OUTFILE "\tApple clang/clang++ 3.0 from Xcode 4.6.1 and gfortran 4.8.2\n\n";
} elsif ($hostname =~ /kite/) {
print OUTFILE "\tApple clang/clang++ 5.1 from Xcode 5.0.2 and gfortran 4.8.2\n\n";
} elsif ($hostname =~ /quail/) {
print OUTFILE "\tgcc, g++ 5.1 from Xcode 5.1 and gfortran 4.8.2\n\n";
} elsif ($hostname =~ /osx1010test/) {
print OUTFILE "\tgcc, g++ 5.1 from Xcode 5.1 and gfortran 4.8.2\n\n";
}
print OUTFILE $section2;
print OUTFILE $section3;
print OUTFILE $section4;

View File

@@ -1,182 +0,0 @@
#!/usr/bin/perl
# makeOuterREADME.pl
# Copyright by The HDF Group.
# All rights reserved.
#
# This file is part of HDF4. The full HDF4 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the files COPYING and Copyright.html. COPYING can be found at the root
# of the source code distribution tree; Copyright.html can be found at the
# root level of an installed copy of the electronic HDF4 document set and
# is linked from the top-level documents page. It can also be found at
# http://hdfgroup.org/HDF4/doc/Copyright.html. If you do not have
# access to either file, you may request a copy from help@hdfgroup.org.
#
use warnings;
use strict;
my $indirectory = ".";
$indirectory = shift;
my $outdirectory = ".";
$outdirectory = shift;
my $outsubdir = shift;
my $version;
my $outfile = "$outdirectory/$outsubdir/README";
open OUTFILE, ">$outfile";
my $hostname="";
my $cmd = "grep \"HDF5 Version\" $indirectory-static/lib/libhdf5.settings";
$_ = `$cmd`;
print OUTFILE $_, "\n";
s/HDF5 Version://;
s/^\s+//;
chomp;
$version = $_;
#print OUTFILE $_, "\n";
my $versionstring= "This directory contains the precompiled HDF5 $version binary distribution\n(include files, libraries, utilities) for";
$cmd = "grep \"Uname information:\" $indirectory-static/lib/libhdf5.settings";
$_ = `$cmd`;
s/Uname information://;
s/^\s+//;
chomp;
print "String to work with is $_\n";
my $platformstring = "";
my $hostnamestring = $_;
my @hostnamestring = split / /, $hostnamestring;
$platformstring = "$hostnamestring[0] ";
if ($indirectory =~ /jam/ || $indirectory =~ /koala/) {
$hostnamestring = $hostnamestring[2];
my $pos = index $hostnamestring, "-";
if ($pos > 0) {
$platformstring .= substr $hostnamestring, 0, $pos;
} else {
$platformstring .= $hostnamestring[2];
}
$platformstring .= " ".$hostnamestring[-3];
} elsif ($indirectory =~ /linew/) {
$platformstring .= "$hostnamestring[2] $hostnamestring[-2]";
} else {
$platformstring .= "$hostnamestring[2] $hostnamestring[-1]";
}
print OUTFILE $versionstring." ".$platformstring.":\n\n";
my $line1;
my $line3;
my $line5;
my $compilerstring="";
my $compilerstring1="";
my $compilerstring2="";
print $indirectory, "\n";
if ($indirectory =~ /ostrich/) {
# $line1 = " hdf5-$version-$outsubdir-16API.tar.gz - Includes C, C++, F90 APIs (using\n";
$line3 = " hdf5-$version-$outsubdir-static.tar.gz - Includes C, C++, F90 APIs (using";
$line5 = " hdf5-$version-$outsubdir-shared.tar.gz - Includes C, C++, F90 APIs (using";
$compilerstring = " gcc, g++, and gfortran 4.4.7)";
}
elsif ($indirectory =~ /platypus/) {
# $line1 = " hdf5-$version-$outsubdir-16API.tar.gz - Includes C, C++, F90 APIs (using\n";
$line3 = " hdf5-$version-$outsubdir-static.tar.gz - Includes C, C++, F90 APIs (using";
$compilerstring1 = " gcc, g++, and gfortran 4.4.7)\n";
if ($indirectory =~ /32/) {
$line5 = " hdf5-$version-$outsubdir-shared.tar.gz - Includes C, C++, F90 and Java APIs (using";
$compilerstring2 = " gcc, g++, and gfortran 4.4.7)\n";
} else {
$line5 = " hdf5-$version-$outsubdir-shared.tar.gz - Includes C, C++, F90 and Java APIs (using";
$compilerstring2 = " gcc, g++, and gfortran 4.4.7 and java 1.8.0_51)\n";
}
}
elsif ($indirectory =~ /moohan/) {
# $line1 = " hdf5-$version-$outsubdir-16API.tar.gz - Includes C, C++, F90 APIs (using\n";
$line3 = " hdf5-$version-$outsubdir-static.tar.gz - Includes C, C++, F90 APIs (using";
$compilerstring1 = " gcc, g++, and gfortran 4.8.5)\n";
if ($indirectory =~ /32/) {
$line5 = " hdf5-$version-$outsubdir-shared.tar.gz - Includes C, C++, F90 and Java APIs (using";
$compilerstring2 = " gcc, g++, and gfortran 4.4.7)\n";
} else {
$line5 = " hdf5-$version-$outsubdir-shared.tar.gz - Includes C, C++, F90 and Java APIs (using";
$compilerstring2 = " gcc, g++, and gfortran 4.8.5 and java 1.8.0_51)\n";
}
}
elsif ($indirectory =~ /emu/) {
# $line1 = " hdf5-$version-$outsubdir-16API.tar.gz - Includes C, C++, F90 APIs (using\n";
$line3 = " hdf5-$version-$outsubdir-static.tar.gz - Includes C, C++, F90 APIs (using";
$line5 = " hdf5-$version-$outsubdir-shared.tar.gz - Includes C, C++, F90 APIs (using";
$compilerstring = " Sun C and C++ 5.12, Sun Fortran 95 8.6)\n";
}
elsif ($indirectory =~ /kite/) {
$line3 = " hfd5-$version-$outsubdir-static.tar.gz - Includes C, C++, F90 APIs (using";
$line5 = " hfd5-$version-$outsubdir-shared.tar.gz - Includes C, C++, F90 APIs (using";
$compilerstring = " Apple clang/clang++ 5.1 from Xcode 5.0.2,
gfortran 4.8.2)\n";
}
elsif ($indirectory =~ /quail/) {
$line3 = " hfd5-$version-$outsubdir-static.tar.gz - Includes C, C++, F90 APIs (using";
$line5 = " hfd5-$version-$outsubdir-shared.tar.gz - Includes C, C++, F90 APIs (using";
$compilerstring = " Apple clang/clang++ 6.0 from Xcode 5.1,
gfortran 4.9.2)\n";
}
elsif ($indirectory =~ /osx1010test/) {
$line3 = " hdf5-$version-$outsubdir-static.tar.gz - Includes C, C++, F90 APIs (using";
$line5 = " hdf5-$version-$outsubdir-shared.tar.gz - Includes C, C++, F90 APIs (using";
$compilerstring = " Apple clang/clang++ 6.1 from Xcode 6.1,
gfortran 4.9.2)\n";
}
elsif ($indirectory =~ /osx1011test/) {
$line3 = " hdf5-$version-$outsubdir-static.tar.gz - Includes C, C++, F90 APIs (using";
$line5 = " hdf5-$version-$outsubdir-shared.tar.gz - Includes C, C++, F90 APIs (using";
$compilerstring = " Apple clang/clang++ 7.0.2 from Xcode 7.0,
gfortran 5.2.0)\n";
}
print OUTFILE $line3;
print OUTFILE $compilerstring1."\n";
if ($line5 ne "") {
print OUTFILE $line5;
print OUTFILE $compilerstring2."\n";
}
#elsif ($indirectory =~ /-16API/) {
# print OUTFILE $line1;
# print OUTFILE $compilerstring;
# print OUTFILE " USES THE VERSION 1.6 DEFAULT API\n";
# print OUTFILE " MAPPING.\n\n";
#}
print OUTFILE " utilities/ - Directory containing the compiled HDF5 utilities.\n";
print OUTFILE " These utilities are STATICALLY linked and will run as is.\n\n";
#print OUTFILE " The tools can be downloaded separately, or ALL in one\n";
#print OUTFILE " compressed file (5-$version-$outsubdir-static-util.tar.gz).\n\n";
print OUTFILE "\n";
print OUTFILE "To obtain the HDF5 distribution, 'unzip' and 'untar' the distribution\n";
print OUTFILE "file:\n\n";
print OUTFILE " gzip -cd <gz file from above> | tar xvf -\n";
#$cmd = "grep \"Configured by:\" $indirectory/$key-static/lib/libhdf5.settings";
#$_ = `$cmd`;
#s/Configured by://;
#s/^\s+//;
#print OUTFILE $_;
#chomp;
#my $hostnamestring = $_;
#s/(^\w+)(\s)(\S+)/$1/;
#s/(^.*)(-)(.*)(200[7-8])(.*)(\s)(\S+)/$1 $5/;
#my $platformstring = $_ . ":\n\n";
#my @hostnamestring = split /@/, $hostnamestring;
#print "Size of hostnamestring is ", scalar @hostnamestring, "\n";
#print $hostnamestring[0] . "\t" . $hostnamestring[2]."\t".$hostnamestring[19]."\n";
#my $platformstring = $hostnamestring[1].":\n\n";
#$hostnamestring = $hostnamestring[1];
#my $pos = index $hostnamestring, ".";
#if ($pos > 0) {
# @hostnamestring = split /\./, $hostnamestring;
# $platformstring = $hostnamestring[0].":\n\n";
#}

View File

@@ -1,7 +1,6 @@
#!/bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
@@ -53,23 +52,23 @@ for compressing the resulting tar archive (if none are given then
information is available in the README_HPC file.
doc -- produce the latest doc tree in addition to the archive.
An md5 checksum is produced for each archive created and stored in the md5 file.
A sha256 checksum is produced for each archive created and stored in the sha256 file.
Examples:
$ bin/release -d /tmp
/tmp/hdf5-1.8.13-RELEASE.txt
/tmp/hdf5-1.8.13.md5
/tmp/hdf5-1.8.13.sha256
/tmp/hdf5-1.8.13.tar
$ bin/release -d /tmp gzip
/tmp/hdf5-1.8.13-RELEASE.txt
/tmp/hdf5-1.8.13.md5
/tmp/hdf5-1.8.13.sha256
/tmp/hdf5-1.8.13.tar.gz
$ bin/release -d /tmp tar gzip zip
/tmp/hdf5-1.8.13-RELEASE.txt
/tmp/hdf5-1.8.13.md5
/tmp/hdf5-1.8.13.sha256
/tmp/hdf5-1.8.13.tar
/tmp/hdf5-1.8.13.tar.gz
/tmp/hdf5-1.8.13.tar.zip
@@ -206,7 +205,7 @@ tar2cmakezip()
# step 3: add LIBAEC.tar.gz, ZLib.tar.gz and cmake files
cp /mnt/scr1/pre-release/hdf5/CMake/LIBAEC.tar.gz $cmziptmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmziptmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.14.4-Source.zip $cmziptmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-2.0.2-Source.zip $cmziptmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/hdf5_plugins-master.zip $cmziptmpsubdir
cp $cmziptmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmziptmpsubdir
cp $cmziptmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmziptmpsubdir
@@ -298,7 +297,7 @@ tar2cmaketgz()
# step 3: add LIBAEC.tar.gz, ZLib.tar.gz and cmake files
cp /mnt/scr1/pre-release/hdf5/CMake/LIBAEC.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.14.4-Source.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-2.0.2-Source.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/hdf5_plugins-master.tar.gz $cmgztmpsubdir
cp $cmgztmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpsubdir
cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpsubdir
@@ -377,7 +376,7 @@ tar2hpccmaketgz()
# step 3: add LIBAEC.tar.gz, ZLib.tar.gz and cmake files
cp /mnt/scr1/pre-release/hdf5/CMake/LIBAEC.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.14.4-Source.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-2.0.2-Source.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/hdf5_plugins-master.tar.gz $cmgztmpsubdir
cp $cmgztmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpsubdir
cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpsubdir
@@ -532,43 +531,43 @@ test "$verbose" && echo " Running tar..." 1>&2
(cd "$tmpdir" && exec tar -ch --exclude-vcs -f "$HDF5_VERS.tar" "./$HDF5_VERS" || exit 1 )
# Compress
MD5file=$HDF5_VERS.md5
cp /dev/null $DEST/$MD5file
SHA256=$HDF5_VERS.sha256
cp /dev/null $DEST/$SHA256
for comp in $methods; do
case $comp in
tar)
cp -p $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.tar
(cd $DEST; md5sum $HDF5_VERS.tar >> $MD5file)
(cd $DEST; sha256sum $HDF5_VERS.tar >> $SHA256)
;;
gzip)
test "$verbose" && echo " Running gzip..." 1>&2
gzip -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.gz
(cd $DEST; md5sum $HDF5_VERS.tar.gz >> $MD5file)
(cd $DEST; sha256sum $HDF5_VERS.tar.gz >> $SHA256)
;;
cmake-tgz)
test "$verbose" && echo " Creating CMake tar.gz file..." 1>&2
tar2cmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.tar.gz 1>&2
(cd $DEST; md5sum CMake-$HDF5_VERS.tar.gz >> $MD5file)
(cd $DEST; sha256sum CMake-$HDF5_VERS.tar.gz >> $SHA256)
;;
hpc-cmake-tgz)
test "$verbose" && echo " Creating HPC-CMake tar.gz file..." 1>&2
tar2hpccmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/HPC-CMake-$HDF5_VERS.tar.gz 1>&2
(cd $DEST; md5sum HPC-CMake-$HDF5_VERS.tar.gz >> $MD5file)
(cd $DEST; sha256sum HPC-CMake-$HDF5_VERS.tar.gz >> $SHA256)
;;
bzip2)
test "$verbose" && echo " Running bzip2..." 1>&2
bzip2 -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.bz2
(cd $DEST; md5sum $HDF5_VERS.tar.bz2 >> $MD5file)
(cd $DEST; sha256sum $HDF5_VERS.tar.bz2 >> $SHA256)
;;
zip)
test "$verbose" && echo " Creating zip ball..." 1>&2
tar2zip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.zip 1>&2
(cd $DEST; md5sum $HDF5_VERS.zip >> $MD5file)
(cd $DEST; sha256sum $HDF5_VERS.zip >> $SHA256)
;;
cmake-zip)
test "$verbose" && echo " Creating CMake-zip ball..." 1>&2
tar2cmakezip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.zip 1>&2
(cd $DEST; md5sum CMake-$HDF5_VERS.zip >> $MD5file)
(cd $DEST; sha256sum CMake-$HDF5_VERS.zip >> $SHA256)
;;
doc)
if [ "${DOCVERSION}" = "" ]; then

View File

@@ -1,10 +1,10 @@
#!/bin/sh
#
# Copyright by The HDF Group.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# Copyright by The HDF Group.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from

View File

@@ -5,7 +5,6 @@ $indent=4;
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,7 +1,6 @@
#!/bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,7 +1,6 @@
#!/usr/bin/env perl
##
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
@@ -77,7 +76,6 @@ $Source = "";
"H5G_obj_t" => "Go",
"H5G_stat_t" => "Gs",
"hsize_t" => "h",
"H5_alloc_stats_t" => "Ha",
"H5_atclose_func_t" => "Hc",
"hssize_t" => "Hs",
"H5E_major_t" => "i", # H5E_major_t is typedef'd to hid_t

View File

@@ -8,12 +8,10 @@ use warnings;
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the files COPYING and Copyright.html. COPYING can be found at the root
# of the source code distribution tree; Copyright.html can be found at the
# root level of an installed copy of the electronic HDF5 document set and
# is linked from the top-level documents page. It can also be found at
# http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have
# access to either file, you may request a copy from help@hdfgroup.org.
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
# Quincey Koziol
# 9 Aug 2013
@@ -247,6 +245,18 @@ while (<>) {
} elsif($_ =~ /^\s*[Ww]arning:.*/) {
$name = $last_c_name;
($toss, $warning, $extra, $extra2) = split /\:/, $_;
# Check for file-scope gcc Fortran warning output
} elsif($_ =~ /f\d\d\d: Warning:/) {
# These are interspersed with the "compiling a file" output
# when compiling with `make -j` and thus difficult to tie to
# any particular file. They are due to things like inappropriate
# build options and don't have a line number.
#
# They start with f, as in f951
$name = "(generic)";
$line = int(rand(1000000)); # Hack to avoid counting as duplictates
($warning) = $_ =~ /\[(.*)\]/x;
# Check for FORTRAN warning output
} elsif($_ =~ /^Warning:.*/) {
$name = $last_fort_name;

View File

@@ -1,76 +0,0 @@
#!/bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://www.hdfgroup.org/licenses.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
# Fix configure file so that it can launch configure testing executable
# via the proper launching command, e.g., yod. (Thus the name yodconfigure
# is used.)
#
# Author: Albert Cheng
if [ "$1" = -f ]; then
FORCEMODE=yes
echo turn FORCEMODE to $FORCEMODE
shift
fi
if [ $# -ne 1 ]; then
echo "Usage: $0 [-f] <configure file>"
echo " -f apply the change even if it has been applied already."
exit 1
fi
confile=$1
if [ ! -w $confile ]; then
echo "$0: $confile is not writable"
exit 1
fi
ACTRY_NAME="ACTRY()"
if grep ^"$ACTRY_NAME"$ $confile >/dev/null 2>&1 && [ "$FORCEMODE" != yes ]; then
echo "$0: $confile is already yodconfigure ready. Use -f to force yodconfigure again."
exit 1
fi
# Insert the ACTRY function after the 1st line which is the #!/bin/sh.
# Change all "eval $ac_try" commands to call ACTRY.
# auto-configure have changed the ac_try syntax from 'eval $ac_try' to
# 'eval "$ac_try"'. Thus requiring two very similar global-substitute.
# The single quotes around EOF tell shell NOT to expand or do substitution in
# the body of ed input.
#
ed - $confile <<'EOF'
1a
# ===inserted by yodconfigure ====
# ACTRY will figure out when it is approprirate to run the command by the
# $RUNSERIAL launcher (e.g., yod -sz 1) and when to just run it as is.
# So far, ./a.out and ./conftest are names of real executable that should
# be run by $RUNSERIAL.
#
# (uncomment the echo line if you want to see what is going on.)
ACTRY()
{
#echo ACTRY: args are: $* > /dev/tty
if [ "$1" = ./a.out -o "$1" = ./conftest ]; then
# echo $RUNSERIAL $* > /dev/tty
$RUNSERIAL $*
else
$*
fi
}
# === end of ACTRY inserted by yodconfigure ====
.
g/eval $ac_try/s/eval/eval ACTRY/
g/eval "$ac_try"/s/eval/eval ACTRY/
w
q
EOF

View File

@@ -1,4 +1,4 @@
cmake_minimum_required (VERSION 3.12)
cmake_minimum_required (VERSION 3.18)
project (HDF5_CPP CXX)
add_subdirectory (src)

View File

@@ -1,6 +1,5 @@
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,4 +1,4 @@
cmake_minimum_required (VERSION 3.12)
cmake_minimum_required (VERSION 3.18)
project (HDF5_CPP_EXAMPLES CXX)
# --------------------------------------------------------------------

View File

@@ -55,7 +55,7 @@ foreach (example ${examples})
-D "TEST_OUTPUT=cpp_ex_${example}.txt"
#-D "TEST_REFERENCE=cpp_ex_${example}.out"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
-P "${HDF_RESOURCES_DIR}/runTest.cmake"
)
endif ()
set_tests_properties (CPP_ex_${example} PROPERTIES FIXTURES_REQUIRED clear_cppex)
@@ -107,7 +107,7 @@ foreach (example ${tutr_examples})
-D "TEST_OUTPUT=tutr_cpp_ex_${example}.txt"
#-D "TEST_REFERENCE=cpp_ex_tutr_${example}.out"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
-P "${HDF_RESOURCES_DIR}/runTest.cmake"
)
endif ()
set_tests_properties (CPP_ex_${example} PROPERTIES FIXTURES_REQUIRED clear_cppex_tutr)

View File

@@ -1,6 +1,5 @@
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,7 +1,6 @@
#! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -10402,13 +10402,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void H5Location::moveLink(const char* src_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>            </span>const Group&amp;
normal'><span style='mso-spacerun:yes'>            </span>const Group&amp;
dst, const char* dst_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>            </span>const
normal'><span style='mso-spacerun:yes'>            </span>const
LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>            </span>const
normal'><span style='mso-spacerun:yes'>            </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10441,13 +10441,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void H5Location::moveLink(const H5std_string&amp; src_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>            </span>const Group&amp;
normal'><span style='mso-spacerun:yes'>            </span>const Group&amp;
dst, const H5std_string&amp; dst_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>            </span>const
normal'><span style='mso-spacerun:yes'>            </span>const
LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>            </span>const
normal'><span style='mso-spacerun:yes'>            </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10480,10 +10480,10 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void H5Location::moveLink(const char* src_name, const char* dst_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>            </span>const
normal'><span style='mso-spacerun:yes'>            </span>const
LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>            </span>const
normal'><span style='mso-spacerun:yes'>            </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10516,13 +10516,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void H5Location::moveLink(const H5std_string&amp; src_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>            </span>const
normal'><span style='mso-spacerun:yes'>            </span>const
H5std_string&amp; dst_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>            </span>const
normal'><span style='mso-spacerun:yes'>            </span>const
LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>            </span>const
normal'><span style='mso-spacerun:yes'>            </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10693,7 +10693,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>const LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>const<span style='mso-spacerun:yes'>  </span>LinkAccPropList&amp;
normal'>const<span style='mso-spacerun:yes'>  </span>LinkAccPropList&amp;
lapl = LinkAccPropList::DEFAULT) </p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10770,13 +10770,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void H5Location::link(const char *curr_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const Group&amp;
normal'><span style='mso-spacerun:yes'>             </span>const Group&amp;
new_loc, const char *new_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10809,13 +10809,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void H5Location::link(const H5std_string&amp; curr_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const Group&amp;
normal'><span style='mso-spacerun:yes'>             </span>const Group&amp;
new_loc, const H5std_string&amp; new_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10848,13 +10848,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void H5Location::link(const char *curr_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const hid_t
normal'><span style='mso-spacerun:yes'>             </span>const hid_t
same_loc, const char *new_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10887,13 +10887,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void H5Location::link(const H5std_string&amp; curr_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const hid_t
normal'><span style='mso-spacerun:yes'>             </span>const hid_t
same_loc, const H5std_string&amp; new_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10932,10 +10932,10 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void H5Location::link(const char *target_name, const char *link_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10968,13 +10968,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void H5Location::link(const H5std_string&amp; target_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
H5std_string&amp; link_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -11085,7 +11085,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void CommonFG::unlink( const char* name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -11119,7 +11119,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void CommonFG::unlink( const H5std_string&amp; name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -11153,7 +11153,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void H5Location::unlink( const char* name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const
normal'><span style='mso-spacerun:yes'>             </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -11187,7 +11187,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void H5Location::unlink( const H5std_string&amp; name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>             </span>const LinkAccPropList&amp;
normal'><span style='mso-spacerun:yes'>             </span>const LinkAccPropList&amp;
lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -11495,7 +11495,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>H5L_info2_t getLinkInfo(const char* link_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-tab-count:1'>               </span>const
normal'><span style='mso-tab-count:1'>               </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -11528,7 +11528,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>H5L_info2_t getLinkInfo(const H5std_string&amp; link_name,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-tab-count:1'>               </span>const
normal'><span style='mso-tab-count:1'>               </span>const
LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -14522,7 +14522,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
normal'>void DSetCreatPropList::setFilter(H5Z_filter_t filter_id, unsigned
int flags,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>        </span>size_t cd_nelmts, const
normal'><span style='mso-spacerun:yes'>        </span>size_t cd_nelmts, const
unsigned int cd_values[])</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -14597,10 +14597,10 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>H5Z_filter_t DSetCreatPropList::getFilter(int filter_number,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>        </span>unsigned int
normal'><span style='mso-spacerun:yes'>        </span>unsigned int
&amp;flags, size_t &amp;cd_nelmts, unsigned int* cd_values,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>        </span>size_t namelen, char
normal'><span style='mso-spacerun:yes'>        </span>size_t namelen, char
name[], unsigned int&amp; filter_config)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -14639,10 +14639,10 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'>void DSetCreatPropList::getFilterById(H5Z_filter_t filter_id,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>        </span>unsigned int
normal'><span style='mso-spacerun:yes'>        </span>unsigned int
&amp;flags, size_t &amp;cd_nelmts, unsigned int* cd_values,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>        </span>size_t namelen, char
normal'><span style='mso-spacerun:yes'>        </span>size_t namelen, char
name[], unsigned int &amp;filter_config)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -19291,10 +19291,10 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
normal'>void H5Library::setFreeListLimits(int reg_global_lim, int
reg_list_lim,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>        </span>int arr_global_lim, int
normal'><span style='mso-spacerun:yes'>        </span>int arr_global_lim, int
arr_list_lim, int blk_global_lim,</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal'><span style='mso-spacerun:yes'>        </span>int blk_list_lim)</p>
normal'><span style='mso-spacerun:yes'>        </span>int blk_list_lim)</p>
</td>
<td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;

View File

@@ -1,4 +1,4 @@
cmake_minimum_required (VERSION 3.12)
cmake_minimum_required (VERSION 3.18)
project (HDF5_CPP_SRC CXX)
#-----------------------------------------------------------------------------
@@ -173,8 +173,8 @@ endif ()
#-----------------------------------------------------------------------------
set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${HDF5_INSTALL_LIB_DIR})
set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${HDF5_INSTALL_INCLUDE_DIR})
set (_PKG_CONFIG_LIBNAME "${HDF5_CPP_LIB_CORENAME}")
set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
@@ -187,8 +187,8 @@ if (BUILD_SHARED_LIBS)
set (_PKG_CONFIG_SH_LIBS "${_PKG_CONFIG_SH_LIBS} -l${HDF5_CPP_LIB_CORENAME}")
endif ()
set (_PKG_CONFIG_REQUIRES "${HDF5_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}")
set (_PKG_CONFIG_REQUIRES_PRIVATE "${HDF5_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}")
set (_PKG_CONFIG_REQUIRES "${HDF5_LIB_CORENAME} = ${HDF5_PACKAGE_VERSION}")
set (_PKG_CONFIG_REQUIRES_PRIVATE "${HDF5_LIB_CORENAME} = ${HDF5_PACKAGE_VERSION}")
configure_file (
${HDF_CONFIG_DIR}/libhdf5.pc.in

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,7 +1,6 @@
// C++ informative line for the emacs editor: -*- C++ -*-
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,7 +1,6 @@
// C++ informative line for the emacs editor: -*- C++ -*-
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,7 +1,6 @@
// C++ informative line for the emacs editor: -*- C++ -*-
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,7 +1,6 @@
// C++ informative line for the emacs editor: -*- C++ -*-
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,7 +1,6 @@
// C++ informative line for the emacs editor: -*- C++ -*-
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

View File

@@ -1,7 +1,6 @@
// C++ informative line for the emacs editor: -*- C++ -*-
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *

Some files were not shown because too many files have changed in this diff Show More