| Commit message (Collapse) | Author | Age | Files | Lines |
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* Add Doxygen for all H5FD_<VFD> initializers
* Add Doxygen for all H5FD_<VFD>_VALUE values
* Mark H5FD_<vfd>_init() calls private in Doxygen
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*
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* 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.
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* Take a stab at using constructors to initialize instead of
function-entry macros. This is a work in progress. It's good enough to
run `many_dsets`.
* Committing clang-format changes
* Add the `many_dsets` benchmark and some scripts I used on jelly for
setting up the build/test environment and for recording/flame-graphing
profiles.
* Committing clang-format changes
* Change my Makefile and environment script to work both on jelly
and on mayll (and probably on Summit).
* Disable clang-format "fix."
* Replace the `if (!H5_TERM_GLOBAL)` test in each FUNC_ENTER_ macro with
`if (true)`.
* Fix bad grammar in a comment.
* Instead of labeling the H5*__init_package routines constructors, fold
each into an initialization routine, H5*_init(), and call each of
the H5*_init() routines. Call most of the H5*_init() routines from
H5_init_library() in an explicit order that I found out earlier by
instrumenting each __init_package routine and running the library
tests. Roll H5FD*__init_package routines into H5FD*_init() routines.
This change ends just-in-time initialization of package dependencies by
package initializers.
Don't track in per-package variables (H5_PKG_INIT_VAR) whether each
package has been initialized. Instead, track in a single library
variable whether the whole library is initialized or not.
Drive the initialization of packages by H5_init_library() with a table
of initializer routines. Also drive the termination of packages by
H5_term_library() with a table.
Perform initialization as needed from FUNC_ENTER_API_INIT(err). This
basically restores the old behavior of that macro.
Delete a bunch of #definitions in H5private.h that have fallen out of
use with these changes.
* Committing clang-format changes
* Undo the bad auto-formatting that appears to have occurred in spite
of my disabling it. Bracket some code in /* clang-format off */ /*
clang-format on */ to prevent a recurrence.
* Remove a diagnostic abort().
* Fix a logic error: print a comma between every package terminator run,
and don't print an initial comma.
* Complete the changes I started in H5_term_library() that undo the bad
auto-formatting.
Stop tracking whether package "tops" were initialized in per-package
variables H5*_top_package_initialize_s. H5_term_library() takes care of
that for them.
Remove H5R_top_term_package() and H5R_term_package(), they don't do
anything.
* Committing clang-format changes
* NFCI. Simplify macro text: replace `if (true) {` with `{`.
* Fix formatting and suppress clang-format on a longer range.
* Quiet some unused label, unused variable complaints that cropped up
after I simplified the FUNC_ENTER_ macros for the sake of performance.
* Committing clang-format changes
* Delete some programs and scripts that don't belong in the pull request.
* Use the right function-entry macro.
* Use a sensible format and disable auto-formatting.
* Stop calling do-nothing initializer H5FS_init(). Delete it.
* Document what changes to make if the default VFD changes.
* While I am here, change an `await_prior` flag on the terminator table
to `true` to match the previous, non-table-driven code that was here.
Found the oversight making the following changes:
NFCI: insert an empty line and copy over slightly-edited comments from
the previous version, where those comments still correctly explained how
library termination operated.
* NFCI: lower a staircase.
* Replace every occurrence of FUNC_ENTER_NOAPI_INIT(...) with H5_PUSH_FUNC
since that is all that that macro does any more.
Quiet a bunch of new warnings by changing FUNC_ENTER_NOAPI(...) to
FUNC_ENTER_NOAPI_NOERR and removing disused `done:` labels.
* NFCI: add curly braces around a multiline statement.
* Quiet a signed/unsigned comparison warning.
* Add some documentation about library initialization and shutdown.
* Make sure that the library is initialized, or else that initialization
is already underway, before performing any VFD's initialization.
* Committing clang-format changes
* Committing clang-format changes
* Reduce differences from `develop` branch.
* Always initialize `tot_init`.
* Committing clang-format changes
* Fix typo: H5SL_init initializes skip lists, not VOL.
* Remove H5_TERM_GLOBAL test in H5T_init. H5T_init was unusual in that
it tested H5_TERM_GLOBAL and exited early if it was set. No other
module initializers did that, and I cannot find any reason that should
be necessary. Tests still pass when I remove it, so away it goes.
* Use HD prefix.
* Add function header comments.
* Drop the intermediate variable, it's only used once.
* Extract subroutine `H5FDperform_init(hid_t (*init)(void))` that
initializes the library, if necessary, before calling its VFD-initializer
argument. Use H5FDperform_init in the definition of the symbols
H5FD_<vfd> (e.g., H5FD_SEC2), which may be evaluated before the library
is initialized, like so:
```
```
I implement H5FDperform_init in its own source file, H5FDperform.c,
and exclude that file from trace processing because the `bin/trace`
cannot deal with the function-pointer type.
* Straggler from last: add new source file src/H5FDperform.c.
* Committing clang-format changes
* Add a missing file to the MANIFEST.
* Switch to FUNC_ENTER_API_NOINIT in H5FDperform_init() and hbool_t in
H5_term_library().
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Implement support for loading of Virtual File Drivers as plugins
Fix plugin caching for VOL connector and VFD plugins
Fix plugin iteration to skip paths that can't be opened
* Enable dynamic loading of VFDs with HDF5_DRIVER environment variable
* Temporarily disable error reporting during H5F_open double file open
* Default to using HDstat in h5_get_file_size for unknown VFDs
* Use macros for some environment variables that HDF5 interprets
* Update "null" and "ctl testing" VFDs
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* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING
file - src and test directories.
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header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email
addresses from library source code (still needs cleaned from other directories).
Misc. warning, style, and whitespace cleanup.
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hdf5_1_10
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
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Clean up code a bit, move new "terminate" VFD callback to new position
in H5FD_class_t struct.
Tested on:
Mac OS X/32 10.6.7 (amazon) w/debug & production
(h5committest not required on this branch)
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Handle external links from symlinked files by adding another check to
look for "child" files for links from the actual location of the "parent" file,
instead of from the location of the symlink.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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copyright notice.
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
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Code cleanup
Description:
Add destructor to match constructor fr VFLs when they are shut down by the
library.
Solution:
Added H5FD_*_term() routines to "undo" changes made in H5FD_*_init()
routines.
Platforms tested:
IBM p690 (copper)
too minor to require h5committest
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Update
Description:
Updated copyright statement in files which hadn't been updated yet.
Platforms tested:
Linux (Only comment change)
Misc. update:
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Purpose:
__DLL__ is a keyword in some platforms and __DLL__ is also defined as a macro for windows DLL applications.
That causes problems.
Description:
Solution:
Use H5_DLL*** to replace __DLL***__ at all header files.
Change the macro defination at H5api_adpt.h.
Platforms tested:
linux2.2.18smp, irix64, solaris 2.7 and windows 2000
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Document bug fix
Description:
IMPORTANT! IMPORTANT! IMPORTANT!
A case where metadata in a file could get corrupted in certain unusual
sitations was detected and fixed.
In certain circumstances, metadata could get cached in the raw data cache,
and if that particular piece of metadata was updated on disk while
incorrectly cached, the new metadata would get overwritten with the stale
metadata from the raw data cache when it was flushed out.
Additionally, I've patched up the raw data cache to be smarter about how
much it caches and how much I/O it triggers, leading to some speedups.
Solution:
Changed the raw data I/O routines which perform caching to require a
parameter with the size of the dataset being accessed and limited the
cache to no more than that many bytes.
Platforms tested:
FreeBSD 4.3 (hawkwind)
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Update
Description:
Changed
#include <hdf_file.h>
construct to
#include "hdf_file.h"
so that the GNU compiler can more easily pick up the dependencies
which it places in the .depend and Dependencies files. Also
regenerated the Dependencies to go along with this.
Platforms tested:
Linux
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could see them
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----------------------
This extensive change is the virtual file layer implementation. I've
ported and tested the sec2, family, and core drivers and only ported
the mpio driver (Albert will test it). So if you need MPIO I would
recommend sticking with the previous version for a while.
You will get a few compile warnings about split and stdio drivers not
being implemented and possibly tracing information not inserted in
some of the drivers. You can safely ignore them but I plan to fix
them.
I'm still working on the split driver because I just realized that it
needs a part of the VFL that isn't written yet.
Documentation is being updated also because there were some minor
changes (mostly just name changes). It should be available on my web
site later this week.
./MANIFEST
./src/Makefile.in
./src/hdf5.h
./src/H5Flow.c [REMOVED]
./src/H5Fstdio.c [REMOVED]
./src/H5Fsec2.c [REMOVED]
./src/H5Fsplit.c [REMOVED]
./src/H5Fmpio.c [REMOVED]
./src/H5Ffamily.c [REMOVED]
./src/H5Fcore.c [REMOVED]
./src/H5MFpublic.h [REMOVED]
./src/H5FD.c [NEW]
./src/H5FDcore.c [NEW]
./src/H5FDcore.h [NEW]
./src/H5FDfamily.c [NEW]
./src/H5FDfamily.h [NEW]
./src/H5FDmpio.c [NEW]
./src/H5FDmpio.h [NEW]
./src/H5FDprivate.h [NEW]
./src/H5FDpublic.h [NEW]
./src/H5FDsec2.c [NEW]
./src/H5FDsec2.h [NEW]
Removed/added files for virtual file layer.
./bin/trace
./src/H5.c
Removed unused public datatypes and added new VFL public
datatypes.
Changed an error message.
./config/BlankForm
./config/dec-flags
./config/gnu-flags
./config/hpux10.20
./config/hpux9.03
./config/irix5.x
./config/irix6.x
./config/solaris2.x
./config/unicosmk
Removed the H5F_OPT_SEEK and H5F_LOW_DFLT constants from the
configuration since they're no longer applicable. The default
file driver is always the sec2 driver and it always optimizes
calls to lseek() or lseek64().
./config/depend.in
C preprocessor errors generated during automatic dependency
building are sent to /dev/null to prevent them from appearing
twice in the make output.
./src/H5AC.c
./src/H5B.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Oshared.c
./src/H5T.c
./src/H5detect.c
./test/ohdr.c
Changed H5F_ADDR_UNDEF to HADDR_UNDEF to be more consistent
with the `haddr_t' datatype which is now a public type.
./src/H5D.c
./src/H5P.c
./src/H5Ppublic.h
./src/H5Tconv.c
./test/cmpd_dset.c
./test/dsets.c
./test/overhead.c
./test/tselect.c
./test/tvltypes.c
The H5P_DATASET_XFER constant was changed to H5P_DATA_XFER
because the properties apply to all types of I/O operations,
not just datasets.
./src/H5B.c
./src/H5Bprivate.h
./src/H5D.c
./src/H5Dpublic.h
./src/H5F.c
./src/H5Farray.c
./src/H5Fistore.c
./src/H5Fprivate.h
./src/H5Fpublic.h
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5R.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Spoint.c
./src/H5Sprivate.h
./test/big.c
./test/h5test.c
./test/istore.c
./testpar/t_dset.c
./testpar/t_file.c
./tools/h5debug.c
./tools/h5ls.c
Modified to work with the virtual file layer by calling H5FD_*
functions instead of H5F_low_* functions and by passing file
access and data transfer properties by object ID instead of
pointer.
Changed H5D_transfer_t to H5FD_mpio_xfer_t since the
COLLECTIVE vs. INDEPENDENT transfer mode is specific to the
MPIO file driver.
Moved MPIO-specific stuff into the MPIO driver.
./src/H5B.c
./src/H5D.c
./src/H5Fprivate.h
The H5F_mpio_* private functions were renamed and placed in
the H5FDmpio driver except those which appeared in H5Smpio.c.
./src/H5E.c
./src/H5Epublic.h
Added major error number H5E_VFL for virtual file layer
related errors.
./src/H5F.c
./src/H5Fprivate.h
Changed the logic that controls whether the boot block is
written. Instead of assuming that the first call to write the
boot block is only to allocate space, I've added a function
argument which makes this explicit.
Changed the way files are compared so that a driver-defined
comparison function can be called. Files which belong to
different drivers are always considered different.
Removed H5F_driver_t since file drivers are now identified by
object ID instead of a special non-user-extendible datatype.
Removed all the hard-coded low-level file properties which
have been replaced by the various file drivers.
./src/H5I.c
./src/H5Iprivate.h
Added the H5I_inc_ref() which was removed a few months ago
since we finally have a use for it.
./src/H5Ipublic.h
Added the H5I_VFL object ID type to identify file drivers in
the virtual file layer.
./src/H5MF.c
./src/H5MFprivate.h
Moved all the allocation/deallocation code into the virtual
file layer which allows file drivers to override much of it.
./src/H5P.c
./src/H5Ppublic.h
Moved file driver-specific code into the various file driver
files.
The H5Pcopy() and H5Pclose() functions make calls into the
virtual file driver to manage the memory for driver-specific
file access and data transfer properties.
./src/H5private.h
./src/H5public.h
The `haddr_t' type is now public.
./test/tfile.c
Added a few more comments.
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