| Commit message (Collapse) | Author | Age | Files | Lines |
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Code cleanup/new feature.
Description:
Split FUNC_LEAVE into API and non-API specific versions. This allows a
solution to compiling this branch with C++, as well as reducing the size
of the binaries produced.
Platforms tested:
FreeBSD 4.7 (sleipnir) w/serial, parallel (including MPE) & thread-safe
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Lots of performance improvements & a couple new internal API interfaces.
Description:
Performance Improvements:
- Cached file offset & length sizes in shared file struct, to avoid
constantly looking them up in the FCPL.
- Generic property improvements:
- Added "revision" number to generic property classes to speed
up comparisons.
- Changed method of storing properties from using a hash-table
to the TBBT routines in the library.
- Share the propery names between classes and the lists derived
from them.
- Removed redundant 'def_value' buffer from each property.
- Switching code to use a "copy on write" strategy for
properties in each list, where the properties in each list
are shared with the properties in the class, until a
property's value is changed in a list.
- Fixed error in layout code which was allocating too many buffers.
- Redefined public macros of the form (H5open()/H5check, <variable>)
internally to only be (<variable>), avoiding innumerable useless
calls to H5open() and H5check_version().
- Reuse already zeroed buffers in H5F_contig_fill instead of
constantly re-zeroing them.
- Don't write fill values if writing entire dataset.
- Use gettimeofday() system call instead of time() system when
checking the modification time of a dataset.
- Added reference counted string API and use it for tracking the
names of objects opening in a file (for the ID->name code).
- Removed redundant H5P_get() calls in B-tree routines.
- Redefine H5T datatype macros internally to the library, to avoid
calling H5check redundantly.
- Keep dataspace information for dataset locally instead of reading
from disk each time. Added new module to track open objects
in a file, to allow this (which will be useful eventually for
some FPH5 metadata caching issues).
- Remove H5AC_find macro which was inlining metadata cache lookups,
and call function instead.
- Remove redundant memset() calls from H5G_namei() routine.
- Remove redundant checking of object type when locating objects
in metadata cache and rely on the address only.
- Create default dataset object to use when default dataset creation
property list is used to create datasets, bypassing querying
for all the property list values.
- Use default I/O vector size when performing raw data with the
default dataset transfer property list, instead of querying for
I/O vector size.
- Remove H5P_DEFAULT internally to the library, replacing it with
more specific default property list based on the type of
property list needed.
- Remove redundant memset() calls in object header message (H5O*)
routines.
- Remove redunant memset() calls in data I/O routines.
- Split free-list allocation routines into malloc() and calloc()-
like routines, instead of one combined routine.
- Remove lots of indirection in H5O*() routines.
- Simplify metadata cache entry comparison routine (used when
flushing entire cache out).
- Only enable metadata cache statistics when H5AC_DEBUG is turned
on, instead of always tracking them.
- Simplify address comparison macro (H5F_addr_eq).
- Remove redundant metadata cache entry protections during dataset
creation by protecting the object header once and making all
the modifications necessary for the dataset creation before
unprotecting it.
- Reduce # of "number of element in extent" computations performed
by computing and storing the value during dataspace creation.
- Simplify checking for group location's file information, when file
has not been involving in file-mounting operations.
- Use binary encoding for modification time, instead of ASCII.
- Hoist H5HL_peek calls (to get information in a local heap)
out of loops in many group routine.
- Use static variable for iterators of selections, instead of
dynamically allocation them each time.
- Lookup & insert new entries in one step, avoiding traversing
group's B-tree twice.
- Fixed memory leak in H5Gget_objname_idx() routine (tangential to
performance improvements, but fixed along the way).
- Use free-list for reference counted strings.
- Don't bother copying object names into cached group entries,
since they are re-created when an object is opened.
The benchmark I used to measure these results created several thousand
small (2K) datasets in a file and wrote out the data for them. This is
Elena's "regular.c" benchmark.
These changes resulted in approximately ~4.3x speedup of the
development branch when compared to the previous code in the
development branch and ~1.4x speedup compared to the release
branch.
Additionally, these changes reduce the total memory used (code and
data) by the development branch by ~800KB, bringing the development
branch back into the same ballpark as the release branch.
I'll send out a more detailed description of the benchmark results
as a followup note.
New internal API routines:
Added "reference counted strings" API for tracking strings that get
used by multiple owners without duplicating the strings.
Added "ternary search tree" API for text->object mappings.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Other platforms/configurations tested?
FreeBSD 4.7 (sleipnir) serial & parallel
Solaris 2.6 (baldric) serial
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Code cleanup
Description:
Clean up warnings with gcc 3.2.1
Platforms tested:
FreeBSD 4.7 (sleipnir) w/C++, changes too small for triple check
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Purpose:
new functions
Description:
H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx.
Platforms tested:
modi4, arabica, eirene
Misc. update:
RELEASE.txt updated.
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Code cleanup/Bug Fix
Description:
Re-do the ID->name code again, taking into account many more weird and
wonderful special cases stumbled across during the last set of test
writing.
Platforms tested:
FreeBSD 4.6 (sleipnir) w and w/o parallel
Linux 2.2.x (eirene) w/FORTRAN & C++
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
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Code cleanup
Description:
Clean up ID->name code:
- Reformat to better match library coding standard
- Changed several algorithms to be more efficient
- Integrated into library more smoothly
Platforms tested:
eirene w/FORTRAN & C++
arabica w/FORTRAN
modi4 w/FORTRAN & parallel
sleipnir
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Purpose:
bug fix
Description:
memory leak regarding the ID to name buffer
Solution:
added a new function H5G_free_ent_name that is called on several places of the library
Platforms tested:
windows 2000
linux, with cpp
solaris, with fortran, cpp
irix64, with parallel, fortran
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Code cleanup
Description:
Changed the last HRETURN* statements in the FUNC_ENTER macros into HGOTO*
macros, which reduces the size of the library binary in certain
configurations by another 10%
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel, IRIX64 6.5 (modi4) serial &
parallel
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Code cleanup
Description:
Change most (all?) HRETURN_ERROR macros to HGOTO_ERROR macros, along with
HRETURN macros to HGOTO_DONE macros. This unifies the error return path
from functions and reduces the size of the library by up to 10% on some
platforms.
Additionally, I improved a lot of the error cleanup code in many routines.
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel and IRIX64 6.5 (modi4) serial &
parallel.
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Bug Fix
Description:
It was possible to create corrupted metadata information (either in memory
or in the file or both) with a parallel I/O program because of the way
metadata writes were being handled for writes out of the metadata cache.
Solution:
Added a dataset transfer property called "block before metadata write"
which is used by the MPI-I/O and MPI-posix drivers to sync up all the
processes before attempting a metadata write. This property is currently
only for metadata writes from the metadata cache.
Platforms tested:
IRIX64 6.5 (modi4) w/parallel
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Bug Fix
Description:
The "dirty" flag for symbol table entries and symbol table nodes was not
being cleared when they were flushed to the file, causing lots of extra
metadata I/O.
Solution:
Reset the symbol table entry & nodes' flags when thy are flushed to disk.
This reduces the number of I/O operations which hit the disk for my test
program from 83 to 53 (i.e. from 393 to 53, overall).
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN & FreeBSD 4.5 (sleipnir) w/C++
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Code cleanup
Description:
Broke the FUNC_ENTER macro into several macros, with more specialized
uses (which followup mail will describe). This was designed to move
most/all of the checks which could be done at compile time to that point,
instead of needlessly performing them (over & over :-) at run-time.
This reduces the library's size (and thus staticly linked binaries) and
has a minor speedup effect also.
Platforms tested:
IRIX64 6.5 (modi4) with parallel & FORTRAN enabled, and additional testing
on FreeBSD and Solaris immediately after the checkin.
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Code cleanup.
Description:
Took Robb's recent ideas for improving the FUNC_ENTER/FUNC_LEAVE macros
equivalents in the SAF library and adapted them to our library. I added
an additional macro which is equivalent to FUNC_ENTER:
FUNC_ENTER_NOINIT - Has the API tracing code, etc. from FUNC_ENTER but
none of the library or interface initialization code. This is to
be used _only_ for static functions and those which explicitly
cannot have the library or interface initialization code enabled
(like the API termination routines, etc.).
This allowed many more of the functions in the library [but not all yet :-(]
to be wrapped with FUNC_ENTER[_NOINIT]/FUNC_LEAVE pairs.
It also reduced the size of the library and executables (by cutting out a
bunch of code which was never executed), I'll e-mail the exact results when
I've finished editing it.
Platforms tested:
IRIX64 6.5 (modi4)
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Code cleanup
Description:
The parallel I/O file driver is optimized to only write metadata with one
process (and broadcast the results to the other processes). This is
currently enabled by a separate call to H5FD_mpio_tas_allsame() before
each metadata write to the file. This can easily lead to problems where
the prelude function call is omitted before the actual write code or, in
a threaded environment, lead to race condititions where the value set is
reset before being used.
Solution:
Since we only want to write metadata from one process, key off of the 'type'
parameter (which has information about whether the data being written it
metadata or raw data) to H5FD_mpio_write() as the method for determining
whether to only write from one process or not.
Platforms tested:
IRIX64 6.5 (modi4)
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Code cleanup
Description:
Clean up the H5B_iterate code to not have a single hard-wired iterator for
each interface which uses a B-tree, instead accept a function pointer which
determines the callback function. This allows additional iterator
callbacks to be defined without requiring additional H5B functions to be
created.
In that spirit, remove the H5B_prune_by_extent call and convert the
H5F_istore callback routine for it into a callback routine for H5B_iterate.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code cleanup
Description:
Clean up warnings from gcc 3.1
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code Cleanup
Description:
Clean up compiler warnings from the last bunch of checkins
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code cleanup
Description:
Get rid of IDs from internal function calls and some small cleanups from
the old-stype => generic property list conversion.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Code cleanup.
Description:
Fix a few compiler warnings from the file creation property list -> generic
property list conversion. Also change a hard-wired value (8) for the
number of B-tree key values to a value that uses the enum's generated by
the compiler.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Purpose:
Changed the file creation property list to the new generic property list.
Platform tested:
IRIX64, SunOS5.7, FreeBSD
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Code cleanup for better compatibility with C++ compilers
Description:
C++ compilers are choking on our C code, for various reasons:
we used our UNUSED macro incorrectly when referring to pointer types
we used various C++ keywords as variables, etc.
we incremented enum's with the ++ operator.
Solution:
Changed variables, etc.to avoid C++ keywords (new, class, typename, typeid,
template)
Fixed usage of UNUSED macro from this:
char UNUSED *c
to this:
char * UNUSED c
Switched the enums from x++ to x=x+1
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Code cleanup (sorta)
Description:
When the first versions of the HDF5 library were designed, I remembered
vividly the difficulties of porting code from a 32-bit platform to a 16-bit
platform and asked that people use intn & uintn instead of int & unsigned
int, respectively. However, in hindsight, this was overkill and
unnecessary since we weren't going to be porting the HDF5 library to
16-bit architectures.
Currently, the extra uintn & intn typedefs are causing problems for users
who'd like to include both the HDF5 and HDF4 header files in one source
module (like Kent's h4toh5 library).
Solution:
Changed the uintn & intn's to unsigned and int's respectively.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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New Features!
Description:
Start migrating the internal use of property lists in the library from the
older implementation to the new generic property lists.
Currently, only the dataset transfer property lists are migrated to the
new architecture, all the rest of the property list types are still using
the older architecture.
Also, the backward compatibility features are not implemented yet, so
applications which use dataset transfer properties may need to make the
following changes:
H5Pcreate(H5P_DATASET_XFER) -> H5Pcreate_list(H5P_DATASET_XFER_NEW)
and
H5Pclose(<a dataset transfer property list>) -> H5Pclose_list(id)
This still may have some bugs in it, especially with Fortran, but I should
be wrapping up those later today.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Bug Fix, Code Cleanup, Code Optimization, etc.
Description:
Fold in the hyperslab speedups, clean up compile warnings and change a
few things from using 'unsigned' or 'hsize_t' to use 'size_t' instead.
Platforms tested:
FreeBSD 4.3 (hawkwind), Solaris 2.7 (arabica), Irix64 6.5 (modi4)
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Code clean/bug fix
Description:
H5FL (free-list manager) code currently is taking an hsize_t as the size
of a memory block to allocate. On many machines, the size of an hsize_t
is greater than the size of a size_t, potentially leading to incorrect
memory allocations in rare circumstances.
Solution:
Changed hsize_t parameters and variables to size_t.
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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Code cleanup.
Description:
Fixed _lots_ (I mean _tons_) of warnings spit out by the gcc with the
extra warnings. Including a few show-stoppers for compression on IRIX
machines.
Solution:
Changed lots of variables' types to more sensible and consistent types,
more range-checking, more variable typecasts, etc.
Platforms tested:
FreeBSD 4.2 (hawkwind), IRIX64-64 (modi4)
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Updating debugging information for new features, etc.
Description:
Lots of the new features added to the library during the last year or so
have been added without updating the debugging routines used by h5debug.
Solution:
Added more of the new features (although not all of them) to the debugging
routines for h5debug. Also included some more information to expand on
the information printed from h5debug.
Platforms tested:
FreeBSD 4.2 (hawkwind)
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Feature symmetry
Description:
A while ago I needed to get the 'type' of data being accessed during writes
to the VFL driver, so I put in code to get the information down there.
Albert asked for the same information during reads, so I've added that in.
Tested:
FreeBSD 4.1.1 (hawkwind)
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Maintainance & performance enhancements
Description:
Re-arranged header files to protect private symbols better.
Changed optimized regular hyperslab I/O to compute the offsets more
efficiently from previous method of using matrix operations.
Added sequential I/O operations at a more abstract level (at the same level
as H5F_arr_read/write), to support the optimized hyperslab I/O.
Platforms tested:
Solaris 2.6 (baldric) & FreeBSD 4.1.1 (hawkwind)
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objects being
cached instead of in separate structures. This reduces the amount of memory
the hash table uses by about half. This is the initial step along the path of
speeding up the metadata caching.
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paramater for
certain return values from the callback.
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"temporary buffer"
code, since the functionality was superceded. See the followup document for
details on the free-list code.
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Bug fix for parallel mode.
Description:
H5FD_mpio_tas_allsame was called for all cases, even when
MPIO is not used for access. That corrupted the internal
file handle structure.
Solution:
Define a macro, IS_H5FD_MPIO(f), for testing if f is opened with
MPIO access. Will call H5FD_mpio_tas_allsame only if this
condition is true.
Platform tested:
O2K, both -64 and -n32 modes.
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form of H5_HAVE_PARALLEL and H5_HAVE_GASS.
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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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----------------------
./src/H5.c [1.3]
./src/H5AC.c [1.3]
./src/H5ACprivate.h [1.3]
./src/H5B.c [1.3]
./src/H5Bprivate.h [1.3]
./src/H5D.c [1.3]
./src/H5F.c [1.3]
./src/H5Farray.c [1.3]
./src/H5Fcore.c [1.3]
./src/H5Ffamily.c [1.3]
./src/H5Fistore.c [1.3]
./src/H5Flow.c [1.3]
./src/H5Fmpio.c [1.3]
./src/H5Fprivate.h [1.3]
./src/H5Fsec2.c [1.3]
./src/H5Fsplit.c [1.3]
./src/H5Fstdio.c [1.3]
./src/H5G.c [1.3]
./src/H5Gent.c [1.3]
./src/H5Gnode.c [1.3]
./src/H5Gprivate.h [1.3]
./src/H5Gstab.c [1.3]
./src/H5HG.c [1.3]
./src/H5HGprivate.h [1.3]
./src/H5HL.c [1.3]
./src/H5HLprivate.h [1.3]
./src/H5MF.c [1.3]
./src/H5MFprivate.h [1.3]
./src/H5O.c [1.3]
./src/H5Oattr.c [1.3]
./src/H5Ocont.c [1.3]
./src/H5Odtype.c [1.3]
./src/H5Oefl.c [1.3]
./src/H5Olayout.c [1.3]
./src/H5Oprivate.h [1.3]
./src/H5Oshared.c [1.3]
./src/H5Ostab.c [1.3]
./src/H5P.c [1.3]
./src/H5R.c [1.3]
./src/H5Smpio.c [1.3]
./src/H5T.c [1.3]
./src/H5Tvlen.c [1.3]
./src/H5private.h [1.3]
./test/dtypes.c [1.3]
./test/gheap.c [1.3]
./test/istore.c [1.3]
./test/lheap.c [1.3]
./test/ohdr.c [1.3]
./tools/h5debug.c [1.3]
File addresses (the `haddr_t' type) are passed by value
instead of by reference. The type is no longer a struct. This
is one of the preliminary changes needed for the Virtual File
Layer stuff.
./src/H5Fprivate.h [1.3]
./src/H5Flow.c [1.3]
Some address functions were rewritten as macros.
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----------------------
./src/H5B.c
./src/H5D.c
./src/H5F.c
./src/H5Farray.c
./src/H5Fcore.c
./src/H5Ffamily.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fprivate.h
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5Gnode.c
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
Changed H5F_block_read/write() to take a file transfer
property list instead of just a parallel I/O mode. This will
allow us to pass additional parameters to the I/O functions
without having so many arguments to worry about.
This fixes a bug I introduced last Friday for parallel HDF5
./src/H5B.c
Fixed decoding of B-tree keys when iterating through the
leaves of the B-tree. This fixes a bug for applications that are
adding new entries to groups and also listing the groups.
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----------------------
./config/depend.in
Fixed automatic dependencies. We were storing dependencies for
*.o files instead of *.lo files after shared libraries were
added.
./config/gnu-flags
./config/linux-gnulibc1
Moved `-march=pentiumpro -mcpu=pentiumpro -malign-double' from
the linux file to this file and caused it to depend on the CPU
name. This fixes one of Elena's bugs.
./src/H5B.c
./src/H5Bprivate.h
./src/H5D.c
./src/H5Dprivate.h
./src/H5Dpublic.h
./src/H5F.c
./src/H5Farray.c
./src/H5Fistore.c
./src/H5Fmpio.c
./src/H5Fprivate.h
./src/H5Fpublic.h
./src/H5Gnode.c
./src/H5P.c
./src/H5RA.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Spoint.c
./src/H5Sprivate.h
./src/H5Tpublic.h
./test/istore.c
Added an H5Dget_storage_size() function that reports the
amount of storage allocated for raw data in a dataset.
Changed H5D_xfer_* to H5F_xfer_* because these properties are
more general than datasets. This also allows some of the
lower-level I/O functions to get this information easier.
./src/H5S.c
./src/H5Sall.c
Added two new functions H5S_all_read() and H5S_all_write()
which are optimizations that copy data directly between file
and memory without having to go through the scatter gather
step. This knocks quite a bit of time off the I/O and
reading/writing entire datasets is a fairly common operation.
./tools/h5ls.c
Reports the logical size of data, the allocated size of data,
and the percent utilization.
./MANIFEST
Removed old pablo files, added new files. Snapshots should now
start to work again.
./src/H5D.c
./src/H5Fmpio.c
Removed two warnings signed vs. unsigned comparisons and check
for overflow.
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----------------------
./config/commence.in
./config/conclude.in
./test/Makefile.in
./tools/Makefile.in
Fixed so private libraries are not installed publicly.
The installation directories `bin', `include', and `lib' are
created mode 755.
./src/H5.c
./src/H5A.c
./src/H5F.c
./src/H5Fcore.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fsec2.c
./src/H5Fstdio.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Ocomp.c
./src/H5Ocont.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Ofill.c
./src/H5Olayout.c
./src/H5Omtime.c
./src/H5Oname.c
./src/H5Osdspace.c
./src/H5Oshared.c
./src/H5Ostab.c
./src/H5R.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Snone.c
./src/H5Spoint.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Vprivate.h
./src/H5Z.c
./src/H5detect.c
./src/H5private.h
./test/chunk.c
./test/dsets.c
./test/dtypes.c
./test/h5test.c
./test/overhead.c
./test/ragged.c
./test/tattr.c
./tools/h5dump.c
./tools/h5findshd.c
./tools/h5ls.c
Changed `__unused__' to `UNUSED' to fix a conflict with GNU
header files.
./src/H5Tpkg.h
./test/h5test.h
Removed __unused__ from forward function declarations.
./src/H5P.c
Removed a comment about restrictions for the type conversion
temporary buffers. Thanks to Quincey, the comment no longer
applied.
./src/H5T.c
Relaxed the H5Tpack() a little so it would pack compound data
structures that had non-transient atomic members.
./tools/h5ls.c
Added a `-g' (or `--group') flag that causes information to be
printed about the specified group instead of the group's
contents. (sort of like Unix's `ls -d'). The `-g' can be used
in combination with `-r' to print information about the group
and its contents.
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----------------------
./src/H5.c
./src/H5A.c
./src/H5AC.c
./src/H5B.c
./src/H5D.c
./src/H5E.c
./src/H5F.c
./src/H5Farray.c
./src/H5Fcore.c
./src/H5Ffamily.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5Gstab.c
./src/H5HG.c
./src/H5HL.c
./src/H5I.c
./src/H5Iprivate.h
./src/H5MF.c
./src/H5MM.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Ocomp.c
./src/H5Ocont.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Ofill.c
./src/H5Olayout.c
./src/H5Omtime.c
./src/H5Oname.c
./src/H5Osdspace.c
./src/H5Oshared.c
./src/H5Ostab.c
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Snone.c
./src/H5Spoint.c
./src/H5Sselect.c
./src/H5T.c
./src/H5TB.c
./src/H5Tbit.c
./src/H5Tconv.c
./src/H5V.c
./src/H5Z.c
./src/H5detect.c
./src/H5private.h
Most of these changes are because the `interface_initialize_g'
variable change from hbool_t to int. It's a one line change.
Changed the way the library is closed so we have more control
over the order the interfaces are shut down. Instead of
registering an atexit() function for every interface in some
haphazard order we just register one: H5_term_library() which
then calls the H5*_term_interface() functions in a
well-defined order.
If the library is closed and then reopened repeatedly by
calling H5close() and H5open() in a loop we only add one copy
of the library termination functions with atexit().
Termination is a two-step process in order to help detect
programming errors that would cause an infinite loop caused by
the termination of one interface waking up some other
previously terminated interface. The first step terminates
the interface and *marks it as unusable*. After all
interfaces are terminated then we mark them all as usable
again. The FUNC_ENTER() macro has been modified to return
failure or to dump core (depending on whether NDEBUG is
defined) if we try to call an interface while it's shutting
down.
./src/H5.c
The H5dont_atexit() function returns failure if it's called
more than once or if it's called too late. However, the error
stack is not automatically printed on failure because the
library might not be initialized yet
./test/chunk.c
./test/flush1.c
./test/flush2.c
./test/iopipe.c
./test/overhead.c
./test/ragged.c
Changed the extra cast for Win32 so we do floating point
division again -- it was just confusion about precedence and
associativity of casting and the C coercion rules. Removed
extra carriage returns inserted by broken operating system.
./src/H5Ffamily.c
Fixed an bug where H5F_fam_write() lowered the EOF marker for
one of the family members causing H5F_fam_read() to read
zeros.
./test/h5test.h [NEW]
./test/h5test.c [NEW]
./test/Makefile.in
./test/bittests.c
./test/cmpd_dset.c
./test/dsets.c
./test/dtypes.c
./test/extend.c
./test/external.c
Support library for test files. This isn't done yet but
Katie's contractions are ~10 minutes apart so I figured I
better back this stuff up just in case I'm not here next
week...
Eventually all test files will understand HDF5_DRIVER to name
the low level file driver and parameters so we can easily test
various drivers. They will also understand HDF5_PREFIX to
prepend to the beginning of file names which is necessary for
testing ROMIO with various drivers. Also, the cleanup function
will know how to use the file name prefix and will understand
different file driver naming schemes like file families. I'm
not sure they'll understand the `gsf:' type prefixes yet.
Note, the external test is completely commented out because
I'm in the middle of modifying it. It will still compile and
run but it doesn't test anything at the moment.
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----------------------
./INSTALL.parallel [NEW]
We're beginning to unify some of the parallel installation
steps. This file will contain general information for
installing the parallel library. It's not complete yet.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
Check for xdr_int() in libnsl required on Solaris when linking
with hdf4. It's found on the Irix system I tested which
complains that `-lnsl' didn't resolve any symbols. Oh well.
Fixed the order of searching for libdf and libmfhdf for hdf4
linking.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5Z.c
Check for compress() in libz in order to find older versions
of the library that will still work for hdf4. Added a
separate check for compress2() that hdf5 will use.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5.c
./src/H5private.h
./src/H5A.c
./src/H5B.c
./src/H5Bprivate.h
./src/H5D.c
./src/H5F.c
./src/H5Farray.c
./src/H5Fcore.c
./src/H5Ffamily.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fprivate.h
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Ocomp.c
./src/H5Ocont.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Ofill.c
./src/H5Olayout.c
./src/H5Omtime.c
./src/H5Oname.c
./src/H5Oprivate.h
./src/H5Osdspace.c
./src/H5Oshared.c
./src/H5Ostab.c
./src/H5R.c
./src/H5RA.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Snone.c
./src/H5Spoint.c
./src/H5Sprivate.h
./src/H5Sselect.c
./src/H5T.c
./src/H5Tbit.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5V.c
./test/bittests.c
./test/gheap.c
./test/hyperslab.c
./test/istore.c
./test/tmeta.c
./test/trefer.c
./test/tselect.c
./tools/h5debug.c
./tools/h5tols.c
Added checks for Posix.1g types like `int8_t'. If not defined
then H5private.h defines them. Changed all `int8' etc. to
`int8_t'.
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5I.c
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
./src/H5TB.c
./src/H5Z.c
Calling H5*_term_interface() resets interface_initialize_g to
FALSE so a subsequent call to H5open() (implied or explicit)
reinitializes global variables properly.
./src/H5private.h
./src/H5Oefl.c
./src/H5S.c
Changed MAX_SIZET, MAX_SSIZET, MAX_HSIZET, and MAX_HSSIZET to
SIZET_MAX, SSIZET_MAX, HSIZET_MAX, and HSSIZE_MAX to they
match the Posix.1 constants in <limits.h>.
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5detect.c
Added 36 more integer hardware conversion functions to the
type conversion table for conversions to/from `long long' and
`unsigned long long'. The `long long' names will be changed
shortly to make them portable to Win32.
Changed H5T_init() to H5T_native_open() and added an
H5T_native_close() to open and close the predefined native
data types.
Increased the initial size of the type conversion table from
64 to 128 entries.
Reordered the 90 new integer conversion functions so the names
that are printed favor `int' over `short' or `long' when two
of them are the same.
./test/dtypes.c
Added hardware and software integer conversion tests for the
56 functions I added recently but not the additional 36
checked in this time. That will come next.
Call H5close() after each test so type conversion statistics
are easier to follow. Try this: $ HDF5_DEBUG=t ./dtypes
Added more debugging output for when things go wrong.
./src/H5private.h
Removed trailing carriage-returns inserted by broken operating
system ;-)
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----------------------
./MANIFEST
Added new Pablo files HDF5record_RT.h and ProcIDs.h
./acconfig.h
./configure [REGENERATED]
./configure.in
./src/H5.c
./src/H5Vprivate.h
./src/H5config.h.in [REGENERATED]
./src/H5private.h
./src/H5public.h
./test/big.c
Added more configuration stuff for the Win32 environment. Removed all
the #ifdef WIN32 from the source and replaced them with OS-independent
stuff. Specifics follow:
Check for non-Posix.1 `st_blocks' field in `struct stat' which is used
by the big file test to decide if the file system supports holes. If
the st_blocks field isn't present then we just skip the test.
Configure checks for <io.h> <sys/resource.h> <sys/time.h> and
<winsock.h> and defines HAVE_IO_H, HAVE_SYS_RESOURCE_H,
HAVE_SYS_TIME_H and HAVE_WINSOCK_H when they're found.
Configure checks whether both <sys/time.h> and <time.h> can be
included and defines SYS_TIME_WITH_TIME if so. Otherwise include only
<sys/time.h> or <time.h> even if both exist.
Configure checks sizeof(__int64) and defines SIZEOF___INT64 to the
result or to zero if __int64 isn't defined. The source uses `long
long' in preference to `__int64'.
Removed null WIN32 definition for `inline' since such a definition
already exists in H5config.h
Protected gettimeofday() calls in debugging code with
HAVE_GETTIMEOFDAY instead of WIN32.
./src/H5F.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fsec2.c
./src/H5Fstdio.h
./src/H5P.c
./src/H5Tconv.c
./src/H5private.h
Removed #include of system files from library source files and
consolodated them into H5private.h where they're protected by various
configuration macros (most of them were duplicated there already
anyway).
./test/big.c
./test/chunk.c
./test/cmpd_dset.c
./test/dsets.c
./test/dtypes.c
./test/extend.c
./test/external.c
./test/fillval.c
./test/flush1.c
./test/flush2.c
./test/iopipe.c
./test/links.c
./test/mount.c
./test/mtime.c
./test/overhead.c
./test/ragged.c
./test/shtype.c
./test/unlink.c
Protected system #include's with #ifdef's from H5config.h.
Undefined NDEBUG since some of the tests rely on assert() to check
return values.
Removed WIN32 definitions for __unused__ since this can be controlled
by the definition of HAVE_ATTRIBUTE in H5config.h
./test/testhdf5.h
Removed the CLEAN_CMD definition because we no longer use it.
Albert's cleanup() functions replaced it.
./test/fillval.c
Initialized auto hid_t variables to fix warnings in error recovery
code when data flow analysis is turned on in compilers.
./test/h5tools.c
Initialized an auto variable to fix a compiler warning.
./test/chunk.c
./test/ragged.c
The WIN32 had some unsigned variables changed to signed because the
compiler generates warnings when coercing unsigned to double(?). I
changed them back to unsigned because they really are unsigned
quantities. If this the change was just to shut up extraneous warnings
then perhaps a compiler flag can do the same; otherwise if the
compiler generates bad code then we should supply a patch file instead
messing up source code with bug work-arounds.
./src/H5detect.c
Protected system #include's with #ifdef's from H5config.h thereby
removing a WIN32.
If getpwuid() doesn't exist (HAVE_GETPWUID) then we assume that
`struct passwd' doesn't exist either (we don't really need it in that
case).
The H5T_NATIVE_LLONG and H5T_NATIVE_ULLONG are defined in terms of
`long long' or else `__int64' or else `long' depending on what's
available.
./src/H5Flow.c
./src/H5Ofill.c
Added __unused__ to some function arguments that aren't used when
assertions are turned off.
./src/H5V.c
Changed an auto variable name in some hand-inlined code to get rid of
a warning about the variable shadowing a previous auto.
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"non-negative/negative"
and also fixed a few more explicit checks against FAIL.
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Replaced FAIL with H5B_INS_ERROR in routine H5B_remove_helper.
Updated code that calls H5B_remove_helper with the proper code.
H5Fmpio.c:
Removed a typo.
H5Gnode.c:
Replaced FAIL with H5B_INS_ERROR in routine H5G_node_remove.
H5Odtype.c:
Put in proper casting to remove compiler warnings.
H5S.c:
Replaced FAIL with H5S_NO_CLASS in routine H5Sget_simple_extent_type.
H5Sselect.c:
Fixed couple typos to remove compiler warnings.
Platform tested:
O2K.
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----------------------
./MANIFEST
./src/H5B.c
./src/H5Bprivate.h
./src/H5G.c
./src/H5Gnode.c
./src/H5Gprivate.h
./test/Makefile.in
./test/unlink.c [NEW]
Finished H5Gunlink() and H5Grename().
./src/H5F.c
./src/H5Fistore.c
./src/H5Fprivate.h
Removed the last memcpy() from the chunk cache.
./src/H5Fistore.c
The offset of a chunk within a dataset is an 8-byte quantity
per dimension instead of 4 bytes.
./src/H5HL.c
Fixed infinite loops in H5HL_remove().
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----------------------
This checkin is to fix a couple bugs for Jim Reus. Some features are
not fully implemented but it shouldn't break anything.
./config/conclude.in
./test/Makefile.in
`make clean' removes object files from the test directory as
well as a couple more *.h5 temp files.
./config/hpux9.03 [NEW]
New config file for HP/UX 9.03
./src/H5B.c
./src/H5Bprivate.h
./src/H5Fistore.c
./src/H5G.c
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5Gstab.c
Not-yet-complete version of object removal.
./src/H5Fistore.c
./src/H5Fprivate.h
Experimental optimizations, disabled by default.
./src/H5Fprivate.h
Default low-level driver was changed to H5F_LOW_SEC instead of
H5F_LOW_STDIO because the sec2 driver is much easier to debug.
./src/H5Fsplit.c
./src/H5G.c
./src/H5Z.c
Changed a couple return statements to HRETURN.
./src/H5Odtype.c
Removed a check for nested compound data types from back when
they weren't implemented that raised an error.
./tools/h5tools.c
Increased temp buffer sizes and added a check for buffer
overflow so we fail an assertion (hopefully). This really
needs to be fixed sometime.
Added support for printing H5T_STRING data types.
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----------------------
./COPYING
Reformatted as text instead of C. Removed zlib crew from the
list of contributors since no zlib code is actually in the
hdf5 library.
./INSTALL
./INSTALL.ascired
./MANIFEST
Minor updates for Beta release including version number
change.
./INSTALL_MAINT
Added information about making a release.
./RELEASE
Updated function list based on public header files.
./bin/checkposix
Got rid of complaints about some obvious things.
./doc/html/H5.api.html
./doc/html/RM_H5F.html
./src/H5F.c
./src/H5Fpublic.h
./test/tfile.c
Changed H5Fget_create_template() and H5Fget_access_template()
to H5Fget_create_plist() and H5Fget_access_plist() since that
conforms better to lots of other names.
./doc/html/Datatypes.html
./doc/html/ExternalFiles.html
./doc/html/Files.html
./doc/html/H5.api.html
./doc/html/H5.sample_code.html
./doc/html/RM_H5F.html
./doc/html/RM_H5Front.html
Changed `template' to `property list', etc.
./doc/html/Ragged.html [NEW]
Documentation for ragged arrays.
./src/H5Iprivate.h
./src/H5Ipublic.h
./src/H5I.c
Changed the scope of some symbols to be more local.
./src/H5.c
./src/H5AC.c
./src/H5D.c
./src/H5E.c
./src/H5F.c
./src/H5Ffamily.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5G.c
./src/H5Gnode.c
./src/H5HG.c
./src/H5I.c
./src/H5O.c
./src/H5Ocomp.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Omtime.c
./src/H5Oname.c
./src/H5P.c
./src/H5S.c
./src/H5Shyper.c
./src/H5Tbit.c
./src/H5Tconv.c
./src/H5V.c
./src/H5Z.c
./src/H5private.h
Fixed some violations of our naming scheme by adding HD to the
beginning of all Posix functions.
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