| Commit message (Collapse) | Author | Age | Files | Lines |
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Code cleanup
Description:
Clean up warnings exposed by compiling on O2K. Also, revert some of Bill
and my changes to the H5S_mpi_opt_types_g, etc. and settle them back into their
original location.
Platforms tested:
h5committested.
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Code cleanup.
Description:
Move many package or internal function prototypes and macro definitions
into tighter scope according to their current use.
Added more comments where appropriate.
Eliminate ancient, unused functions.
Added a couple "accessor" functions to get parts of data structures which
were moved out of scope.
Platforms tested:
h5committested
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New feature/enhancement
Description:
Chunked datasets are handled poorly in several circumstances involving
certain selections and chunks that are too large for the chunk cache and/or
chunks with filters, causing the chunk to be read from disk multiple times.
Solution:
Rearrange raw data I/O infrastructure to handle chunked datasets in a much
more friendly way by creating a selection in memory and on disk for each chunk
in a chunked dataset and performing all of the I/O on that chunk at one time.
There are still some scalability (the current code attempts to
create a selection for all the chunks in the dataset, instead of just the
chunks that are accessed, requiring portions of the istore.c and fillval.c
tests to be commented out) and performance issues, but checking this in will
allow the changes to be tested by a much wider audience while I address the
remaining issues.
Platforms tested:
h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
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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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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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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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Code cleanup
Description:
Move operations on each type of selection into the source code file for
each selection type (all->H5Sall.c, hyperslab->H5Shyper.c, etc.)
Remove central H5S_select_<foo> operations, instead calling the operations
through function pointers in each selection (a much more object-oriented
approach).
Platforms tested:
FreeBSD 4.6 (sleipnir)
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Large code cleanup/re-write
Description:
This is phase 1 of the data I/O re-architecture, with the following changes:
- Changed the selection drivers to not actually do any I/O, they
only generate the sequences of offset/length pairs needed for
the I/O (or memory access, in the case of iterating or filling
a selection in a memory buffer)
- Wrote more abstract I/O routines which get the sequence of offset/
length pairs for each selection and access perform the I/O or
memory access.
Benefits of this change include:
- Removed ~3400 lines of quite redundant code, with corresponding
reduction in the size of library binary.
- Any selection can now directly access memory when performing I/O,
if no type conversions are required, instead of just "regular"
hyperslab and 'all' selections, which speeds up I/O.
- Sped up I/O for hyperslab selections which have contiguous lower
dimensions by "flattening" them out into lesser dimensional objects
for the I/O.
No file format or API changes were necessary for this change.
The next phase will be to create a "selection driver" for each type of
selection, allowing each type of selection to directly call certain
methods that only apply to that type of selection, instead of passing
through dozens of functions which have switch statements to call the
appropriate method for each selection type. This will also reduce
the amount of code in the library and speed things up a bit more.
Phase 3 will involve generating an MPI datatype for all types of selections,
instead of only "regular" hyperslab and 'all' selections. This will
allow collective parallel I/O for all I/O operations which don't
require type conversions. It will also open up the door for allowing
collective I/O on datasets which require type conversion.
Phase 4 will involve changing the access pattern to deal with chunked
datasets in a more optimal way (in serial).
Phase 5 will deal with accessing chunked datasets more optimally for
collective parallel I/O operations.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/ parallel & C++ and IRIX64 6.5 (modi4) w/parallel
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Bug fix.
Description:
Return H5S_all_opt_possible() prototype to original position in H5Spkg.h,
it is not related to parallel I/O.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code Cleanup
Description:
Removed some compiler warnings.
Solution:
In a few cases, NULL was being returned when a FAIL was supposed to
be returned instead. There were some header files which needed to be
included in a few of the sources. A couple of if-then statements had
assignments in the conditional part. The compiler warned that they
should have extra "()"s around them. Made the code check the values
instead.
Platforms tested:
Linux (parallel) Modi4 (parallel)
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Code cleanup
Description:
Previously, the I/O pipeline (pline), external file list (efl) and fill-
value (fill) structs were passed down the raw data function call chain,
even into and/or through functions which didn't use them. Since all three
of these pieces of information are available from the dataset creation
property list, just pass the dataset creation property list down the
function call chain and query for the information needed in a particular
function.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code cleanup
Description:
Fix incorrect include from <H5Sprivate.h> to "H5Sprivate.h"
Platforms tested:
Just eyeballed it.
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Purpose:
New feature
Description:
Fill-value's behaviors for contiguous dataset have been redefined.
Basicly, dataset won't allocate space until it's necessary. Full details
are available at http://hdf.ncsa.uiuc.edu/RFC/Fill_Value, at this moment.
Platforms tested:
Linux 2.2.
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New Feature
Description:
Added new H5Dfill() routine to fill the elements in a selection for a
memory buffer with a fill value. This is a user API wrapper around some
internal routines which were needed for the fill-value modifications
from Raymond as well as Pedro's code for reducing the size of a chunked
dataset.
Platforms tested:
FreeBSD 4.5 (sleipnir) [and IRIX64 6.5 (modi4) in parallel, in a few
minutes]
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Bug Fix & Code Cleanup
Description:
The MPI-IO optimized transfer routines
(H5S_mpio_spaces_read/H5S_mpio_space_write) are not being invoked in all
the cases where they could be used.
Additionally, the code for determining if an optimized transfer is wrapped
into the actual I/O transfer routine in a very confusing way.
Solution:
Re-enabled MPI-IO optimized transfer routines in all the cases where they
should work.
Extracted all the pre-conditions for optimized transfers into separate
routines from the transfer routines.
Platforms tested:
FreeBSD 4.5 (sleipnir) & IRIX64 6.5 (modi4)
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Bug Fix & Feature
Description:
The selection offset was being ignored for optimized hyperslab selection
I/O operations.
Additionally, I've found that the restrictions on optimized selection
I/O operations were too strict and found a way to allow more hyperslabs
to use the optimized I/O routines.
Solution:
Incorporate the selection offset into the selection location when performing
optimized I/O operations.
Allow optimized I/O on any single hyperslab selection and also allow
hyperslab operations on chunked datasets.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Bug Fix
Description:
If a non-zero fill-value is used for a chunked dataset, any non-existent
chunked read with an "all" selection (or a contiguous hyperslab selection)
will return zero for those instead of the user's fill-value.
Solution:
Fixed I/O code to pass down fill-value to "optimized" I/O routines, so it
will be available to fill the user's buffer with.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Bug fix & feature add
Description:
Added new API function H5Sget_select_type to determine type of selection in
a dataspace. Return values are defined by the H5S_sel_type enumerated type
in H5Spublic.h
Also, hyperslab operations involving a "all" or "none" selection are not
generating the correct resulting selections.
Solution:
Added more code to make hyperslab operations against an "all" or "none"
selection generate the correct results.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code speedups, etc.
Description:
Bring in new algorithms and data structures for dealing with hyperslabs.
This speeds up the hyperslab I/O for non-regular hyperslabs by a huge
amount.
Currently, the new API functions are ifdef'ed out, pending discussion
and consensus approval.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Bug fix
Description:
H5S_select_elements is not actually putting the new point on the list of
points selected when there are no points currently selected and the
'append' operation is chosen.
Solution:
Add new point to list correctly.
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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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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Purpose:
Parallel Bug Fixes
Description:
Was out of sync with header file re-arrangements I checked in last night.
Solution:
Fixed to use new header files, etc.
Platforms tested:
O2K (modi4)
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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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