| 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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Purpose:
Cleanup H5Tget_native_type code
Description:
improve code cosmetics.
Solution:
Platforms tested:
modi4, eirene, arabica
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Fix Windows portability bug
Description:
"long long" is not defined on Windows.
Solution:
Use our internal definition of "long_long" instead.
Platforms tested:
eyeballed.
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Code Cleanup
Description:
A function was returning "NULL" instead of "FAIL" for an error
condition. Renamed the variable "class" to "h5_class" since class is
a keyword in C++ and might mess up with a C++ compiler...
Platforms tested:
Eirene pp (too small a change for 3 tests)
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Code cleanup
Description:
Cleaned up some error values that were incorrect, added some assertions
and refactored the integer & floating-point native conversions some.
Platforms tested:
FreeBSD 4.7 (sleipnir), too small for h5committest
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Purpose:
Add new functions
Description:
add H5Tget_native_type and H5Tis_variable_str.
Platforms tested:
arabica, eirene, modi4
Misc. update:
MANIFEST and release_docs/RELEASE 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
[ i s this a bug fix? feature? ...]
Description:
the copy of a symbol table entry was done with a shallow copy, in H5T_copy
this was causing an exception on the free call of the ID to name buffer
replaced a shallow copy of a symbo l a edescribe the bug, or describe the new feature, etc]
Solution:
[details about the changes, algorithm, etc...]
[Please as detail as you can since your own explanation is
better than others guessing it from the code.]
Platforms tested:
windows 2000
solaris with cpp, fortran
irix64, with fortran, parallel i r
[machines you have tested the changed version. This is absolute
important. Test it out on at least two or three different platforms
such as Big-endian-32bit (SUN/IRIX), little-endian-32(LINUX) and
64-bit (IRIX64/UNICOS/DEC-ALPHA) would be good.]
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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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Purpose:
bug fix in 'ID to name' function
Description:
the function replace_name was only checking for immutable datatypes
Solution:
added a new function H5T_is_named, that checks for named datatypes
Platforms tested:
windows 2000, linux, solaris with Fortran
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Purpose:
Added 'ID to name' support
Description:
There is a new API function H5Iget_name
Most of the changes are on H5G.c , regarding the symbol table entry struct H5G_entry_t
which has 2 new fields 'name' and 'old_name'
A new private function was introduced H5G_ent_copy, that does a deep copy
between 2 symbol table entries
The test file is getname.c
Platforms tested:
windows 2000, Linux, Solaris
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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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Purpose:
Merged from 1.4 branch
Description:
API tracing improvements
Platforms tested:
Linux (--disable-hsizet didn't work before my changes and still doesn't
work, but --enable-hsizet is fine).
Note: This checkin includes temporary code in H5FDmpiposix.c to turn
off GPFS byte range token prefetches on ASCI/Blue. Once the HDF5 API
supports the necessary prerequisite functionality this temporary code
can be migraged up above HDF5.
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Code cleanup
Description:
Clean up a few warnings which were showing up with --enable-production
turned on.
Platforms tested:
FreeBSD 4.6 (sleipnir) 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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Code cleanup
Description:
Created a new H5I function which combined the some of the functionality of
H5I_get_type and H5I_object: H5I_object_verify.
Using this new function in the library trims another ~200 lines of code off
the library and makes the resulting binaries smaller and faster also.
Platforms tested:
FreeBSD 4.6 (sleipnir)
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Code cleanup
Description:
Make a "H5T_t *" parameter into a "const H5T_t *" parameter.
Platforms tested:
FreeBSD 4.6 (sleipnir)
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Code cleanup
Description:
Removed more compiler warnings, etc.
Platforms tested:
Linux 2.2.x (eirene) w/parallel
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Code cleanup
Description:
Clean up some compiler warnings...
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Purpose:
Bug #774 fix
Description:
H5Tenum_valueof and H5Tenum_nameof functions did not fail
when non-existing name or non-existing value were supplied.
This happened because binary search algorithm did not check
if value or name found during the search were equal to the supplied
one.
Solution:
Added an appropriate check condition.
Platforms tested:
Solaris 2.7 and Linux 2.2.18
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Bug Fix
Description:
H5Dcreate and H5Tcommit allow "empty" compound and enumerated types (i.e.
ones with no members) to be stored in the file, but this causes an assertion
failure and is somewhat vapid.
Solution:
Check the datatype "makes sense" before using it for H5Dcreate and
H5Tcommit.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Bug fix (bug #777)
Description:
Current code allows a compound datatype to be inserted into itself.
Solution:
Check if the ID for the member is the same as the ID for the compound
datatype and reject it if so.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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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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Update API tracing information
Platforms tested:
Linux 2.2 (eirene)
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Code cleanup
Description:
Clean up warnings from gcc 3.1
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Purpose:
New feature
Description:
Added a query function H5Tget_member_index for compound and enumeration
data types, to retrieve member's index by its name.
Platforms tested:
Linux 2.2
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Purpose:
Bug fix(#697)
Description:
Variable-length string wasn't treated as string.
Solution:
Added character set and padding into VL string type.
Platforms tested:
FreeBSD
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Code cleanup
Description:
Cleanup compiler warnings found by the SGI compiler and gcc 3.0
Platforms tested:
FreeBSD 4.5 w/gcc 3.0 (hack) && IRIX64 (modi4)
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Bug fixes
Description:
This checkin addresses two separate bugs:
#1 - When a compound datatype with a VL datatype as a field is used
to read or write data, the datatype conversion paths added to
the table of paths were treating the VL datatypes somewhat too
genericly - they weren't dicriminating between VL datatypes used
in different files and therefore there was the possibility that
a path in the table having information for one file could get used
with a second file, causing errors or core dumps (if the first
file was closed before the later file used the path).
#2 - When composite (compound, array or VL) datatype paths in the datatype
conversion table are being tested to see if they can be used for
the current datatypes being converted, they can cause additional
conversion paths to be registered in the conversion path table.
Since this causes the global table to change size and entries to
move around, it is possible that the local variables tracking a
potential path could become incorrect as the global table was
changed out from underneath them.
Both bugs fixed are described in bug #703
Solution:
Two separate fixes:
#1 - Changed H5T_cmp to differentiate between VL datatypes in different
files and not to return datatypes in two different files as equal.
#2 - Note size of global table before evaluating datatype paths. Then,
after the appropriate path has been chosen, check if the size of
the global table has changed and recompute the position of the path
chosen in the table if necessary.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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More optimizing for byte order conversion. Mostly just making code
easier to follow by simplifying Duff's device coding of the loops.
I also split the conversion function into two functions with different
names so output from H5T debugging indicates whether the optimized or
unoptimized case was invoked.
2002-01-25 10:47:13 Robb Matzke <matzke@arborea.spizella.com>
* H5T_init_interface: Registered conversion function H5T_conv_order_opt() under two
names. H5T debugging will report the conversion
function as either "ibo(opt)" or "fbo(opt)".
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Bug Fix
Description:
H5Tinsert was allowing compound datatype fields to be inserted past the end
of the datatype.
Solution:
Added range check in H5T_insert
Platforms Tested:
FreeBSD 4.4 (sleipnir)
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Code cleanup
Description:
Tweaked internal error handling macros to reduce the size of the library's
object code by about 10-20%.
Also cleaned up some compiler warnings...
Platforms tested:
FreeBSD 4.4 (sleipnir)
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Purpose:
Modify H5Fclose behavior
Description:
The HDF5 actual file close behaves in several ways in terms of if there
are still objects(dataset, group, datatype) opened in file.
Solution:
Added a new file access property, file close degree. It has four values,
H5F_CLOSE_DEFAULT
H5F_CLOSE_WEAK
H5F_CLOSE_SEMI
H5F_CLOSE_STRONG
The way a file is closed is decided by these values.
Platforms tested:
IRIX64 6.5, SunOS 5.6, FreeBSD 4.4
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Purpose:
a minor bug on H5T.c
Description:
should be HEREUTRN_ERROR(...,...,int,...)
instead of HERUTRN_ERROR(...,...,int*,...)
Solution:
change HERETURN_ERROR(...,...,NULL,...) into HERETURN_ERROR(...,...,FAIL,...)
Platforms tested:
windows 2000
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Code cleanup
Description:
Windows is generating hundreds of warnings from some of the practices in
the library. Mostly, they are because size_t is 32-bit and hsize_t is
64-bit on Windows and we were carelessly casting the larger values down to
the smaller ones without checking for overflow.
Also, some other small code cleanups,etc.
Solution:
Re-worked some algorithms to eliminate the casts and also added more
overflow checking for assignments and function parameters which needed
casts.
Kent did most of the work, I just went over his changes and fit them into
the the library code a bit better.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Bug fix for code cleanup... :-)
Description:
Fix a few problems introduced in my previous code cleanup.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Code cleanup
Description:
Got rid of IDs from internal API functions and also got rid of API calls
from internal functions.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Purpose:
Switch from old property list to new generic property list.
Description:
Mainly changed H5Pcreat, H5Pclose, H5Pcopy.
Platforms tested:
IRIX64 6.5, FreeBSD, SunOS 5.7.
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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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Feature shift
Description:
Take out the v1.2.x compatibility stubs and put in the hooks for v1.4.x
compatibility when needed.
Platforms tested:
FreeBSD 4.3 (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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Documentation
Description:
H5Tget_member_type in v1.2.x returns the base type of array fields in
compound datatypes, not an array type itself.
Solution:
Changed to emulate this behavior in v1.4.x when the --enable-hdf5v1_2
flag is given during configuration.
Platforms tested:
FreeBSD 4.3 (hawkwind)
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Code Cleanup
Description:
Changed POSIX function calls to the HD* way of doing things. Checked
with checkposix and tested on Linux.
Platforms tested:
Linux
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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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Bug fix (sort of)
Description:
The RCSID string in H5public.h was causing the C++ code problem as it
was included multiple times and C++ did not like multiple definitions
of the same static variable.
Solution:
Since we don't really make use of the RCSID strings as we have not
installed it in all source files, we decided to remove it.
Platforms tested:
eirene (linux), modi4 (IRIX64-64) both serial and parallel modes.
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