Refactor generic property list initialization code to put property list
specific routines in property list modules, instead of scattered to the four
winds. Also, introduce property list class initialization objects, to make
adding new property list classes in the library easier.
Fix daily test failure by using H5Pget_elink_prefix() API routine instead
of looking at the "raw" generic property list information.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/C++ & FORTRAN
Linux/64 2.4 (mir) w/build-all & 1.6 compat
upgrade.
Description:
Changed the error report of read and write to HSYS_GOTO_ERROR to report
system error messages.
Platforms tested:
heping, osage, copper.
Description: Made small changes to sec2 driver to reflect that VMS systems ino_t is 1dim array
of size 3; all changes are marked with H5_VMS variable.
Defined HDremove macro for VMS to remove multiple versions of the files.
Solution:
Platforms tested: heping, VMS server
Misc. update:
Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
upgrade.
Description:
Changed all appropriate error stack calls to the new HSYS_ERROR macro
call in order to push system error message to the stack too.
Platforms tested:
heping.
Misc. update:
Code tweak
Description:
Add in a couple of minor changes from Elena's version of pushing the
system error information on the error stack.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Feature.
Description:
Added HSYS_ERROR macro to retrieve and push system error message to
the error stack.
Added the related H5E_SYSERRSTR error code.
This allows system error messages be shown to users too. Thus
give a better explanation of what the errors are.
Platforms tested:
h5committested.
Code cleanup
Description:
Clean up various warnings reported by the Windows team.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Description: Removed PABLO from the source
Solution:
Platforms tested: arabica with 64-bit, copper with parallel,
heping with GNU C and C++ and PGI fortran (but
I disabled hl, there is some weird problem only
on heping: F9XMODFLAG is not
propagated to the Makefile files
Misc. update:
Description: In file H5FDsec2.c and H5FDlog.c, there's statements like
H5_ASSIGN_OVERFLOW(file->eof,sb.st_size,off_t,haddr_t);
It assumes sb.st_size from h5_stat_t is of type off_t. But on Windows, it
has type __int64. So the H5_ASSIGN_OVERFLOW statement may cause problem.
Instead of trying to do switch between Windows and other systems in H5FDsec2.c
and H5FDlog.c, define a substituting type in H5private.h to fix the problem.
On Windows, this type is __int64; on other systems, it is off_t.
Platforms tested: fuss. Simple fix. Already did h5committest for v1.6.
Bug fix.
Description:
Fix off-by-one error in Core VFL driver which would cause spurious address
or size overflow errors when an odd valued address or size was checked.
Platforms tested:
FreeBSD 4.10 (sleipnir)
Linux 2.4 (heping)
Solaris 2.7 (arabica)
Code cleanup & minor optimization
Description:
Re-work the way interface initialization routines are specified in the
library to avoid the overhead of checking for them in routines where there is
no interface initialization routine. This cleans up warnings with gcc 3.4,
reduces the library binary size a bit (about 2-3%) and should speedup the
library's execution slightly.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/gcc34
h5committest
Bug fix/code cleanup
Description:
Copy Robb's feature in SSlib that checks that the name of the function
used in the FUNC_ENTER macro is actually the name of function.
Fixed a bunch of typos & copy-n-pasto's for functions with incorrect names.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
too minor to require h5committest
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
Bug fix/optimization
Description:
Address slowdown in MPI-I/O file metadata operations that was introduced
mid-stream. We now _require_ a POSIX compliant parallel file system for the
MPI-I/O file driver (as well as for the MPI-POSIX file driver).
Also optimized file open operation when the file is being created by
reducing the number of collective & syncronizing calls.
Additionally, refactor the MPI routines into a common place, eliminating
duplicated code.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
h5committest
Code cleanup, bug fixes
Description:
Wrap up rest of changes necessary for fixing the "short" MPI-I/O read
problem that Robb reported.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
Bug fix.
Description:
The stdio filer driver is not reducing the file's size in the manner
that the sec2 driver does.
Solution:
Copy code from the sec2 for handling this properly.
Platforms tested:
h5committested
New feature.
Description:
Allow the file to shrink as well as expand when flushing a file before
closing it.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
New Feature
Description:
Added support for the lock and unlock function calls for file
drivers. Only FPHDF5 uses this feature. All of these drivers don't
define lock or unlock methods.
Platforms tested:
Linux, Modi4, Sol
Misc. update:
Bug Fix
Description:
Metadata cache in parallel I/O can cause hangs in applications which
perform independent I/O on chunked datasets, because the metadata cache
can attempt to flush out dirty metadata from only a single process, instead
of collectively from all processes.
Solution:
Pass a dataset transfer property list down from every API function which
could possibly trigger metadata I/O.
Then, split the metadata cache into two sets of entries to allow dirty
metadata to be set aside when a hash table collision occurs during
independent I/O.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel
Misc. update:
Updated release_docs/RELEASE
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
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
Purpose:
New API functions
Description:
Added API functions to return pointer to low-level file handle
(H5Fget_vfd_handle and H5FDget_vfd_handle) and related property list
setting functions(H5Pset_family_offset and H5Pset_multi_type).
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
Code cleanup
Description:
Combined H5P_isa_class and H5I_object functionality into a new internal
H5P API function: H5P_object_verify, which checks that a property list is
the appropriate class and then returns the property list object associated
with the property list ID.
This reduces the source code by about 200 LOC and trims the library binary
some more.
Platforms tested:
FreeBSD 4.6 (sleipnir)
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
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.
Purpose:
correct a typo in the H5FD_sec2_flush.
Description:
fd is not defined. It should be file->fd
Solution:
Platforms tested:
windows 2000, linux 2.2.18smp
Code cleanup
Description:
Changed a few direct calls to posix functions to use proper wrapper macros.
Also, changed method of extending file to use ftruncate().
Platforms tested:
FreeBSD 4.6 (sleipnir) && IRIX64 6.5 (modi4)
New feature.
Description:
Added a "small data" block allocation mechanism to the library, similar to
the mechanism used for allocating metadata currently.
See the RFC for more details:
http://hdf.ncsa.uiuc.edu/RFC/SmallData/SmallData.html
This reduces the number of I/O operations which hit the disk for my test
program from 19 to 15 (i.e. from 393 to 15, overall).
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
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.
New Feature
Description:
The VFL flush function is called immediately before a file is closed.
This can cause duplicate syncronization actions to occur, if the VFL
close function also performs them.
Solution:
Added 'closing' parameter to VFL 'flush' operation. This allows the VFL
flush function to bypass operations that will be duplicated within the VFL
close function.
Additionally, use the 'closing' parameter to bypass calls to MPI_File_sync()
when set. Since MPI_File_close() also syncronizes the file, this avoids
the terrible performance hit taken when calling MPI_File_sync() as the file
is closing.
Platforms tested:
IRIX64 6.5 (modi4)
Code cleanup
Description:
Platform dependent code related to the struct stat and fstat
calls polluted source codes. Hard to maintain.
Solution:
Platform dependent code are moved to H5private.h and then internal
code can #include H5private.h. Repeat those macro definition for
the stdio and multi drivers since they area examples for writing
a virtual file driver. They must not use any internal code.
Platforms tested:
eirene (parallel), modi4 (serial including gass driver.)
Purpose:
fix a windows bug
Description:
1. To create a >4GB file, fstati64 has to be used instead of fstat.
change fstat to fstati64 for WIN32 macroes. Some discussions are going on
the general issue on how to better handle with WIN32 or other similar platform.
This check-in is just a reminder not to forget the windows bug.
2. erase a WIN32 macro(include winsock2.h) at h5detect.c. It is not a problem now.
Solution:
use fstati64 instead of fstat for win32.
Platforms tested:
windows2000(confirmed at linux machine eirene)
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
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)
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.
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)
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)
Bug fix.
Description:
On some systems (linux when not using gcc) 'dev_t' is not actually
a scalar variable. This causes the code which compares dev_t's in
the file drivers to not compile. Also the H5_inline flag was not being
set correctly in the H5private.h file.
Solution:
Set the H5_inline flag to '' (i.e. define it, but don't assign it a value)
if it is not currently defined.
Use DEV_T_IS_SCALAR flag from configure to correctly compare dev_t's using
memcmp instead of a scalar flag.
Platforms tested:
FreeBSD 4.3 (hawkwind), Linux 2.4.2 (chiba city cluster at Argonne)
