| Commit message (Collapse) | Author | Age | Files | Lines |
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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
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Code optimization
Description:
Revised dataspace selections to use a more "object oriented" mechanism
to set the function pointers for each selection and selection iterator. This
reduces the amount and number of times that dataspace selection info has to
be copied.
Additionally, change hyperslab selection information to be dynamically
allocated instead of an inline struct.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Refactor code
Description:
Move chunk and contiguous cached raw data from file information to dataset
information. This simplifies a number of internal interfaces, aligns the
code with it's purpose better and should allow more optimizations to the
chunked data I/O performance.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir)
h5committest
Misc. update:
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Code optimization & bug fix
Description:
When dimension information is being stored in the storage layout message
on disk, it is stored as 32-bit quantities, possibly truncating the dimension
information, if a dimension is greater than 32-bits in size.
Solution:
Fix the storage layout message problem by revising file format to not store
dimension information, since it is already available in the dataspace.
Also revise the storage layout data structures to be more compartmentalized
for the information for contiguous, chunked and compact storage.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
Solaris 2.7 (arabica)
h5committest
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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
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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
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Code cleanup
Description:
Clean up compiler warnings, especially the 'FUNC' variable not used which
comes out in production mode.
Solution:
Had to add a new FUNC_ENTER_NOAPI_NOINIT_NOFUNC macro for those non-API
functions which don't need the 'FUNC' variable defined. (This will be _so_
much easier when C99 is standard on all our supposed platforms, since it has a
__FUNC__ macro... )
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor for h5committest (although there were lots of files changed, the
change was minor in each one)
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Bug fix
Description:
Code was using an internal DXPL with collective I/O turned on during
independent I/O operations to fill dataset on disk.
Solution:
Switched to internal DXPL with independent I/O
Platforms tested:
FreeBSD 4.9 (sleipnir)
FreeBSD 4.9 (sleipnir) w/parallel
Linux 2.4 (verbena) w/fortran & C++
Solaris 2.7 (arabica) w/64-bit extensions enabled
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Bug fix
Description:
When datasets are deleted from a file, they are removed from the sieve
buffer, but instead of invalidating only the part of the sieve buffer affected,
the sieve buffer code would throw away the entire sieve buffer, potentially
including other raw data in the buffer that hadn't been written to disk yet.
Solution:
Improve the sieve buffer clearing code to handle partial invalidations.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Refactoring code
Description:
Refactored "IS_H5FD_MPIO || IS_H5FD_MPIPOSIX || IS_H5FD_FPHDF5" combination
of macros in many places into single IS_H5FD_MPI macro, which has the same
definition, but should be easier to maintain.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Code cleanup
Description:
Clean up various minor warnings in the library.
Platforms tested:
FreeBSD 4.8 (sleipnir)
too small to need h5committest
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Code cleanup/Feature removal
Description:
Remove "round robin" writing of metadata in MPI VFDs (and a couple of other
places). This never really worked the way I hoped it would and it causes
problems on certain machines.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/parallel
Too small for triple check.
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Update code
Description:
Move "PABLO_MASK" definition above header file inclusion to avoid problems
with inline functions in header files.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Bug fix
Description:
An earlier checkin changed some of the assumptions about single block
hyperslabs, causing them to fail in odd ways.
Solution:
Fix errors with single block hyperslabs by keying off of count==1 instead
of stride==1.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/parallel
h5committested
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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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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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Code Improvements/Bug Fixes
Description:
Comparison of equality of a double/float variable to 0.0 is not
guaranteed to work and is bad practice.
In H5Fcontig.c, a warning was given by a statement like:
x = (++x) % y;
This could be confusing to a compiler I suppose.
In H5RS.c, a typedef of a structure was being tagged by the compiler
as "useless" because it had the form:
typedef struct foo {
int var1;
/* ... */
}; /* <--- note no name for this typedef */
The statement "typedef struct foo foo" is already in the header file.
Solution:
Test that the absolute value of the variable is < a very small
positive number.
Changed "x = (++x) % y" to "++x; x %= y;" instead.
Removed the "typedef" from the structure in the H5RS.c file.
Platforms tested:
Modi4 (Parallel & Fortran)
Verbena (C++ & Fortran)
Arabica (Fortran)
Misc. update:
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New feature.
Description:
Added ability to free space used for storing raw data for both contiguous
and chunked datasets.
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).
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Update
Description:
Final support addition for FPHDF5. Wherever there was an equivalent
MPIO or MPIO/POSIX call/check, I placed an FPHDF5 call/check there as
well, with the appropriate #ifdefs in place.
The hdf5.h is updated with the H5FDfphdf5.h driver #include.
Platforms tested:
Linux & Modi4
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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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Bug fix/Code cleanup/New Feature
Description:
Correct problems with writing fill-values to external storage and allocate
the data storage at the correct times.
Also, mostly straighten out the strange code which allocates and fills
raw data storage for datasets. Things are still a bit odd in that the
fill-values for chunked datasets are written when the space is allocated,
instead of in a separate routine, but there are two reasons for this:
it's inefficient (especially in parallel) to iterate through all the chunks
twice, and (more importantly) the space needed to store compressed chunks
isn't known until we've got a buffer of compressed fill-values ready to
write to the chunk.
Additionally, add in the H5D_SPACE_ALLOC_INCR and H5D_SPACE_ALLOC_DEFAULT
setting for the "space time", which incorporate the previous behavior of
the space allocation for chunked datasets.
The default settings for the different types of dataset storage are now
as follows:
Contiguous - Late
Chunked - Incremental
Compact - Early
This checkin also incorporates a change to the behavior of external data
storage in two ways - fill-values are _never_ written to external storage
(under the assumption that writing fill-values is triggered by allocating
space in an HDF5 file, and since space is not allocated in the file, the
fill-values should not be written) and external data files are now created
if they don't exist when data is written to them. The fill-value will
probably need to be revisited at some time in the future, this just seemed
like the safer course currently.
I think I cleaned up some compiler errors also, before getting bogged down
in the fixes for the space allocation and fill-values.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/serial & parallel. Will be testing on IRIX64
6.5 (modi4) in serial & parallel shortly.
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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:
Make the sieve buffer managed by the free-list code.
Platforms tested:
FreeBSD 4.6 (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:
Change variable casts to use H5_ASSIGN_OVERFLOW, or check for overflow
before the cast with H5_CHECK_OVERFLOW.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Purpose:
eliminate warnings on win32
Description:
some conversion warnings were being issued
Solution:
added some type casts
Platforms tested:
w2000, linux
changed the HDmemset to include a cast in win32; this was just to eliminate a compiler
warning. probably the macro can also be used in unix
#ifdef WIN32
#define HDmemset(X,C,Z) memset((void*)(X),C,Z)
#else /* WIN32 */
#define HDmemset(X,C,Z) memset(X,C,Z)
#endif /* WIN32 */
the list of previous warnings was
D:\disk_w\hdf5\src\H5FDstdio.c(659) : warning C4244: 'initializing' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Fcontig.c(435) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Fcontig.c(497) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Fcontig.c(915) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Fcontig.c(982) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(912) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(995) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(1936) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(2019) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(2862) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(2864) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(2948) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(3690) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(3692) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(3776) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(5167) : warning C4244: '+=' : conversion from '__int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Tvlen.c(371) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
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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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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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Document bug fix
Description:
IMPORTANT! IMPORTANT! IMPORTANT!
A case where metadata in a file could get corrupted in certain unusual
sitations was detected and fixed.
In certain circumstances, metadata could get cached in the raw data cache,
and if that particular piece of metadata was updated on disk while
incorrectly cached, the new metadata would get overwritten with the stale
metadata from the raw data cache when it was flushed out.
Additionally, I've patched up the raw data cache to be smarter about how
much it caches and how much I/O it triggers, leading to some speedups.
Solution:
Changed the raw data I/O routines which perform caching to require a
parameter with the size of the dataset being accessed and limited the
cache to no more than that many bytes.
Platforms tested:
FreeBSD 4.3 (hawkwind)
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Bug Fix.
Description:
Setting a non-zero userblock size was causing raw data caching code to
break.
Solution:
Changed from using absolute end-of-address-space offsets in cache size
calculations to relative offsets.
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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Clean up code.
Description:
Cleaned up various compiler warnings.
Platforms tested:
FreeBSD 4.2 (hawkwind)
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Small code optimization
Description:
Removed some unnecessary buffer assignments.
Platforms tested:
Solaris 2.6 (baldric)
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Bug Fix
Description:
Some of the HRETURN types were incorrect. They were NULL when
they should have been FAIL.
Solution:
Changed the NULLs to FAILs.
Platforms tested:
Linux
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Code optimization
Description:
Minor tweaks throughout the optimized regular hyperslab code to increase
speed. This set of improvements increase the benchmark time from taking
~5.46 seconds to ~4.50 seconds, or around a 20% further speedup.
Platforms tested:
Solaris 2.6 (baldric)
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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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Bug Fix
Description:
Use H5FD_get_eoa instead of H5FD_get_eof to check for reading off the end
of the allocated file space. Using H5FD_get_eof was causing the Stream
VFD to fail.
Solution:
Switched from using H5FD_get_eof to H5FD_get_eoa
Platforms tested:
FreeBSD 4.1.1 (hawkwind)
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Rearrange code
Description:
The data sieve buffering code for contiguously stored datasets was
wedged in the H5F_arr_read/H5F_arr_write routines.
Solution:
Created a new H5Fcontig.c to hold I/O routines for contiguously stored
datasets (like H5Fistore.c for chunked dataset I/O routines) and moved
data sieving code into those routines.
Platforms tested:
Solaris 2.6 (i.e. baldric)
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