Code cleanup/refactoring/potential bug fix
Description:
Migrate "template macro" changes from development branch back into this
branch, since they give about a 20% speedup for integer & floating-point type
conversions. The also avoid a potential alignment bug on the Crays...
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest not necessary, since the changes are already verified in the
development branch.
Bug fix
Description:
Correct the size of the buffer needed for the destination value to use
the actual destination type size.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
Bug fix
Description:
The VL type conversion routine attempt to align it's destination buffer to
an offer that will work for both hvl_t and char * types, but the algorithm used
fails to work correctly on Cray machines.
Solution:
Give up on attempting to align the buffer when it's allocated on the stack.
Just dynamically allocate it instead.
Platforms tested:
FreeBSD 4.9 (sleipnir)
Cray SV1 (wind)
Bug fix
Description:
H5T_BKG_TEMP was accidentally removed from library code, but is used by
application's datatype conversion routines.
Solution:
Revert removal of H5T_BKG_TEMP.
Platforms tested:
h5committest
Bug fix
Description:
Fix "unaligned access" warning on IA64 (and alpha, probably) machines.
Solution:
Make certain that temporary destination buffer is aligned on correct
boundary for type conversion.
Platforms tested:
IA64 Linux cluster (titan)
too small for h5committest
Bug fix
Description:
Aligned data is not being detected by type conversion routines correctly
on some Crays, causing corrupted data during I/O.
Solution:
Add extra checking for strange pointer behavior on Crays.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Cray SV1 (wind)
Cray T3E (hubble)
Cray T90 (gypsy)
Description: H5Tget_native_type fails for multiple kinds of datatype on Cray; it fails
fix-length string type, too.
Platforms tested: Cray, h5committest
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
Code cleanup.
Description:
Break up the ~9350 line H5T.c module into smaller pieces, which contain
code for a particular feature or support for a datatype class.
This should make the "main" H5T code (still in H5T.c) easier to support,
as well as removing some of the "minor" routines from the user applications
which don't use them (my rough estimates show about 4% reduction (~30K on
a FreeBSD machine) in optimized, staticly-linked binaries for very simple
programs)
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir)
Misc. update:
Update MANIFEST
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 & bug fix
Description:
Cleanup another set of warnings on Windows and also fix mis-placed assertion
that caused the daily tests to fail.
Platforms tested:
IRIX64 6.5 (modi4) w/-n32
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
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.
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)
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
Purpose:
Bug fix.
Description:
For nested VL datatype, the heap object of VL elements lower than top level
weren't freed.
Solution:
Read in the content of heap object for VL elements and free them in
function H5T_conv_vlen.
Platforms tested:
eirene
Purpose:
Bug Fix.
Description:
VL type memory leak when data is overwritten.
Solution:
Free heap objects holding old data.
Platforms tested:
Linux 2.2(eirene), IRIX 6.5(paz).
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.
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)
Purpose:
eliminating the compiler warnings in Windows
Solution:
I am eliminating the compiler warnings in Windows.
the last 2 were:
1)
if((oid_list = H5MM_malloc(oid_count*sizeof(hid_t)))==NULL)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL,
"memory allocation failed");
D:\disk_w\hdf5\src\H5F.c(2590) : warning C4047: '=' : 'int ' differs in levels
of indirection from 'void *'
on the HGOTO_ERROR call , I replaced the NULL with FAIL
2)
*((float*)d) = *((double*)s);
D:\disk_w\hdf5\src\H5Tconv.c(6426) : warning C4244: '=' : conversion from 'double ' to 'float ', possible loss of data
I added the type cast
*((float*)d) = (float) *((double*)s);
we have now 0 errors 0 warnings on Windows !
Platforms tested:
w2000, linux
Code cleanup
Description:
Got rid of the "H5T_BKG_TEMP" setting that was used internally to the
library, since temporary background buffers are now handled by the
individual conversion routines instead of in a global background buffer.
No APIs were changed or affected by this.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Bug fix
Description:
When several level deep nested compound & VL datatypes are used, the data
in the nested compound datatypes is incorrectly sharing the same "background
buffer", causing data corruption when the data is written to the file.
Solution:
Allocate a separate background buffer for each level of the nested types
to convert. (Also allocate temporary background buffers for array
datatypes, where this sort of problem could occur also)
Added more regression tests to check for these errors.
Platforms tested:
FreeBSD 4.5 (sleipnir) & Solaris 2.6 (baldric)
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 10:48:54 Robb Matzke <matzke@arborea.spizella.com>
* H5T_conv_order: Removed Duff's device consisting of >500 lines of code. Unrolled
two loops by hand resulting in <300 lines of code
which is a few percent faster and far easier to read.
Bug Fix
Description:
Replace an 'if' statement taken out in commit earlier today which was
necessary for routing around endian conversions when zero elements were
converted.
Platforms tested:
IRIX64 6.5 (modi4)
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)
Bug Fix
Description:
Byte swapping routine was core dumping when attempting to convert 0
elements.
Solution:
Don't try to byte swap when there is nothing to do... :-)
Apologies to Kent for my comments on Friday about testing his checkins,
especially when it was I who needed to do moer testing. :-/
Platforms tested:
Solaris 2.7 (arabica)
Code improvement
Description:
The byte swapping routine for data conversion was inefficient.
Solution:
Applied a number of optimizations which should yield around a 2-3 times
faster algorithm.
Platforms tested:
Solaris 2.6 (baldric)
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)
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)
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)
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
Bug Fix
Description:
The 'carry' variable in the general floating point-to-floating point
conversion routine wasn't getting initialized correctly and was causing
problems while converting certain sequences of floating point numbers
on the Cray SV1.
Solution:
Added 'else carry=0;' line to always reset the carry variable to a known
value.
Platforms tested:
Cray SV1 (killeen)
2001-02-03 00:19:25 Robb Matzke <matzke@llnl.gov>
* H5T_conv_f_f: Fixed a bug where I had forgotten to increment the floating-point
exponent if rounding the significand resulted in a
carry. Thanks to Guillaume Colin de Verdiere for
finding this one!
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)
Bug Fix
Description:
More descrimination is necessary for the type of background buffer needed.
Compound types need H5T_BKG_TEMP and vlen & array types need H5T_BKG_YES.
Solution:
Make the internal routine be more specific about the background type set.
Platforms tested:
FreeBSD 4.2 (hawkwind)
Bug fix
Description:
Non-optimized conversions have a memory overwrite bug when the destination
size of a compound datatype is greater than the source size.
Solution:
Corrected direction of walking through the destination array for final
copying.
Platforms tested:
FreeBSD 4.2 (hawkwind) & Cray J90 (killeen)
Bug Fix
Description:
Compound datatypes weren't reading background data properly when used
with array or vlen fields.
Solution:
Changed to always read background information from file in those situations.
Platforms tested:
FreeBSD 4.2 (hawkwind)
Code addition
Description:
The dumper needs to know when a datatype needs to be reclaimed, so I
added a small helper function to detect if a particular datatype is or
contains a particular class of datatypes.
Platforms tested:
Linux 2.2.16-3smp (eirene)
Patch on the patch of my code cleanup... :-)
Description:
Fix compiler problems with previous code patching...
Platforms tested:
Linux 2.2.16-3smp (eirene)
