| Commit message (Collapse) | Author | Age | Files | Lines |
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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
Description:
Free blocks of space in the file which were merged with a block before them
were not updating the free list information correctly, allowing space in
the file to over-allocated and potentially corrupted.
Solution:
Correct address of free block during merging.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir)
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Code cleanup
Description:
Clean up compile warnings.
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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Purpose:
Performance improvement for compact dataset.
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
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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)
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Code cleanup/New Feature
Description:
Improve the space allocation in the file by re-using freed space more
effectively.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/serial & parallel
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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)
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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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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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New feature.
Description:
Added MPI-posix VFL driver. This driver uses MPI to coordinate actions, but
performs I/O directly with posix sec(2) I/O functions. This driver should
_NOT_ be used if the file accessed is not on a parallel filesystem.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/parallel & IRIX64 6.5 (modi4) w/parallel
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Code improvement
Description:
Some small code cleanups and took out the code the was turning off the
metadata cache for parallel I/O (!)
Platforms tested:
IRIX64 6.5 (modi4) w/parallel
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Bug fix.
Description:
H5P_get was reading a 'hsize_t' field into a 'size_t' variable, causing
problems on the HP's and Windows.
Solution:
Changed the variable to be an hsize_t
Platforms tested:
HP/UX 11.0 (kelgia)
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Code cleanup
Description:
Allow H5FD_free to return successfully (but ignore) freeing objects with
size 0.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Bug fix.
Description:
Added extra check to locations where metadata and "small data" blocks were
being returned to the file's list of free space to avoid freeing 0-sized
blocks. This should fix the problems in last night's daily tests.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code Improvement
Description:
Split the metadata accumulator code into two parts: one for allowing writes
of the accumulator buffer during reads (when the buffer is dirty and needs
to be flushed to disk in order to hold the new metadata being read in) and
another for only allowing writes of the buffer during writes.
This allows the MPI-I/O VFL driver to use the metadata accumulator (but
only during writes) and benefit from the reduced number of metadata I/O
operations that it brings.
Platforms tested:
IRIX64 6.5 (modi4) w/parallel
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Code cleanup/bug fix
Description:
Unused space in the file was being "dropped on the floor" when the metadata
or "small data" block was moved to a new location in the file and there was
unused space in the old block.
Solution:
Put the space left in the allocation block into the free list of space for
the file. This allows it to be [potentially] reused and sometimes allows
the file to be smaller.
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
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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++
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Code improvement
Description:
Now that the metadata accumulator is working correctly, the buffer size
tends to get rather large and stay there.
Solution:
Put a throttle on the accumulator buffer to reduce its size back down when
it isn't needed.
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN & FreeBSD 4.5 (sleipnir) w/C++
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Code improvement
Description:
The metadata aggregation code in the library was not terribly smart about
extending contiguous regions of metadata in the file and would not extend
them as far as possible. This causes space in the file to be wasted, also.
Solution:
Be smarter about extending the space used in the file for metadata by
checking whether new metadata blocks allocated in the file are at the end
of the current metadata aggregation region and append them to the metadata
region if so. This has the nice side benefit of reducing the number of
bytes we waste in the file and reducing the size of the file by a small
amount in some cases.
This reduces the number of I/O operations which hit the disk for my test
program from 53 to 19 (i.e. from 393 to 19, overall).
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
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Code cleanup/bug fix
Description:
The "metadata accumulator" cache in the library (which is designed to catch
small metadata writes/reads and bundle them together into larger I/O
buffers) was incorrectly detecting the important case of metadata pieces
being written sequentially to the file, adjoining but not overlapping.
Additionally, the metadata accumulator was not being used to cache data
read in from disk, only caching writes.
Solution:
Fix accumulator to correctly cache adjoining metadata writes and also to
cache metadata read from disk.
Between these two fixes, the number of I/O requests which resulted in actual
reads/writes to the filesystem dropped from 393 requests to 82 for the
particular test I was using. :-)
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN & FreeBSD 4.5 (sleipnir) w/C++
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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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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
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Code cleanup
Description:
Clean up warnings on IRIX64 6.5 (modi4)
Platforms tested:
IRIX64 6.5 (modi4)
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New feature
Description:
Add 'closing' parameter to H5FDflush and VFL "flush" functions, per
http://hdf.ncsa.uiuc.edu/RFC/VFLFlush/VFLFlush.html
Platforms tested:
IRIX64 6.5 (modi4)
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Back out changes.
Description:
Back out changes to VFL 'flush' API function, pending review.
Platforms tested:
IRIX64 6.5 (modi4)
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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)
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Bug Fix
Description:
The H5Gget_objinfo() function was not setting the 'fileno' field in the
H5G_stat_t struct passed in.
Solution:
Added a "file serial number" to each file currently open in the library
and put that in the 'fileno' field. If a file is opened twice (with
H5Fopen) and the VFL driver detects that it is the same file (i.e. the
two file structures have the same "shared file info" in the library's
memory structures), they will have the same serial number.
This serial number has two drawbacks:
- If a VFL driver doesn't/can't detect that two calls to H5Fopen with
the same file actually _are_ the same file, each will get a
different serial number
- If the same file is closed and re-opened, the serial number will be
different.
It is be possible to fix the second drawback for many VFL drivers, but it
would be a lot of effort and probably isn't worth it until we've got a
good reason to do it. Dunno if we'll ever be able to fix the first
drawback...
Platforms tested:
FreeBSD 4.5 (sleipnir)
VS: ----------------------------------------------------------------------
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Bug Fix
Description:
When file space was returned to the file space free-list for reuse,
occasionally raw data allocations which used space from the free-list
would overlap with the metadata accumulator and get over-written with
the cached information in the accumulator, corrupting the data.
Solution:
Check if the space about to be recycled on the free-list is going to be
used for raw data and also overlaps with the metadata accumulator cache,
avoiding using space that fits those criteria.
This fixes bug #701
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Bug fix
Description:
Fix another typo from today's big "overflow" commit.
Platforms tested:
Solaris 2.6 (baldric)
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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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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)
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Purpose:
Generic Property List Change
Description:
Changed file access list to the new generic list.
Platforms tested:
IRIX64, SunOS5.7, FreeBSD
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Kludge
Description:
Since we're only about halfway through converting the internal use of
property lists from the "old way" to the generic property lists, we turned
off snapshots to avoid exposing lots of API changes to users, until the
APIs settled down.
Getting the snapshots rolling again seems to have become a priority, so
some changes are going to have to be made now that were going to be
postponed until we were completely finished with the conversion. This
requires that the old API functions be able to deal with both the old
and new property lists smoothly.
Solution:
Kludge together the property list code so that they can transparently handle
dealing with both the old and new property lists
Platforms tested:
FreeBSD 4.4 (hawkwind)
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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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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)
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Bug Fix
Description:
In certain circumstances, raw data was inadvertantly attempted to be read
from the metadata cache. This was caught with an assertion failure (i.e.
core dump) in the development branch or an eventual sequence of errors in
the release branch.
Solution:
Corrected off-by-one error in metadata caching code.
Platforms tested:
FreeBSD 4.3 (hawkwind)
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Bug fix... (sorta)
Description:
Added --enable-linux-lfs configure flag to have better control over whether
the enable large file support on Linux machines. Also removed the
-malign-double flag for gcc since it can potentially cause errors which
are difficult to detect.
Platforms tested:
Linix 2.2 & 2.4 (eirene and dangermouse)
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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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Clean up compiler warnings.
Description:
Just code neatening mostly, some casts, etc.
Platforms tested:
FreeBSD 4.3 (hawkwind)
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Bug fix for Pablo integration
Description:
Several API functions were using FUNC_ENTER, without using FUNC_LEAVE,
HRETURN or HRETURN_ERROR to leave the function. (Using "plain" 'return'
statements instead).
Solution:
Changed return statements to FUNC_LEAVE, HRETURN or HRETURN_ERROR, as
appropriate.
Platforms tested:
FreeBSD 4.3 (hawkwind)
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Code cleanups
Description:
Fixed a small number of warnings and also took out the H5private.h
header from H5Ppublic.h
Platforms tested:
FreeBSD 4.3 (hawkwind)
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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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Feature
Description:
The allocation by alignment (H5Pset_alignment) feature code somehow
got dropped in some 1.3.x version.
Solution:
Re-implemented it with "new and improved" algorithm. It keeps track
of "wasted" file-fragment in the free-list too.
Platforms tested:
modi4(parallel).
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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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2000-12-29 09:06:02 Robb Matzke <matzke@llnl.gov>
* H5FD_query: Marked `flags' argument as /*out*/
2000-12-29 09:05:49 Robb Matzke <matzke@llnl.gov>
* H5FDquery: Marked `flags' argument as /*out*/
2000-12-29 09:03:39 Robb Matzke <matzke@llnl.gov>
* H5FD_open: Reindented a line or two.
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Backward compatibility code
Description:
Add in code to allow the library to emulate the v1.2 API and behavior.
Platforms tested:
FreeBSD 4.2 (hawkwind)
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