| Commit message (Collapse) | Author | Age | Files | Lines |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Convert object header cache client to use the new metadata journaling
cache, which included adding a new client for handling continuation chunks.
Added "real" protect calls around modifying chunks in object headers.
Switched a few more metadata cache library API routines to drop the
file pointer, when it is not needed (pinning/unpinning entries, etc.)
Fixed bug in journaling cache handling of 'image_len' callbacks and
also changed cache to retry deserializing entries when the entry's size is
larger than the speculative size initially tried.
Retrying for 'image_len' callbacks has problems with the 'multi' VFD,
so the h5dump and FORTRAN 'multi' tests are commented out, until the changes to
the 'multi' VFD from the file free space branch are brought back into the
trunk.
Currently, the 'h5recover' tool has a bug which requires it to be run
twice before replaying the journal "sticks". However, this is from an earlier
checkin, since the code in the branch already has this behavior... :-(
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.5.4 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring revisions 14800:14900 from trunk into metadata journaling branch
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.5.2 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring changes from trunk from the time the branch was created (r14280)
up to the 1.8.0 release (r14525) back into the metadata journaling branch.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
|
|
|
|
|
|
|
|
|
| |
journaling
superblock extension message. Created the file src/H5Omdj_msg.c and
moved journaling superblock extension message to it.
Tested serial on Phoenix, and parallel on Kagiso.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
note that both the H5C and H5C2 code have been updated.
Also checked in code to track journaling status in the super block.
Note that this code has not been tested -- but as best I can tell,
it does not break the existing regression tests.
Tested serial (debug and production) on Phoenix. Also tested parallel
on kagiso.
Note that regression test fails on kagiso (but not on phoenix) if
the cache2 serial tests are configured to use the core file driver.
Thus this code is check in with the core file driver optimization
of the cache2 tests disabled. To turn it on, set the USE_CORE_DRIVER
#define to TRUE.
|
|
|
|
|
|
| |
metadata
journaling branch. This version may not compile.
|
|
|
|
|
|
|
|
|
|
| |
Removed the stream-vfd from the basic library code.
(The stream-vfd source files are not removed yet but the MANIFEST has been
updated to NOT release those stream-vfd source files.)
Platforms tested:
Kagiso and smirom.
Then test the release tar ball in kagiso.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Break up H5D source file into H5D/H5Dint/H5Ddeprec
Attempt fix for "szip noencoder" build failure.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Move H5Pregister our of old "compat v1.6" section and add it to the
versioned symbols.
Add simple regression test for H5Pregister1()
Split H5P.c source file into H5P/H5Pint/H5Pdeprec files.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Add H5Rget_obj_type() to the API versioning and switch internal
routines to use H5Rget_obj_type2()
Misc. other code cleanups, etc.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
AIX/32 5.3 (copper)
Solaris/32 2.10 (linew)
Mac OS X/32 10.4.10 (amazon)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Fix problem with dataspace messages where the version of the format
for a dataspace message could depend on the "use the latest format" flag from
the file after it was initially created.
Also, move debuging routine into separate file.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Mac OS X/32 10.4.10 (amazon)
Solaris/32 2.10 (linew)
|
|
|
|
|
|
|
|
|
|
|
| |
Rename H5Titerate.c source file to H5Tvisit.c, which is more
descriptive of routine(s) in file.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Mac OS X/32 10.4.10 (amazon)
|
|
|
|
|
|
|
|
|
|
|
|
| |
Fix problem with datatype messages where the version of the format
for a datatype message could depend on the "use the latest format" flag from
the file after it was initially created.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Mac OS X/32 10.4.10 (amazon)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Initial checkin of API version macro generation script (bin/make_vers),
along with configuration file (src/H5vers.txt) and generated header
(src/H5version.h). Right now, no version macros are defined, since the main
source code and tests need to be adjusted to pay attention to the macros
defined.
Also, fixed makefile for generating error header files when used with
GNU make.
Tested on:
Mac OS X/32 10.4.10 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
|
|
|
|
|
|
|
|
|
|
|
|
| |
Add small interface to "wrap" a static buffer (usually on the stack), but
still allow for buffers larger than the static buffer to be allocated. This
can eliminate _many_ short-lived buffer allocations in situations where the
buffer is a predictable size (or at least a "very likely" size).
Also, some minor code cleanups, particularly in the SOHM caching code.
Tested on:
Mac OS X/32 10.4.10 (amazon)
|
|
|
|
|
|
|
|
|
|
| |
Refactor fill value buffer code into one location, for better long-term
maintenance.
Tested on:
Mac OS X/32 10.4.10 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Add "fail if unknown" and "mark if unknown" flags to object header messages.
This gives the library a clean way to tell older libraries that a message should
not be just ignored if it's unknown, but that other actions should occur.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
|
|
|
|
|
|
|
|
|
|
| |
Rename new error handling API routines from H5E<foo>_stack() to
H5E<foo>2().
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Change H5[D|G|T]<foo>_expand() "temporary" API routines to
H5[D|G|T]<foo>2() "versioned" routines. Also added
H5[D|G|T](create|commit)_anon() routines to continue to allow "anonymous"
objects to be created in a file.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Move ref. count of # of links to an object out of the object header's
prefix and make it a header message instead (since it's a "rare" occurence),
eliminating some more space for each object in the file.
Inserting this "ref. count" message exposed a flaw in the library's
mechanism for locating a message to promote to another chunk and replace
with a continuation message, which required some additional work to fix.
It's still not completely robust, but it's working for more cases now and
detects failures robustly.
Reduced the minimum size of an object header chunk to just enough to
contain a header message prefix and continuation message.
Tested on:
FreeBSD/32 6.2 (duty)
|
|
|
|
|
|
|
|
| |
Add new object header message to track attribute information (unused
currently).
Tested on:
Mac OS X/32 10.4.8 (amazon)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Revise latest form of superblock format pretty drastically, to
eliminate unused fields and move rarely used fields into superblock extension.
Finished removing last vestiges of references to (never used) i"shared"
object header message ID.
Added object header messages for non-default v1 B-tree 'K' values
and for driver info.
Updated testfiles to reflect size changes, etc.
Various minor cleanups, etc.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
|
|
|
|
| |
Ran reconfigure to generate the Makefile.in files.
|
|
|
|
|
|
|
|
|
| |
object header
information, rather than storing it directly in the superblock.
This should make future updates to the superblock much less painful.
Tested on Windows, kagiso, and smirom.
|
|
|
|
|
|
|
|
|
|
|
|
| |
Add support for deleting all the attributes on an object, when they
are dense and possibly shared.
Also, add some testing routines, for better error detection.
Should fix daily test failures also...
Tested on:
FreeBSD/32 6.1 (duty)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Add more tests for checking that writing to shared attributes works
correctly. (Looks like it still has a bug when dense storage is used, which
I'll correct shortly).
Add testing routine to shared message code, to retrieve reference count for
a shared message.
Add fractal heap 'op' callback for efficiently computing the hash value of
an existing encoded message in the shared message fractal heap.
Various minor cleanups and warning placations.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Add support for opening attributes in dense and/or shared storage by
index.
Move routines for building and operating on tables of attributes into
separate source module.
Fix bug where reverting from "dense" to "compact" storage would 'unshare'
attributes.
Minor code cleanups, etc.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
|
|
|
|
|
|
|
|
|
|
|
| |
Migrate "internalish" attribute operations into new source code file.
Add test & basic support for opening attributes in dense storage (shared
attributes not tested or supported yet).
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Add first pass of "dense" attribute storage to objects. Lots of parts of
this are stubbed out, but all the tests are passing and I'll work on the corner
cases soon.
Eliminated several unused parameters from object header message callback
routines.
Other, miscellaneous code cleanups, etc. (and probably some things I've
forgotten about... :-)
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
AIX/32 5.? (copper)
|
|
|
|
|
|
|
|
|
|
|
| |
Migrate more object header routines to use the H5O_msg_ prefix and put
them into the src/H5Omessage.c code module.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
AIX/32 5.? (copper)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Propagate object creation properties up into group, dataset and named
datatype property lists, when those property lists are retrieved for
existing objects in a file.
Also, add H5Tget_create_plist() API routine, to allow named datatype
property lists to be retrieved for named datatypes.
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
|
|
|
|
|
|
|
|
|
|
|
| |
Add # of attributes to the object info struct and deprecate
H5Aget_num_attrs().
Tested on:
FreeBSd/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Add src/H5Oalloc.c file forgotten in previous object header checkin
Break out more object header routines into separate file (debugging routines
this time).
Fix "//" style comment in recent ISOHM source changes.
Fix 'size_t' vs. 'unsigned' problem (visible in 64-bit testing) in recent
ISOHM test changes.
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
|
|
|
|
|
|
|
|
|
|
| |
moved to
H5Opublic.h.
Updated Makefile.am, reconfigured.
Tested on kagiso.
|
|
|
|
|
|
|
|
|
|
|
|
| |
This feature is still in progress; Shared Object Header Messages are not
complete as a feature and are not thoroughly tested. There are still
"TODO" comments in the code (comments with the word "JAMES" in them,
so as not to be confused with other TODO comments).
Hopefully this checkin will reduce the liklihood of conflicts as I finish
implementing this feature.
All current tests pass on juniper, copper (parallel), heping, kagiso, and mir.
|
|
|
|
|
|
|
|
| |
Move compact storage routines into separate file, to make room for internal
routines that operate on links within group operations.
Tested on:
Linux/32 2.6 (chicago)
|
|
|
|
|
|
|
|
| |
Rename new H5Gcopy() routine to H5Ocopy() as discussed in last Friday's
design discussion.
Tested on:
Linux/32 2.6 (chicago)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
|
|
|
|
|
| |
Altix (cobalt). There's a configure
option --enable-direct-vfd/--disable-direct-vfd to enable/disable Direct I/O support. The default
is enabled. There's a small test in test/vfd.c. Another way to test it is to set environment
variable HDF5_DRIVER to "direct" and run "make check" in the test/ directory. There'll be some
further improvement in the following checkin including allowing user to provide memory boundary
value, file block size, and copying buffer size.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Add the "use the latest version of the format" support to datatype
messages. And a regression test to check that it's working.
Also, found that we have been over-allocating space for compound datatype
messages (when they have array datatypes or can use the latest version of the
format) and trimmed the size back.
Clean up datatype & dataspace encode/decode routines by having them
allocate & release "fake" file structures, which gets them out of needing to
"know" about the internals of file structures.
Other minor whitespace/formatting cleanups, etc.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
File format is not stable, don't keep files produced!
Description:
First stage of checkins modifying the format of groups to support creation
order. Implement "dense" storage for links in groups.
Try to clarify some of the symbols for the H5L API.
Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest
file format options (including "dense" link storage in groups)
Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation
order tracking in groups (although no index on creation order yet).
Remove --enable-group-revision configure flag, as file format issues are
now handled in a backwardly/forwardly compatible way.
Clean up lots of compiler warnings and other minor formatting issues.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-v1.6 compa
Mac OSX/32 10.4.8 (amazon)
AIX 5.3 (copper) w/parallel & FORTRAN
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Break out a bunch of the misc. routines that were in src/H5.c into more
specific modules.
Add optimized fletcher32 checksum routine, for checksumming metadata as
well as raw data.
Tested On:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Will test further after checkin...
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Several changes, all mooshed together:
- Add support for "tiny" objects - which can be stored in the heap
ID itself, instead of in the heap data blocks.
- Flesh out support for compressed direct blocks, but comment it
out until John's got some metadata cache changes in place to
support it.
- Add support for applying I/O pipeline filters to 'huge' objects
- Refactor 'huge' object code to store information for 'huge' objects
directly in the heap ID, when there are I/O pipeline filters
applied to the heap (and the heap ID is large enough to hold the
information)
- Update h5debug tool to correctly handle 'huge' & 'tiny' objects.
- Misc. other code cleanups, etc.
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/64 2.4 (mir)
Solaris/64 2.9 (shanti)
|
|
|
|
|
|
|
|
|
| |
Rename some files, to better align with the names of the functions within
them.
Tested on:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
|
|
|
|
|
|
|
|
|
|
|
|
| |
Initial revision to add support for "huge" objects in the heap (which are
actually stored directly in the file, but are tracked with v2 B-tree that is
accessed through heap header).
Testing:
FreeBSD 4.11 (sleipnir)
Linux/64 2.4 (mir)
Linux/32 2.4 (heping)
Mac OS X.4 (amazon)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Users can create external links using H5L_create_external(). These links
point to an object in another HDF5 file. Users can alter the behavior of
external links or create new kinds of links by registering callbacks
using the H5L interface.
Added tests, tools support, etc.
Also a number of other, minor changes have been made (some restructuring of
the H5L interface, for instance).
Additional documentation and examples are forthcoming.
|
|
|
|
|
|
|
|
|
|
|
| |
Refactored free space manager to use metadata cache for serialized free
space sections. This speeds up the fractal heap test considerably...
Tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4/32 (chicago)
Linux 2.4/64 (mir)
Mac OS X (amazon)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Feature
Description:
Revised Link APIs.
Solution:
New link APIs use H5L*
H5*create_expand do not create links to the objects created; this must
be done manually with H5Llink.
Added APIs to link an object given its ID (H5Llink), to copy links (H5Lcopy),
and changed creation APIs (H5Lcreate_hard and H5Lcreate_soft) and query
API (H5Lget_linkinfo instead of H5Gget_objinfo).
All old APIs are still supported in H5Gdeprec.c .
Platforms tested:
sol, mir, copper
Misc. update:
Forgot to update MANIFEST and release docs. Will do after checkin.
|
|
|
|
|
|
|
|
|
|
|
| |
Makefile cleanup
Description:
Cleaned up where files were distcleaned
Platforms tested:
mir (change only affects distclean)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Code checkpoint
Description:
Checkpoint fractal heap improvements, as well as move the free space
manager code that it's using into a separate package.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4/64 (mir) w/C++ & FORTRAN
Linux 2.4/32 (heping)
Solaris 2.9 (shanti)
AIX 5.? (copper) w/FORTRAN & parallel
|