| Commit message (Collapse) | Author | Age | Files | Lines |
|
|
|
|
|
|
| |
Aligning code with changes made in VOL branch. This will make porting
non VOL related changes from trunkto the 1.8 branch much easier.
tested h5commitest.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r25084, 25088, 25092, 25097 from trunk to 1.8 branch:
r25084:
Begin process of migrating from using property list IDs internally to the
library to using the internal generic property list data structure.
r25088:
Introduce "file I/O info" struct, to hold file & dxpl pointers, and start
propagating up through library.
r25092:
More migration to using H5F_io_info_t pointers and away from using
property list IDs internally. Also, clean up some compiler warnings in the
cache code.
r25097:
Make progress toward moving from DXPL IDs to property list structures
within the library. Also move the signature location code from the H5F
package to the H5FD package, where it's a better fit. Also, clean up some
more compiler warnings along the way.
Tested:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(h5committested on trunk)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r24995 and r24998 from the trunk to the 1.8 branch:
r24995:
Improve checks for NULL buffer from user during H5Dread/H5Dwrite calls.
r24998:
Check in Neil's changes for correctly handling case where library is
reinitialized through a deprecated routine.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/serial & paralle
(change has baked on trunk for >7 days)
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r24476 from trunk to 1.8 branch:
Remove duplicate "intent" flags from top & shared file structures, leaving
them only in the shared file structure.
Tested on:
Mac OSX/64 10.9.0 (amazon) w/gcc 4.8, both parallel & serial
(too minor to require h5committest)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Tested: jam, koala, ostrich, platypus (h5committest)
Log from r24140:
Purpose: Remove problematic abandonment of error stack
Description:
H5Fis_hdf5 uses H5F_locate_signature to check if the file is hdf5. If it does
not locate the signature, H5F_locate_signature would issue an error and return
HADDR_UNDEF. H5Fis_hdf5 does not consider it an error if the signature is not
found, so it does not issue an error or clear the stack. The filled stack could
then cause issues later on.
Changed H5F_locate_signature to return herr_t, not issue an error if the
signature is not found, and added a parameter for a pointer to the signature
address that the function fills in.
Tested: jam, koala, ostrich (h5committest)
|
|
|
|
|
|
|
|
|
| |
of code from the trunk. It fixes the problem by first iterating
through all opened datasets and groups to see if any of them uses the filter. If it finds one, the function fails with a message.
Then the function flushes all opened files.
Tested with h5committest.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r21133 from trunk to 1.8 branch:
More code cleanups to reduce coupling between packages that use the H5F
internal routines, but really aren't part of the H5F "package".
Tested on:
FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode
FreeBSD/64 8.2 (freedom) w/gcc4.6, w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (koala) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r20219 from trunk to 1.8 branch:
Tell the VFL flush call that the file will be closing, allowing
the VFDs to avoid sync'ing the file (particularly valuable in parallel).
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
|
|
|
|
| |
Tested: jam (open_file_pool branch tested with h5committest)
|
|
|
|
|
|
|
|
|
|
| |
Bring metadata accumulator fixes and tests into 1.8
Description:
Changes consist of addition of tests for H5Faccum.c source code,
as well as some fixes that address some discovered bugs in the
metadata accumulator on several corner cases.
Tested:
h5committested
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r19587 from trunk to 1.8 branch:
Address issue with object headers being created getting evicted from
the metadata cache cache before they are completely initialized. This is
done by pinning the object header in the cache until it is completely
initialized and attached to a group.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r19247 from trunk to 1.8 branch:
Bring r19246 from Coverity branch to trunk:
Improve metadata "accumulator" for files to track the dirty region within
the accumulator data. This allows the accumulator to drop clean data and
reduces the number of I/O operations when it is dirtied.
This is progress toward Bz#1142 - speeding up the fheap test (which it
doesn't help much, actually, but it does help other aspects of file I/O).
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r18702 from trunk to 1.8 branch:
Bring r18672 from metadata journaling "merging" branch to trunk:
Mostly changes to move to only using one 'user data' parameter for
calls to H5AC_protect(), along with some minor reformatting code cleanups.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
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 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r18505 from trunk to 1.8 branch:
Move code to free superblock data structure into separate routine, in
preparation for upcoming metadata journaling -> trunk merging.
Tested on:
FreeBD/32 6.3 (duty) w/debug
(h5committested on trunk)
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r18502 from trunk to 1.8 branch:
Bring r18501 from metadata journaling "merging" branch to trunk:
Extract data structure 'destroy' routines from metadata cache client
'destroy' callbacks.
Tested on:
FreeBSD/32 6.3 (duty) w/debug
(h5committested on trunk)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r18357 from trunk to 1.8 branch:
Bring r18356 from metadata journaling merge branch to trunk:
Converge metadata journaling branch with trunk with a bunch of v1 B-tree
changes:
- Remove H5ACprivate.h header from H5Bprivate.h header
- Revise v1 B-tree client callbacks
- Get rid of H5B_serialize() by bringing it into H5B_flush()
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r17939 from trunk to 1.8 branch:
Handle external links from symlinked files by adding another check to
look for "child" files for links from the actual location of the "parent" file,
instead of from the location of the symlink.
Tested on:
FreeBSD/32 6.3 (duty)
(h5committested on trunk)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r17885 from trunk to 1.8 branch:
Convert 'huge' fractal heap object management code to use refactored
v2 B-tree routines.
Also, switch internal representation of 'sizeof_addr' and 'sizeof_size'
in files to be uint8_t's instead of size_t's, since they are stored in single
bytes in the file format.
Various other minor compiler warning cleanups and error call tweaks.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk
|
|
|
|
|
|
|
|
|
|
| |
Bring r17461 from trunk to 1.8 branch:
Fix a few more problems when the user block is not aligned properly.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r17408, 17411, 17412, 17413 & 17414 from trunk back to 1.8 branch:
r17408:
Move flush operation on mounted file hierarchy into H5Fmount module.
r17411:
Make H5AC_flush just flush the cache and make H5AC_dest perform the
proper parallel synchronization before destroying the cache. Also, further
discriminate between 'closing' and 'non-closing' actions in H5F_flush.
r17412:
Seperate 'flush' functionality from 'destroy' functionality at the
H5F level also.
r17413:
Remove vestigial intermediate routine for flushing file and move it
into API routine. Also, remove private, unused (now) 'H5F_FLUSH_DOWN' symbol
from public header file.
r17414:
Flush the core VFD's buffer before closing the file, also flush the
metadata accumulator before reseting it. Write the driver info message out
in the superblock flush routine more directly, instead of using wrapper
routine, since the wrapper routine won't work when the superblock is being
shutdown.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest performed on trunk)
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r17393 and r17398 from trunk to 1.8 branch:
Bring back more changes from the file free space branch to the trunk. (17393)
First set of changes to move VFD 'truncate' call out of H5F_flush and defer
it until the file is closed. (17398)
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk)
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r17365 from trunk to 1.8 branch:
Final merge of changes from sblock_mdc branch back to trunk. The
superblock is now managed by the metadata cache.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest performed on trunk)
|
|
|
|
|
|
|
|
|
|
| |
Bring r17336 from trunk to 1.8 branch:
Bring more changes from the file_free_space branch into the trunk.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk)
|
|
|
|
|
|
|
|
|
| |
Bring r17341 from trunk to 1.8 branch:
Tweaks to comments, to better align with changes on sblock_mdc branch
Tested on:
Just eyeballed, only tweaks to comments
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r17146 from trunk to 1.8 branch:
Bring a bunch of misc. improvements & tweaks from the revise_chunks
branch back to the trunk, so that future merges won't be so painful.
Tested on:
FreeBSd/32 6.3 (duty)
(h5committested on trunk)
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r17138 from trunk into 1.8 branch:
Disable use of temporary file space allocation when using a parallel VFD,
until we've made changes to broadcast the new address of the metadata when it
is relocated down into 'normal' file space.
Tested on:
Mac OS X/32 10.5.8 (amazon)
(h5committested on trunk)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r17010,17017,17021-17022,17029-17031,17035 back from trunk:
"temporary" file allocation space changes.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
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 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
Versions of the library between 1.3.0 and 1.6.3 have a bug which prevents them
from opening any file that does not have the root group's symbol table
information cached in the root group's entry in the superblock. Prior to 1.8
this was not an issue as this information was always cached. However, 1.8.0
stopped writing this information (which is not required by the file format
specification), and these older versions can therefore not read files created or
last written by versions 1.8.0 to 1.8.2. This fix modifies the library to once
again add this information to the superblock (when using the old file format).
Tested: jam, linew, smirom (h5committest)
|
|
|
|
|
|
|
|
| |
necessary as Quincey pointed out.
I took it out and used the driver address instead.
Tested on jam - simple change.
|
|
|
|
|
|
|
|
|
|
|
|
| |
is opened and closed with
v1.8 library, v1.8 library writes the driver info block in the superblock. But v1.6
doesn't write it. This caused the data after the superblock to be overwritten. The
solution is to use a flag to indicate when the original file doesn't have the driver
info, v1.8 library doesn't write it either.
Tested on jam. I have some trouble to access smirom and linew using h5committest.
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
Some files apparently exist in the wild which have corrupt symbol table messages
on the root group. These files can be opened by 1.6 (which uses the cached
information in the superblock) but not by 1.8. This patch fixes 1.8 and 1.9 so
they can now open these files, and will correct them if necessary. Also fix
some potential (rare) problems with array datatype versions.
Tested: jam (parallel; h5committest not working on linew or smirom)
|
|
|
|
|
|
|
|
| |
H5Dget_access_plist
functions to 1.8 branch
Tested: kagiso, jam (trunk version tested with h5committest)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r15800 back from trunk:
- File free space branch changes through r15794
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (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/Intel compilers w/default API=1.6.x,
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 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
mounted files.
Description:
Moved mount table from top file structure to shared file structure. Moved
parent out of mount table and back into top file structure. mounted files can
now be accessed from any handle of the parent file. Changes to how files are
closed. Stricter cycle checking on mounted files. Removed unused function
H5F_has_mount().
Tested:
kagiso, smirom, linew (h5committest)
|
|
|
|
|
|
|
| |
1. src/H5F.c, src/H5system.c: formulate path for mainfile
2. src/H5Lexternal.c: add search for target file
3. configure.in: add H5_HAVE_WINDOW_PATH
4. test/links.c: add tests for external link
|
|
|
|
|
|
|
|
| |
Further cleanups & simplifications to prepare for next phase of work.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.5.1 (amazon)
|
|
|
|
|
|
|
|
|
|
|
| |
Various code cleanups and refactor recent changes for h5stat to fit
into the existing library data structures better.
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
New feature.
Description:
Added routines to report on the amount of storage for:
1) 1.6 btree and heap storage info for groups
2) 1.8 btree, fractal heap storage info for groups, attributes and SOHM table
3) btree storage for chunked datasets
4) 1.8 superblock extension size.
Platform tested:
h5committested.
|
|
|
|
|
|
|
| |
Cleanup handling of file consistency/status flags a bit.
Tested on:
FreeBSD/32 6.2 (duty)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
The main purpose of this checkin was to eliminate the
space used for tracking creation time indices when there is no way they
can be used (i.e. attributes can't be shared in the file and the user hasn't
turned on attribute creation tracking), however there were some other minor
changes which crept in:
- Fix a cache locking deadlock when a shared attribute and one of its
components end up in the same fractal heap direct block.
(This is fixed the "slow" way for right now, until John has time
to add support for readers/writer locking to the cache.
- Optimize attribute copying when a copy will be kept during a v2 B-tree
search.
- When freeing a block on disk, attempt to merge it with the metadata
and "small data" aggregators.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 6.2 (duty)
|
|
|
|
|
|
|
|
|
|
|
|
| |
Fix bug in external links when "strong" file close degree is used.
Make external link callbacks use standard error reporting mechanisms.
Other minor code cleanups...
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 6.2 (duty)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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)
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Further cleanups to superblock code:
- Move most of the ISOHM-specific code into the H5SM module
- Make only one checksum, for combined superblock & driver info
block
Minor other cleanups, etc.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 6.2 (duty)
|
|
|
|
|
|
|
|
|
|
| |
Straighten out some of the code for handling superblocks, in preparation
for revising the format of the latest version of the superblock before the
beta release.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 6.2 (duty)
|
|
|
|
|
|
|
|
|
| |
copyright notice.
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
|
|
|
|
|
|
|
|
|
|
| |
Add support for inserting attributes into creation order index.
Also, update support for dense link & attribute storage in h5debug.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
|
|
|
|
|
|
|
|
|
| |
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.
|
|
|
|
|
|
|
|
|
|
|
| |
version of
superblock).
Tried to standardize sizes and added #defines to H5Fpkg.h so that hopefully
the code is a little easier to read.
Of course this is a file format change.
Tested on Windows, juniper, smirom, kagiso.
|
|
|
|
|
|
|
|
|
|
|
|
| |
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)
|
|
|
|
|
|
|
|
|
|
|
| |
SOHM table
version and size information into the superblock to eliminate a read when
loading it.
This is a file format change, and hopefully the last one (knock on wood).
Tested on kagiso and Windows (mostly just a SOHM change).
|