| Commit message (Collapse) | Author | Age | Files | Lines |
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H5Pset_istore_k() will validate the "ik" value to not exceed the max v1 btree entries (2 bytes)
The same check for H5Pset_sym_k() "ik" value.
h5committested.
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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.
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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)
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Merged r24993 from the trunk.
Adds core VFD write tracking functionality. When enabled, the core VFD
will track dirty regions of the file and only write out the changed
regions. The new H5Pget/set_core_write_tracking() API call controls this
feature. A new "core_paged" VFD target was added to the check-vfd target
in test/Makefile.am that runs all tests with the new write tracking
functionality.
Tested on:
32-bit LE linux (jam)
64-bit LE linux (koala)
64-bit BE linux (ostrich)
Each platform was tested with HDF5_DRIVER set to "core" and "core_paged".
Jam was also tested with the standard sec2 driver.
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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)
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Bring r24256 & r24261 from trunk to 1.8 branch:
Switch H5I internal data structure from using hash table to skip lists.
Also, a few misc. cleanups.
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 2.11 (emu) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (ostrich) w/C++ & FORTRAN, w/threadsafe, in debug mode
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Bring r23713 and r23717 from trunk to 1.8 branch:
Clean up warnings, switch library code to use Standard C/POSIX wrapper
macros, remove internal calls to API routines, update checkapi and checkposix
scripts.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
Big-Endian Linux/64 (ostrich)
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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.
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Bring r22915 from trunk to 1.8 branch:
Bring Coverity changes back to trunk:
r20399:
Change parse_command_line to free hand structure on error and only "leave()" at end of main.
r20400:
Purpose: Fix coverity issue 592
Description: Added void cast to call to H5F_sfile_assert_num() in
H5F_term)interface(). There is no need to check the return value of this
function in general, and there would be nothing to do even if it did fail.
r20401:
Added free(src_sizes) and free(src_offset). --gh
Tested on:
Mac OSX/64 10.8.2 (amazon) w/C++, FORTRAN, threadsafe
(too minor for h5committest)
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Bring r22608 from trunk to 1.8 branch:
Switch propert list/class iteration from internal to external form of
iteration, cleaning up and simplifying the code a bit.
Bring other general improvements from plist_encode_decode branch back to
trunk.
Clean up many warnings.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/gcc 4.7, debug and C++ & FORTRAN
(too minor to require h5committest)
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Bring r22219 from trunk to 1.8 branch: (with release manager's blessing)
Merge "file image" changes from feature branch back to trunk.
Tested on:
h5committested
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Bring r21135 from trunk to 1.8 branch:
More code cleanups to reduce coupling with the H5F package.
Tested on:
FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode
(h5committested on trunk)
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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
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Bring r21126 from trunk to 1.8 branch:
Clean up some compiler warnings, but mainly an interim checkin on the
path of reducing code coupling in the library by removing most of the places
which were accessing H5F package definitions.
Tested on:
Mac OS X/32 10.6.8 (amazon) w/debug
FreeBSD/32 8.2 (loyalty) w/debug
FreeBSD/64 8.2 (freedom) w/debug
Linux/32 2.6 (jam) w/debug
Linux/64 2.6 (koala) w/debug
Linux/64 2.6 (heiwa) w/debug
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Tested: jam (open_file_pool branch tested with h5committest)
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Bring r18031 from trunk to 1.8 branch:
Bring r18030 from merge_metadata_journaling branch to trunk:
Bring "brush clearing" changes (whitespace & style issues, mostly) from
metadata_journaling branch to the "merging" branch, to converge the trunk and
the metadata_journaling branch.
Also, some other minor cleanups along the way.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
(h5committested on trunk)
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Bring r17971 from trunk to 1.8 branch:
Allow the core VFD to properly support opening backing store files through
symbolic links and have the external links in the file be treated in the same
way as for the sec2 driver.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk)
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Bring r17943 from trunk to 1.8 branch:
Finish refactoring v2 B-trees so that they can have client callback
context provided to the encode/decode callbacks.
Tested on:
FreeBSD/64 6.3 (liberty)
(h5committested on trunk)
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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)
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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
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Bring r17402 & r17403 from trunk to 1.8 branch:
r17402:
Switch from using a 'flags' parameter to the flush routine(s), to just
using a single 'closing' boolean parameter, since that's all we're doing with
the flags anyway and this makes things more obvious.
r17403:
Eliminate 'closing' flag to dataset flush routine, since all cached
dataset information has already been flushed when a file is closed and the
datasets themselves will be closed (and the dataset caches destroyed).
Skip calling more flush routines when the file is closing, in preparation
for eventual separation of the 'flush' concept from the 'shutdown the cache'
concept.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest performed on trunk)
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Bring r17400 from trunk to 1.8 branch:
Refactor H5F_flush into two routines, one which handles the recursion/
iteration necessary to handle mounted files; and one which just handles the
flush operation for a single file.
Also, remove H5F_FLUSH_INVALIDATE and switch all code to depend on
H5F_FLUSH_CLOSING.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk)
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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)
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Bring r17313 from trunk to 1.8 branch:
Bring back various minor code cleanups from the file free space branch
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 (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
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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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)
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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
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Bring r16367 back from trunk:
Refactor internal address encode/decode routines slightly, to allow for
more flexible use.
Tested on:
Mac OS X/32 (amazon)
FreeBSD/32 (duty)
(too minor to require h5committest)
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external links.
Description: Added H5Pset/get_elink_cb to allow the user to specify a callback
function to be called whenever an external link is traversed. Added
H5Pset/get_elink_acc_flags to allow the user to specify the file access flags
to use to open the target file of an external link. All these properties are set on a LAPL.
Tested: jam (trunk version tested with h5committest)
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Bring r16182 back from trunk:
Rename internal routines, variables, macros, typedefs, etc. for chunked
dataset storage from "istore" to some variant of "chunk" or "btree".
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
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H5Dget_access_plist
functions to 1.8 branch
Tested: kagiso, jam (trunk version tested with h5committest)
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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
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Description: Fixes a possible datatype id leak that could occur during compound
datatype conversion, or more precisely, when unregistering those conversions.
Datatype ids normally registered by the library are no longer visible to the
application via H5Fget_obj_ids and H5Fget_obj_count.
Tested: kagiso, linew, smirom (h5committest)
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H5Fget_obj_count to ssize_t and modified
C++ and Fortran API functions. This is for bug #1245.
Tested on kagiso - I've tested the same change using h5committest.
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Bring r15676 back from trunk:
Centralize all macros for declaring "magic numbers"/signatures for
objects in the file into src/H5Fprivate.h, so it's easier to know what
values have already been defined, etc.
Tested on:
Mac OS X/32 10.5.5 (amazon)
Too minor to require h5committest
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reference count
> 1.
Description: Added a new field 'app_count' to H5I_id_info_t struct, to track
the reference count on an id due to the application. the old 'count' field
tracks the total. Generally any id visible to the application gets placed
in app_count. Added app_ref boolean parameter to H5I_inc_ref, H5I_dec_ref,
H5I_register, H5I_clear_type, and a few other functions, to specify whether
the operation(s) being performed on the id(s) are due to the application
(TRUE) or not (FALSE). Test added for this case.
Tested: kagiso, smirom, linew (h5committest)
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Bring back revision 15211 from trunk:
Update the gcc flags for version 4.3
Clean up warnings
Tested on:
Mac OS X/32 10.5.3 (amazon)
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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
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Add H5Lvisit_by_name() API routine to library.
Eliminated all (five!) other group traversal routines and changed them
all to use the new API routine.
Cleaned up output of h5ls & h5stat:
- Issue error when requesting recursive traversal of a file
with the "group info" flag, but no group given
- Print info about root group in all(?) appropriate situations
- Don't print "verbose" information about root group until the
root group is in the list of objects to display
(mostly because h5ls & h5stat had a different twist on traversing the
groups in a file that the other utilities)
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Take further advantage of the readers/writer locking in the metadata cache
and push the locking of the local heap up to the routines which call B-tree
routines, which should drastically lower the number of metadata cache protect/
unprotect calls.
Tested on:
Mac OS X/32 10.4.9 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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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)
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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)
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Eliminate some unnecessary properties for unused aspects of superblock.
Tested on:
Mac OS X/32 10.4.8 (amazon)
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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)
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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.
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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)
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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).
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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.
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Clean up initialization of H5F & H5L APIs.
Tested on:
Linux/64 2.6 (chicago2)
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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
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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.
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