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* [svn-r12803] Description:Quincey Koziol2006-10-2321-645/+790
| | | | | | | | | | | | | | Finish new version of the I/O pipeline message, which is much smaller than the previous version. This version is used with the "use the latest version of the format" flag. Closed several memory leaks/overruns (found with valgrind). Also, lots of compiler & formatting cleanups. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12802] Description:Quincey Koziol2006-10-232-23/+27
| | | | | | | | | | Clean up code in passing... Tested on: Linux/32 2.4 (heping) Linux/64 2.4 (mir) FreeBSD/32 4.11(sleipnir) Mac OS/32 10.4.8 (amazon)
* [svn-r12801] Description:Quincey Koziol2006-10-233-335/+478
| | | | | | | | | | | | Fix several errors in the "latest version" of the object header format changes and enable the new version when requested now. Clean up several confusing or duplicated sections of code. Tested on: Linux/32 2.4 (heping) Linux/64 2.4 (mir) FreeBSD/32 4.11 (sleipnir)
* [svn-r12792] Fixed a Makefile.am to clean up a test file generated by the ↵James Laird2006-10-205-889/+890
| | | | | | | | | | | Packet Table compression test. Tested that the file is removed on juniper and heping. Running reconfigure also regenerated the H5E* files (I think this means somebody updated these files but didn't run reconfigure).
* [svn-r12788] Enable the algorithm of Direct driver to read data in fragment ↵Raymond Lu2006-10-191-36/+76
| | | | | | | | from file. If the application requests large data from file, to avoid using too much of memory for copying data from library's own aligned buffer to application's (unaligned) buffer, this step is done in fragment. The next step checkin is to handle writing data in fragment.
* [svn-r12783] Took out the function H5FD_direct_alloc that was added ↵Raymond Lu2006-10-191-47/+1
| | | | | | | yesterday. This function would be redundant because the allocation function in H5FD.c H5FD_real_alloc actually has handled the aligned allocation.
* [svn-r12777] Added support to aligned file space allocation. The alignment ↵Raymond Lu2006-10-181-1/+47
| | | | | | should be set through H5Pset_alignment.
* [svn-r12776] The internal change is to make the 3 parameters of ↵Raymond Lu2006-10-182-24/+200
| | | | | | | | H5Pset_fapl_direct be a structure and passed through driver info functions in H5FD_direct_open, H5FD_direct_read, and H5FD_direct_write. The external change is to add a new API function H5Pget_fapl_direct to query 3 control values, the memory boundary, file system block size, and the maximal buffer size for copying data.
* [svn-r12774] Modified flush code in the metadata cache to allow it toJohn Mainzer2006-10-1812-178/+995
| | | | | | | | | | | | | | | | | handle flush callbacks which can dirty other entries, and resize and/or rename the target entry. This feature is needed by the fractal heap code. Also added associated test code. H5Commit tested. Test failed on heping, but the error appears to be a syntax error in an un-related file. Tests on copper & sol passed, along with tests on phoenix.
* [svn-r12771] Description:Quincey Koziol2006-10-174-151/+453
| | | | | | | | | | | | | | | | | More fixes to make the I/O & memory operations more efficient when loading & flushing object header chunks. Add in concept of a chunk having a "gap" at the end - unused space that is not large enough to hold a full null message that describes it. Clean up formatting a bit. Latest version of object header format not enabled yet, still working on a few bugs... Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12770] Description:Quincey Koziol2006-10-163-374/+359
| | | | | | | | | | | | | | | Overhaul usage of object header chunks to reduce I/O operations and memory allocations. The object header prefix is now stored in the first object header chunk's "image" in memory. Also, lots of formatting cleanups. Taught h5debug tool about new object header format (which isn't enabled just yet). Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12769] Description:Quincey Koziol2006-10-161-53/+50
| | | | | | | | | | | Move object header creation past several internal possibilities for errors, making the routine more resistant to errors encountered. Also, various formatting/compiler warning cleanups. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12768] Description:Quincey Koziol2006-10-166-26/+26
| | | | | | | | | | Add 'initval' parameter to "lookup3" checksum routine (and implicitly to the metadata checksum routine), to allow chaining several checksums together easily (which isn't used by these modules, but will be used in my next checkin) Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12767] Description:Quincey Koziol2006-10-164-14/+16
| | | | | | | | Code cleanup to improve formatting & reduce compiler warnings. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12766] Made two changes to Direct I/O VFD: first added 3 parameters to ↵Raymond Lu2006-10-162-124/+170
| | | | | | | | H5Pset_fapl_direct to control memory boundary, file block size, and maximal copy buffer size; second in H5FD_direct_write and H5FD_direct_read, the library checks whether data buffer is aligned. If it is, then write and read the data directly instead of making a copy buffer.
* [svn-r12761] Description:Quincey Koziol2006-10-166-388/+444
| | | | | | | | | | Refactor object header macros, in preparation for updating the format. Tested on: Mac OS/PPC 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir) w/thread-safe Linux/32 2.4 (heping) w/C++ & FORTRAN Linux/64 2.4 (mir) w/1.6 compat & build-all
* [svn-r12760] Description:Quincey Koziol2006-10-161-3/+253
| | | | | | | | | | | | Speculatively attempt to read in the entire first chunk in object header with the object header prefix. If successful (which it is most of the time), this reduces by 1 the # of I/Os required to read in the object header. Since the object header typically was taking 2 I/Os, this should cut the number of I/O operations when opening an object's header in half. Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/C++ & FORTRAN
* [svn-r12756] Description:Quincey Koziol2006-10-127-113/+94
| | | | | | | | | | | | | | Clean up some object header code in advance of more major changes in the near future. Fix small initialization error in attribute message name buffer copy. Tweak down the default # of messages for new object headers. Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/FORTRAN & C++ Mac OS/32 10.4.8 (amazon)
* [svn-r12755] The line "#define _XOPEN_SOURCE 600" is recommended for ↵Raymond Lu2006-10-121-2/+3
| | | | | | posix_memalign function but causes compiling error on copper. Comment it out. It only gives a warning on SGI Altix.
* [svn-r12741] Added support for direct I/O to check-vfd. The direct VFD is ↵James Laird2006-10-106-891/+891
| | | | | | | | | | only tested if it is enabled. Added Direct VFD status to the configure summary. Removed a line left over from pablo support. Oops!
* [svn-r12740] Description:Quincey Koziol2006-10-109-391/+374
| | | | | | | | | | | Update datasets and the layout, attributes and fill-value object header messages to use the latest version of the file format flag. Tested on: FreeBSD 4.11 (sleipnir) Linux/64 2.4 (mir) Linux/32 2.4 (heping)
* [svn-r12739] Added Direct I/O driver to VFD. It's only supported by SGI ↵Raymond Lu2006-10-1011-10/+1056
| | | | | | | | | | 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.
* [svn-r12738] Description:Quincey Koziol2006-10-102-2/+2
| | | | | | | | Tweak down some of the static array definitions for new & re-loaded object header data structures, to reduce memory use in common cases. Tested on: Linux/32 2.6 (chicago)
* [svn-r12736] Description:Quincey Koziol2006-10-098-358/+340
| | | | | | | | | | | | | | | | | | | Add "use the latest format" support for dataspace object header encode/ decode routines and clean up format a bit for the latest format (new to 1.8.x releases) Remove storing 'perm' parameter for array datatypes in memory and the file, and add test to make certain that if any user applications are attempting to store them, we get some reports back. (Should be unlikely, since the RefMan says that the parameter is not implemented and is unsupported). Carry those changes into the tests, etc. Clean up a bunch more compiler warnings. Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/FORTRAN & C++ Linux/64 2.4 (mir) w/enable-1.6-compat
* [svn-r12733] Description:Quincey Koziol2006-10-091-1/+1
| | | | | | | | | | Use calloc() instead of malloc(), in order to fail a bit more gracefully on errors. Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/FORTRAN & C++ Linux/64 2.4 (mir) w/enable-1.6-compat
* [svn-r12732] Description:Quincey Koziol2006-10-091-1/+1
| | | | | | | | | | | Fix error with passing in new root indirect block instead of NULL pointer to protect of previous root direct block, when converting heap to use a root indirect block. Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/FORTRAN & C++ Linux/64 2.4 (mir) w/enable-1.6-compat
* [svn-r12730] Add _WIN32 macro since some windows applications need to use ↵MuQun Yang2006-10-061-1/+1
| | | | this macro rather than WIN32.
* [svn-r12727] 1. Cleaning up the comments of the source code.MuQun Yang2006-10-062-92/+90
| | | | | | | 2. Using H5Dmpio_Debug macro to reflect the debugging information of new parallel IO supports. They are very minor changes. Tested at heping. t_pflush2 failed. Others passed.
* [svn-r12723] Fix a bug where return values were overwritten in H5F_dest, and ↵James Laird2006-10-051-1/+13
| | | | | | | | | | | | | | another bug exposed by that one in which closing a read/write file ID wouldn't flush the cache if there was another file handle open. This caused problems when the second file handle was read-only; neither would actually flush the cache. Now all read/write file handles flush the cache when the close, but only when the file is going to be destroyed is the cache destroyed. This way read-only file handles keep the cache open but it is always clean. Tested on mir, heping, sol, and copper (parallel)
* [svn-r12719] Configured external links to (by default) use the FAPL of the ↵James Laird2006-10-041-2/+11
| | | | | | | | | | parent file, rather than H5P_DEFAULT. This lets them be used with stdio and directio drivers. Tested on mir and juniper (check-vfd takes a long time!).
* [svn-r12715] Incorporated a user-submitted patch to better detect the 'tr' ↵James Laird2006-10-036-866/+870
| | | | | | | | | | | | utility and quote its arguments. Also checks for the 'socket' library on Solaris. If this patch passes the Daily Tests and makes the user happy, I'll port it back to the 1.6 branch. Tested on mir and sol.
* [svn-r12712] Description:Quincey Koziol2006-10-031-196/+283
| | | | | | | | | | Finish 'use the latest version of the format' changes to the datatype object header message. Compound and enumerated types will now be encoded more efficiently by packing the field names & member offsets better. Tested on: Linux 2.6/32 (chicago) Linux 2.6/64 (chicago2)
* [svn-r12708] Description:Quincey Koziol2006-10-0313-332/+547
| | | | | | | | | | | | | | | | | | | 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)
* [svn-r12707] Description:Quincey Koziol2006-10-025-66/+118
| | | | | | | | | Further minor modifications to the file format for tracking links in groups. This is tentatively the "final" file format for groups. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12706] Description:Quincey Koziol2006-10-0230-173/+164
| | | | | | | | | Clean up some of the warnings on 64-bit Linux... Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2) Too minor to require h5committest
* [svn-r12705] Description:Quincey Koziol2006-10-023-112/+104
| | | | | | | | | | | | Fix file handle destroy routine to not attempt to flush out partially initialized file handles (when opening a file fails). Tested on: (until they finished testing, this time... :-) FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/64 2.4 (mir) w/1.6 compat Linux/32 2.4 (heping) w/FORTRAN & C++ Mac OSX/32 10.4.8 (amazon)
* [svn-r12703] Using int64_t in H5Lpublic.h caused errors on Windows, where ↵James Laird2006-10-022-16/+21
| | | | | | | | | | | | int64_t is only defined in H5private.h. Moved definition of int64_t from H5private.h to H5public.h as a temporary solution. Tested on heping and Windows (windows also needed H5Gdense.c and H5Gbtree2.c to be added to hdf5 project).
* [svn-r12702] Description:Quincey Koziol2006-10-022-59/+79
| | | | | | | | | | | | | | | | | Add test to fractal heaps to exercise issues with opening the same heap through two different file handles. Fix issues with file handle contexts in metadata cache callbacks for heap components. Fix bug in file close handling where cached information was being invalidated even when another file handle was open to the file. Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/64 2.4 (mir) w/1.6 compat Linux/32 2.4 (heping) w/FORTRAN & C++ Mac OSX/32 10.4.8 (amazon)
* [svn-r12701] Description:Quincey Koziol2006-10-022-55/+46
| | | | | | | | Clean up formatting/whitespace Tested on: Mac OSX/32 10.4.8 (amazon) Too minor to require full h5committest
* [svn-r12700] Alert:Quincey Koziol2006-10-0258-2622/+4755
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* [svn-r12699] Description:Quincey Koziol2006-10-023-66/+122
| | | | | | | | | | | Fix problems with opening a fractal heap multiple times, from different file handles. 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 Mac OS/32 10.4.8 (amazon)
* [svn-r12694] Fixed a couple of typos in the comment block for H5Oincr_refcount.James Laird2006-09-291-2/+2
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* [svn-r12693] Changed return values of H5O*_refcount functions to be herr_t ↵James Laird2006-09-291-7/+9
| | | | | | | | instead of int. Mostly cosmetic change. Testing on mir.
* [svn-r12692] Removed code that was used to support lazy allocation of file spaceJames Laird2006-09-284-89/+2
| | | | | | | since HDF5 no longer allocates file space lazily. Tested on mir; should be only a cleanup, since the code isn't called from anywhere.
* [svn-r12686] Added compression to Packet Tables. Now both C and C++ packet ↵James Laird2006-09-261-0/+1
| | | | | | | | | | | | | | | | tables have an extra parameter that sets the deflate filter. Added tests, made examples use the new APIs. Cleaned up include files a little and removed some casts that I hope are superfluous. If anybody encounters strange errors in the packet table tests where the chunk size is set to some extremely large value, please let me know, but I was unable to reproduce this error on any system. Tested on mir, heping, sol, juniper, VS 6.0. Looked for the chunk size error on several other systems a month or two ago.
* [svn-r12681] Description:Quincey Koziol2006-09-261-178/+180
| | | | | | | Encode/decode object references in portable way. Tested on: Solaris/64 2.9 (shanti)
* [svn-r12680] Description:Quincey Koziol2006-09-2523-450/+816
| | | | | | | | | Review, revise & checkin in Peter's latest round of object copy changes, which add basic support for datasets & attributes with reference datatypes. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12670] Snapshot version 1.8 release 0 (alpha5)HDF Admin2006-09-161-2/+2
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* [svn-r12669] Description:Quincey Koziol2006-09-152-10/+22
| | | | | | | | Use a slightly less efficient method of computing the log2() on SGI IRIX64, in order to avoid a compiler bug when optimizations are turned on. Tested on: SGI IRIX64 6.5 (atlantia)
* [svn-r12668] Description:Quincey Koziol2006-09-157-54/+57
| | | | | | | Re-run 'bin/reconfigure' script after recent checkins Tested on: none - shouldn't have any affect on compilation
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