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* [svn-r12452] Purpose:James Laird2006-07-051-0/+2
| | | | | | | | | | | | | | | | | | | | | | 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.
* [svn-r11686] Purpose:Quincey Koziol2005-11-071-13/+11
| | | | | | | | | | | | | | | | | | | New feature Description: Add in baseline "object copy" code from Peter [in the form of a new API routine: H5Gcopy()]. There's still some work to do (like handling variable- length datatypes and possibly support for references) and it hasn't been tested on mounted files yet, but the core functionality is there and working correctly. I've also got a set of patches to update the 1.6 branch with tweaks to keep the branches mostly in sync, but Elena will kill me if I import them before the 1.6.5 release is out... :-) Platforms tested: FreeBSD 4.11 (sleipnir) h5committested
* [svn-r11593] Purpose:Quincey Koziol2005-10-211-1/+17
| | | | | | | | | | | | Code cleanup Description: Clean up & standardize a bit in preparation for coding standards discussion. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-2/+2
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Trim trailing whitespace, which is making 'diff'ing the two branches difficult. Solution: Ran this script in each directory: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r9727] Purpose:Quincey Koziol2004-12-291-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-) Description: Generally speaking, this is the "signed->unsigned" change to selections. However, in the process of merging code back, things got stickier and stickier until I ended up doing a big "sync the two branches up" operation. So... I brought back all the "infrastructure" fixes from the development branch to the release branch (which I think were actually making some improvement in performance) as well as fixed several bugs which had been fixed in one branch, but not the other. I've also tagged the repository before making this checkin with the label "before_signed_unsigned_changes". Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel & fphdf5 FreeBSD 4.10 (sleipnir) w/threadsafe FreeBSD 4.10 (sleipnir) w/backward compatibility Solaris 2.7 (arabica) w/"purify options" Solaris 2.8 (sol) w/FORTRAN & C++ AIX 5.x (copper) w/parallel & FORTRAN IRIX64 6.5 (modi4) w/FORTRAN Linux 2.4 (heping) w/FORTRAN & C++ Misc. update:
* [svn-r7211] Purpose:Quincey Koziol2003-07-111-1/+1
| | | | | | | | | | | Code cleanup Description: Various code cleanups suggested by lint tool Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r7029] Purpose:Quincey Koziol2003-06-121-1/+2
| | | | | | | | | | | | | New feature/Bug fix Description: Add new fill time value - H5D_FILL_TIME_IFSET which writes the fill value to a dataset if the user has defined one, otherwise not writing the fill value to the dataset. Platforms tested: FreeBSD 4.8 (sleipnir) serial & parallel h5committest
* [svn-r6546] Purpose:Bill Wendling2003-03-311-11/+13
| | | | | | | | | | | | Update Description: Updated copyright statement in files which hadn't been updated yet. Platforms tested: Linux (Only comment change) Misc. update:
* [svn-r6269] Purpose:Quincey Koziol2003-01-131-4/+4
| | | | | | | | | | | | | Code cleanup Description: Various code cleanups to allow the development branch to be compiled with a C++ compiler (i.e. CC=g++ ) Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir) C++
* [svn-r6062] Raymond Lu2002-11-071-0/+1
| | | | | | | | | | | | Purpose: New function. Description: H5Dget_offset returns the offset of a dataset's data relative to the beginning of a file. Platforms tested: arabica(simple function, one test should be enough.) Misc. update: RELEASE.txt
* [svn-r5931] MuQun Yang2002-09-201-17/+17
| | | | | | | | | | | | Purpose: __DLL__ is a keyword in some platforms and __DLL__ is also defined as a macro for windows DLL applications. That causes problems. Description: Solution: Use H5_DLL*** to replace __DLL***__ at all header files. Change the macro defination at H5api_adpt.h. Platforms tested: linux2.2.18smp, irix64, solaris 2.7 and windows 2000
* [svn-r5926] Purpose:Quincey Koziol2002-09-131-7/+7
| | | | | | | | | | | | | API name change Description: Change all "space time" references to "alloc time", including API functions and macro definitions, etc. Platforms tested: FreeBSD 4.6 (sleipnir) w/C++ Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/parallel & FORTRAN
* [svn-r5894] Purpose:Quincey Koziol2002-08-271-2/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix/Code cleanup/New Feature Description: Correct problems with writing fill-values to external storage and allocate the data storage at the correct times. Also, mostly straighten out the strange code which allocates and fills raw data storage for datasets. Things are still a bit odd in that the fill-values for chunked datasets are written when the space is allocated, instead of in a separate routine, but there are two reasons for this: it's inefficient (especially in parallel) to iterate through all the chunks twice, and (more importantly) the space needed to store compressed chunks isn't known until we've got a buffer of compressed fill-values ready to write to the chunk. Additionally, add in the H5D_SPACE_ALLOC_INCR and H5D_SPACE_ALLOC_DEFAULT setting for the "space time", which incorporate the previous behavior of the space allocation for chunked datasets. The default settings for the different types of dataset storage are now as follows: Contiguous - Late Chunked - Incremental Compact - Early This checkin also incorporates a change to the behavior of external data storage in two ways - fill-values are _never_ written to external storage (under the assumption that writing fill-values is triggered by allocating space in an HDF5 file, and since space is not allocated in the file, the fill-values should not be written) and external data files are now created if they don't exist when data is written to them. The fill-value will probably need to be revisited at some time in the future, this just seemed like the safer course currently. I think I cleaned up some compiler errors also, before getting bogged down in the fixes for the space allocation and fill-values. Platforms tested: FreeBSD 4.6 (sleipnir) w/serial & parallel. Will be testing on IRIX64 6.5 (modi4) in serial & parallel shortly.
* [svn-r5324] Pedro Vicente Nunes2002-05-021-1/+0
| | | | | | | Purpose: updated some comments regarding Code Warrior , removed other debugging comments Platforms tested: w2000
* [svn-r5170] Raymond Lu2002-04-111-1/+32
| | | | | | | | | | | Purpose: New feature Description: Fill-value's behaviors for contiguous dataset have been redefined. Basicly, dataset won't allocate space until it's necessary. Full details are available at http://hdf.ncsa.uiuc.edu/RFC/Fill_Value, at this moment. Platforms tested: Linux 2.2.
* [svn-r5168] Pedro Vicente Nunes2002-04-111-1/+3
| | | | | | | | | | | | | | | | | | | | | | Purpose: H5Dset_extent API function Description: 1 new public function: H5Dset_extent, that allows shrinking a dataset several private functions that free the previously allocated chunks H5F_istore_prune_by_extent, H5B_prune_by_extent : removes the chunks H5F_istore_initialize_by_extent : initializes them with the fill value H5S_select_fill is used to fill the selection in the memory buffer Platforms tested: Windows 2000 SUN( arabica) LINUX (eirene) IRIX64 (modi4)
* [svn-r5152] Purpose:Quincey Koziol2002-04-091-0/+2
| | | | | | | | | | | | | | | New Feature Description: Added new H5Dfill() routine to fill the elements in a selection for a memory buffer with a fill value. This is a user API wrapper around some internal routines which were needed for the fill-value modifications from Raymond as well as Pedro's code for reducing the size of a chunked dataset. Platforms tested: FreeBSD 4.5 (sleipnir) [and IRIX64 6.5 (modi4) in parallel, in a few minutes]
* [svn-r4921] Pedro Vicente Nunes2002-02-071-0/+1
| | | | | | | | | | | | | Description: modified the below files to inlude a new public function H5Dset_extend, similar to H5Dextend, but it can lower the dimension this function requires 2 more new private functions: H5D_set_extend H5S_set_extend Platforms tested:
* [svn-r4312] Purpose:Quincey Koziol2001-08-061-9/+0
| | | | | | | | | Feature shift Description: Take out the v1.2.x compatibility stubs and put in the hooks for v1.4.x compatibility when needed. Platforms tested: FreeBSD 4.3 (hawkwind)
* [svn-r3781] Purpose:Bill Wendling2001-04-051-2/+2
| | | | | | | | | | | | | | | | | | 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
* [svn-r3005] Purpose:Quincey Koziol2000-11-271-0/+9
| | | | | | | | 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)
* [svn-r1576] Added H5Dvlen_get_buf_size function.Quincey Koziol1999-08-191-0/+1
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* [svn-r1568] Changes since 19990730Robb Matzke1999-08-101-9/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- This extensive change is the virtual file layer implementation. I've ported and tested the sec2, family, and core drivers and only ported the mpio driver (Albert will test it). So if you need MPIO I would recommend sticking with the previous version for a while. You will get a few compile warnings about split and stdio drivers not being implemented and possibly tracing information not inserted in some of the drivers. You can safely ignore them but I plan to fix them. I'm still working on the split driver because I just realized that it needs a part of the VFL that isn't written yet. Documentation is being updated also because there were some minor changes (mostly just name changes). It should be available on my web site later this week. ./MANIFEST ./src/Makefile.in ./src/hdf5.h ./src/H5Flow.c [REMOVED] ./src/H5Fstdio.c [REMOVED] ./src/H5Fsec2.c [REMOVED] ./src/H5Fsplit.c [REMOVED] ./src/H5Fmpio.c [REMOVED] ./src/H5Ffamily.c [REMOVED] ./src/H5Fcore.c [REMOVED] ./src/H5MFpublic.h [REMOVED] ./src/H5FD.c [NEW] ./src/H5FDcore.c [NEW] ./src/H5FDcore.h [NEW] ./src/H5FDfamily.c [NEW] ./src/H5FDfamily.h [NEW] ./src/H5FDmpio.c [NEW] ./src/H5FDmpio.h [NEW] ./src/H5FDprivate.h [NEW] ./src/H5FDpublic.h [NEW] ./src/H5FDsec2.c [NEW] ./src/H5FDsec2.h [NEW] Removed/added files for virtual file layer. ./bin/trace ./src/H5.c Removed unused public datatypes and added new VFL public datatypes. Changed an error message. ./config/BlankForm ./config/dec-flags ./config/gnu-flags ./config/hpux10.20 ./config/hpux9.03 ./config/irix5.x ./config/irix6.x ./config/solaris2.x ./config/unicosmk Removed the H5F_OPT_SEEK and H5F_LOW_DFLT constants from the configuration since they're no longer applicable. The default file driver is always the sec2 driver and it always optimizes calls to lseek() or lseek64(). ./config/depend.in C preprocessor errors generated during automatic dependency building are sent to /dev/null to prevent them from appearing twice in the make output. ./src/H5AC.c ./src/H5B.c ./src/H5D.c ./src/H5F.c ./src/H5G.c ./src/H5Gent.c ./src/H5Gnode.c ./src/H5HG.c ./src/H5HL.c ./src/H5O.c ./src/H5Oattr.c ./src/H5Odtype.c ./src/H5Oefl.c ./src/H5Oshared.c ./src/H5T.c ./src/H5detect.c ./test/ohdr.c Changed H5F_ADDR_UNDEF to HADDR_UNDEF to be more consistent with the `haddr_t' datatype which is now a public type. ./src/H5D.c ./src/H5P.c ./src/H5Ppublic.h ./src/H5Tconv.c ./test/cmpd_dset.c ./test/dsets.c ./test/overhead.c ./test/tselect.c ./test/tvltypes.c The H5P_DATASET_XFER constant was changed to H5P_DATA_XFER because the properties apply to all types of I/O operations, not just datasets. ./src/H5B.c ./src/H5Bprivate.h ./src/H5D.c ./src/H5Dpublic.h ./src/H5F.c ./src/H5Farray.c ./src/H5Fistore.c ./src/H5Fprivate.h ./src/H5Fpublic.h ./src/H5Gnode.c ./src/H5Gpkg.h ./src/H5HG.c ./src/H5HL.c ./src/H5O.c ./src/H5R.c ./src/H5Sall.c ./src/H5Shyper.c ./src/H5Smpio.c ./src/H5Spoint.c ./src/H5Sprivate.h ./test/big.c ./test/h5test.c ./test/istore.c ./testpar/t_dset.c ./testpar/t_file.c ./tools/h5debug.c ./tools/h5ls.c Modified to work with the virtual file layer by calling H5FD_* functions instead of H5F_low_* functions and by passing file access and data transfer properties by object ID instead of pointer. Changed H5D_transfer_t to H5FD_mpio_xfer_t since the COLLECTIVE vs. INDEPENDENT transfer mode is specific to the MPIO file driver. Moved MPIO-specific stuff into the MPIO driver. ./src/H5B.c ./src/H5D.c ./src/H5Fprivate.h The H5F_mpio_* private functions were renamed and placed in the H5FDmpio driver except those which appeared in H5Smpio.c. ./src/H5E.c ./src/H5Epublic.h Added major error number H5E_VFL for virtual file layer related errors. ./src/H5F.c ./src/H5Fprivate.h Changed the logic that controls whether the boot block is written. Instead of assuming that the first call to write the boot block is only to allocate space, I've added a function argument which makes this explicit. Changed the way files are compared so that a driver-defined comparison function can be called. Files which belong to different drivers are always considered different. Removed H5F_driver_t since file drivers are now identified by object ID instead of a special non-user-extendible datatype. Removed all the hard-coded low-level file properties which have been replaced by the various file drivers. ./src/H5I.c ./src/H5Iprivate.h Added the H5I_inc_ref() which was removed a few months ago since we finally have a use for it. ./src/H5Ipublic.h Added the H5I_VFL object ID type to identify file drivers in the virtual file layer. ./src/H5MF.c ./src/H5MFprivate.h Moved all the allocation/deallocation code into the virtual file layer which allows file drivers to override much of it. ./src/H5P.c ./src/H5Ppublic.h Moved file driver-specific code into the various file driver files. The H5Pcopy() and H5Pclose() functions make calls into the virtual file driver to manage the memory for driver-specific file access and data transfer properties. ./src/H5private.h ./src/H5public.h The `haddr_t' type is now public. ./test/tfile.c Added a few more comments.
* [svn-r1566] Changed C++ "operator" keyword to "op"Quincey Koziol1999-08-101-1/+1
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* [svn-r1374] Added in code to support the H5Diterate function, which I've got ↵Quincey Koziol1999-06-241-0/+6
| | | | | | | to add tests for now. Also, I revised some of the code for hyperslab I/O, which should provide a modest speedup in situations with lots of hyperslabs.
* [svn-r1332] Fixes to get the VL datatypes working. The only function ↵Quincey Koziol1999-06-111-0/+1
| | | | | | currently working is H5Tvlen_create().
* [svn-r1240] Changes since 19990427Robb Matzke1999-04-301-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./tools/h5ls.c Added a `--address' (`-a') switch which causes h5ls to display file addresses for raw data. For contiguous datasets it's just a nice simple number, but for chunked datasets it's a list of logical dataset coordinates, file addresses, filter masks, and storage sizes. Changed `--dump' switch to `--data'. ./src/H5D.c ./src/H5F.c ./src/H5Fprivate.h Enhanced the indexed-storage B-tree iterator so it can dump raw data addresses (and other info) to the standard error stream. Added H5Ddebug() so h5ls has a way to dump addresses for datasets. I'm not sure what else this API function should do, so I think we should discuss it before we document it. So far, h5ls is the only thing that uses it, and we can easily change that. ./src/H5Tconv.c ./test/dtypes.c Finally had a chance to verify Paul's H5T_conv_s_s (general string to string conversions) bug fixes and incorporate them into H5T_conv_f_f (general floating-point to floating-point conversions) and H5T_conv_i_i (general integer to integer conversons). Thanks Paul. ./src/H5D.c ./src/H5S.c ./src/H5Sprivate.h Added performance timers around data space read and write callbacks. They were already there for the gather/scatter callbacks. The timings for read/write callbacks are displayed along with gather/scatter when data space debugging is turned on. ./bin/iostats Updated to print totals. Added a `--fast' option that doesn't do any output except the totals and is much faster. ./bin/trace Changed __unused__ to UNUSED to match source code. ./config/gnu-flags Updated error message for pgcc. I've sent bug reports to the pgcc people but the new version still has the same bug. ./configure.in ./config/conclude.in ./config/depend.in Fixed dependencies for non-GNU makes when run in a directory other than the hdf5 source tree. Updated GNU `make dep' rules to copy the distributed dependencies for non-GNU makes into the source tree when run in some other directory.
* [svn-r1204] Changes since 19990415Robb Matzke1999-04-231-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./config/depend.in Fixed automatic dependencies. We were storing dependencies for *.o files instead of *.lo files after shared libraries were added. ./config/gnu-flags ./config/linux-gnulibc1 Moved `-march=pentiumpro -mcpu=pentiumpro -malign-double' from the linux file to this file and caused it to depend on the CPU name. This fixes one of Elena's bugs. ./src/H5B.c ./src/H5Bprivate.h ./src/H5D.c ./src/H5Dprivate.h ./src/H5Dpublic.h ./src/H5F.c ./src/H5Farray.c ./src/H5Fistore.c ./src/H5Fmpio.c ./src/H5Fprivate.h ./src/H5Fpublic.h ./src/H5Gnode.c ./src/H5P.c ./src/H5RA.c ./src/H5Sall.c ./src/H5Shyper.c ./src/H5Smpio.c ./src/H5Spoint.c ./src/H5Sprivate.h ./src/H5Tpublic.h ./test/istore.c Added an H5Dget_storage_size() function that reports the amount of storage allocated for raw data in a dataset. Changed H5D_xfer_* to H5F_xfer_* because these properties are more general than datasets. This also allows some of the lower-level I/O functions to get this information easier. ./src/H5S.c ./src/H5Sall.c Added two new functions H5S_all_read() and H5S_all_write() which are optimizations that copy data directly between file and memory without having to go through the scatter gather step. This knocks quite a bit of time off the I/O and reading/writing entire datasets is a fairly common operation. ./tools/h5ls.c Reports the logical size of data, the allocated size of data, and the percent utilization. ./MANIFEST Removed old pablo files, added new files. Snapshots should now start to work again. ./src/H5D.c ./src/H5Fmpio.c Removed two warnings signed vs. unsigned comparisons and check for overflow.
* [svn-r1051] changed the HDF5DLL and HDF5GLOBAL to __DLL__ and __DLLVAR__Patrick Lu1999-02-021-9/+9
| | | | also exported all globals and non static functions to the dll
* [svn-r1032] Changes since 19990118Robb Matzke1999-01-211-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./tools/h5tools.c Strings are not converted to null-padding before being printed; they are printed with whatever byte values appear in the file. ./tools/h5ls.c Now able to display attribute data type and data. Added a `-f' or `--full' switch which causes the full name of each object to be displayed instead of just the base name. Added a `-r' or `--recursive' switch that recursively prints the contents of groups, avoiding cycles. More bulletproofing for non-printable characters in things like object names, attribute names, and comment strings. We don't want listing a file to send termal escape sequences because it's sometimes possible to execute commands that way. Since h5ls doesn't usually use quotes around object names we must sometimes escape space characters. External files are listed in a table to make the output less confusing. ./tools/h5tools.c ./tools/h5tools.h Changed h5dump() to h5dump_dset() and added h5dump_mem(). Also make h5dump_fixtype() public. ./test/dtypes.c Wrote some data to an attribute to test h5ls attribute printing. ./src/H5ACprivate.h ./src/H5Apublic.h ./src/H5Dprivate.h ./src/H5Dpublic.h ./src/H5Epublic.h ./src/H5Fprivate.h ./src/H5Fpublic.h ./src/H5Gprivate.h ./src/H5HLprivate.h ./src/H5Oprivate.h ./src/H5Ppublic.h ./src/H5RApublic.h ./src/H5Rpublic.h ./src/H5Spublic.h ./src/H5Tpkg.h ./src/H5Tpublic.h ./src/H5Vprivate.h ./src/H5Zpublic.h ./src/H5private.h ./src/H5public.h Reindented function prototypes after `HDF5API' was added. Also rewrapped long lines. ./src/H5Flow.c Added an `#ifdef WIN32' around an unused variable. ./src/H5api_adpt.h Removed extra carriage returns inserted by "broken" operating system. ./src/H5Dprivate.h ./src/H5Oprivate.h ./src/H5Vprivate.h ./src/H5private.h Removed extraneous inclusion of H5api_adpt.h since it's included in H5public.h which is included by everything. ./src/Makefile.in Added H5api_adpt.h to the list of public header files to fix broken `make install'.
* [svn-r1030] added necessary info to export functions to dllPatrick Lu1999-01-211-9/+9
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* [svn-r529] Changes since 19980722Robb Matzke1998-07-221-10/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./src/H5.c Handle hid_t of type H5_TEMPBUF, arguments usually called tbuf_id. Added array tracing where the array rank is stored in a simple data space. Just use the name of the data space argument when declaring the array argument: herr_t H5Sselect_hyperslab (hid_t space_id, H5S_seloper_t op, const hssize_t start[/*space_id*/], const hsize_t _stride[/*space_id*/], const hsize_t count[/*space_id*/], const hsize_t _block[/*space_id*/]) and when the program runs you'll see array values printed: H5Sselect_hyperslab(space=218103813, op=H5S_SELECT_SET, start=0xbfffef4c {0}, _stride=NULL, count=0xbfffef44 {64}, _block=NULL) = SUCCEED; Added more symbolic data types to the tracing output. ./src/H5A.c ./src/H5Apublic.h ./src/H5D.c ./src/H5Dpublic.h ./src/H5F.c ./src/H5Fpublic.h ./src/H5G.c ./src/H5Gpublic.h ./src/H5P.c ./src/H5Ppublic.h ./src/H5S.c ./src/H5Sall.c ./src/H5Shyper.c ./src/H5Spoint.c ./src/H5Spublic.h ./src/H5Sselect.c ./src/H5Ssimp.c ./src/H5TB.c ./src/H5V.c Changed some API argument names to be more consistent with other API functions and to produce better tracing output. Reformatted some long lines. Indented printf statements. ./tools/h5ls.c Fixed warnings about unsigned vs. signed comparisons.
* [svn-r411] Added data-transfer-mode to various function to specify whichAlbert Cheng1998-06-071-3/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | mode to use for data transfer. Currently, INDEPENDENT transfer is the default mode. Collective is supported for files opened via the MPIO driver. Specific changes to individual files follow. H5D.c: Replaced previous kludge of passing xfer_mode via the file access_mode with xfer_mode function parameter all the way to the low level I/O drivers. H5Dprivate.h: The H5D_xfer_t.xfer_mode is now used in serial and parallel modes. Removed the "HAVE_PARALLEL" macro condition to support it. H5Dpublic.h: Added H5D_XFER_DFLT as a new value for H5D_transfer_t and removed the HAVE_PARALLEL condition macro to make the H5D_transfer_t definition available to both serial and parallel version. H5B.c: H5F.c: H5Farray.c: H5Fcore.c: H5Ffamily.c: H5Fistore.c: H5Flow.c: H5Fmpio.c: H5Fsec2.c: H5Fsplit.c: H5Fstdio.c: H5Gnode.c: H5HG.c: H5HL.c: H5O.c: H5Sprivate.h: H5Ssimp.c: debug.c: Added xfer_mode to the argument lists of the following routines to specify data transfer mode. Then updated calls to these routines with appropriate transfer mode. Whenever cases that collective mode is inappropriate (e.g. object header read-write, flush), H5D_XFER_DFLT is used. The H5D_XFER_DFLT mode is currently acting the same as the independent mode. H5F_block_read H5F_block_write H5F_arr_read H5F_arr_write H5F_core_read H5F_core_write H5F_fam_read H5F_fam_write H5F_mpio_read H5F_mpio_write H5F_low_write H5F_low_read H5F_sec2_read H5F_sec2_write H5F_split_read H5F_split_write H5F_stdio_read H5F_stdio_write H5S_simp_fgath H5S_simp_fscat H5S_simp_read H5S_simp_write H5Fprivate.h: H5P.c: Removed access_mode field from struct H5F_access_t type. The access-mode was the initial design to control independent or collective I/O mode. It is now supported by the data transfer mode.
* [svn-r353] Changes since 19980414Robb Matzke1998-04-171-19/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./html/Compression.html [NEW] ./html/Datasets.html ./html/H5.format.html ./html/H5.user.html Documented compression. A couple of the H5P functions aren't quite implemented yet but they're coming soon... ./src/H5Dprivate.h ./src/H5E.c ./src/H5Epublic.h ./src/H5Farray.c ./src/H5Fistore.c ./src/H5Fprivate.h ./src/H5MF.c ./src/H5MFprivate.h ./src/H5O.c ./src/H5Ocomp.c [NEW] ./src/H5Oprivate.h ./src/H5P.c ./src/H5Ppublic.h ./src/H5Sprivate.h ./src/H5Ssimp.c ./src/H5Z.c [NEW] ./src/H5Zprivate.h [NEW] ./src/H5Zpublic.h [NEW] ./src/Makefile.in ./src/hdf5.h ./test/dsets.c ./test/istore.c Compression is now mostly working. Don't try to open a compressed dataset though because the compression message won't be read. ./html/Datatypes.html ./html/H5.api.html ./src/H5.c ./src/H5private.h ./src/H5D.c ./src/H5T.c ./src/H5Tconv.c ./src/H5Tpkg.h ./src/H5Tprivate.h ./src/H5Tpublic.h Added timing support. When compiled with H5T_DEBUG defined the library will print conversion bandwidths when the library closes. The H5Tregister functions take a string as the first argument so the statistics output is meaningful. ./MANIFEST Added new files. ./configure.in ./src/H5config.h.in Check for getrusage(). Check for compress2() in libz.a and the zlib.h header file. Added `z' to the debug list. ./src/H5B.c ./src/H5Bprivate.h ./src/H5Gnode.c ./src/debug.c Cleaned up some indentation and added support to print istore B-trees. From the debugger, give the B-tree address and the dimensionality from the layout message of the object header. ./src/h5ls.c The oid is printed as w:x:y:z where w and x are the file ID and y and z are the OID within the file. You can give z or y*2^32+z as an argument to the debugger to print the object header for the object. ./src/H5AC.c Cleaned up statistics and made them match those reported by H5T and H5Z. ./src/H5MM.c ./src/H5MMprivate.h ./src/H5Fistore.c Finally got rid of a couple of long-standing const cast warnings.
* [svn-r343] First implementation of collective access support.Albert Cheng1998-04-131-0/+8
| | | | | | | | | | | | | | | | | | | | | | | | | H5D.c Changed H5D_write and H5D_read to recognize collective transfer requests. Current algorithm puts the xfer-mode in the file->mpio structure. Not thread safe. Need to revise it to pass transfer parameter as a function parameters to the lower levels. H5Dprivate.h H5Dpublic.h Added xfer_mode to the transfer property list structure. Added defination of transfer modes, H5D_XFER_INDEPENDENT and H5D_XFER_COLLECTIVE. H5Farray.c Added code to handle collective access requests. Currently works for one contiguous block at a time. Need to revise it with the MPIO low level calls to combine all blocks as one truely collective call. H5P.c H5Ppublic.h Added H5Pset_xfer and H5Pget_xfer routines that can set and get the transfer mode of a data transfer property list.
* [svn-r338] Changes since 19980407Robb Matzke1998-04-081-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./src/H5B.c ./src/H5D.c ./src/H5Dprivate.h ./src/H5Dpublic.h ./src/H5F.c ./src/H5Farray.c ./src/H5Fcore.c ./src/H5Ffamily.c ./src/H5Fistore.c ./src/H5Flow.c ./src/H5Fprivate.h ./src/H5Fpublic.h ./src/H5Fsec2.c ./src/H5Fsplit.c ./src/H5Fstdio.c ./src/H5G.c ./src/H5Gent.c ./src/H5Gnode.c ./src/H5HG.c ./src/H5HL.c ./src/H5MF.c ./src/H5MFprivate.h ./src/H5O.c ./src/H5Ocont.c ./src/H5Odtype.c ./src/H5Oefl.c ./src/H5Olayout.c ./src/H5Oname.c ./src/H5Oprivate.h ./src/H5Osdspace.c ./src/H5Oshared.c ./src/H5Ostab.c ./src/H5P.c ./src/H5Ppublic.h ./src/H5S.c ./src/H5Sprivate.h ./src/H5Spublic.h ./src/H5Ssimp.c ./src/H5Tconv.c ./src/H5Tpkg.h ./src/H5V.c ./src/H5Vprivate.h ./src/H5private.h ./src/H5public.h ./src/h5ls.c ./test/cmpd_dset.c ./test/dsets.c ./test/extend.c ./test/external.c ./test/hyperslab.c ./test/iopipe.c ./test/istore.c ./test/shtype.c ./test/tfile.c ./test/th5s.c Anything having to do with the size of a dataset now uses the types `hsize_t' and `hssize_t' which must be the same size and at least as large as `size_t'. This isn't fully tested yet, so hsize_t and hssize_t are defined as size_t and ssize_t in H5public.h. Setting them to larger values will trip up gcc versions less than 2.8.1 on x86 platforms. Documented unused function formals with `__unused__' before the formal name. This also has the effect of supressing warning messages for gcc since it's defined to be `__attribute__((unused))' in the H5private.h file. ./src/debug.c ./src/h5ls.c If the file name contains a `%' then the file is opened as a file family with H5P_DEFAULT for the file member access property list. ./src/h5ls.c The group name is optional, defaulting to `/'. ./src/hdf5.h Added some missing public header files.
* [svn-r324] Change H5A (atoms) to H5I (IDs)Quincey Koziol1998-03-171-1/+1
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* [svn-r305] Changes since 19980304Robb Matzke1998-03-051-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./MANIFEST New files ./html/extern1.gif [NEW] ./html/extern1.obj [NEW] ./html/extern2.gif [NEW] ./html/extern2.obj [NEW] ./html/Datasets.html Documented external raw data storage. ./html/Datasets.html ./html/chunk1.gif [NEW] ./html/chunk1.obj [NEW] Added a picture and better description for chunking since it seems that people are thinking chunks are fixed-size at the file level instead of at the array level. ./src/H5D.c ./src/H5Dpublic.h ./test/external.c Changed H5Dget_create_parms() to H5Dget_create_plist(). ./src/H5D.c ./src/H5Farray.c ./src/H5Fprivate.h ./src/H5Oefl.c ./src/H5Oprivate.h ./src/H5Sprivate.h ./src/H5Ssimp.c ./test/external.c ./test/istore.c External raw data file I/O for contiguous storage is now working. The library supports segments of various sizes which can be scattered throughout multiple files in any order. ./test/Makefile.in Remove more temporary files.
* [svn-r214] Changes since 19980203Robb Matzke1998-02-031-0/+1
| | | | | | | | | | | ---------------------- ./src/H5C.c ./src/H5Cprivate.h ./src/H5D.c ./src/H5Dpublic.h Added H5Dget_create_parms(), trying to stay one step ahead of Elena ;-)
* [svn-r213] Changes since 19980130Robb Matzke1998-02-031-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./MANIFEST Added H5Fmpio.c. One way to check that you've properly included new files is to run `./bin/release none', then unpack the resulting tar file somewhere and try to compile it. The tar file will be ./releases/hdf-5.0.0a.tar. ./config/freebsd2.2.1 ./config/linux Added `-ansi' ./acconfig.h Added definitions for PHDF5 and HAVE_PARALLEL. ./configure.in Added minimal support for parallel build. Kim and Albert will have to flesh this out or I can do it if they're more specific about what they need. ./config/commence.in Added default value for $(RUNTEST) ./config/conclude.in `make test' uses value of $(RUNTEST) to run test cases. ./src/Makefile.in Added PARALLEL_SRC for conditional compilation of H5Fmpio.c ./src/H5D.c ./src/H5Dpublic.h Added H5Dget_type() for Elena NOTE: These changes require that configure be rerun. If you're using GNU make it will happen automatically, otherwise do it by hand.
* [svn-r209] Changes since 19980130Robb Matzke1998-01-301-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./INSTALL Added instructions for which C flags to set for debugging. ./src/H5C.c ./src/H5Cpublic.h H5Cset_chunk() takes const pointer. ./src/H5D.c ./src/H5Dprivate.h ./src/H5Dpublic.h Added H5Dextend() to extend the dimensions of a dataset. ./src/H5Osdspace.c ./src/H5P.c ./src/H5Pprivate.h ./src/H5Ppublic.h ./test/cmpd_dset.c ./test/dsets.c ./test/th5p.c Added the optional `maxdims' argument to H5Pcreate_simple() and defined constant H5P_UNLIMITED which can appear in the maxdims. Added `const' to arguments. Implemented H5Pcopy() Removed the unused file argument from H5P_modify. Added H5P_extend(). Removed the `flags' field from simple data types and we determine if the `max' or `perm' arrays are valid by looking at the pointer. Cleaned up the H5O_sdspace_debug output. ./src/H5T.c Fixed a printf format. ./MANIFEST ./test/Makefile.in ./test/extend.c [NEW] Added a test for multi-dimensional unlimited dimensions.
* [svn-r185] Changes since 19980128Robb Matzke1998-01-281-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./src/H5D.c ./src/H5Dpublic.c Added H5Dget_space(). ./src/H5Gstab.c ./src/H5H.c Fixed a comparison with size_t against <0. ./src/H5P.c ./src/H5Pprivate.h ./src/H5Ppublic.h Changed `intn' to `int' for public function args and returns. H5Pget_hyperslab() returns the dimensionality. ./test/testhdf5.h Clears error stack more frequently. ./src/H5Psimp.c ./test/cmpd_dset.c Impelementing data space conversion.
* [svn-r164] Changes since 19980122Robb Matzke1998-01-221-17/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./src/*.h Fixed indentation where indent(1) screwed up. This isn't by any means the final say, but it's better than it was. ./src/H5A.c ./src/H5Aprivate.h ./src/H5Apublic.h ./src/H5C.c ./src/H5D.c ./src/H5E.c ./src/H5F.c ./src/H5G.c ./src/H5M.c ./src/H5P.c ./src/H5T.c ./src/H5Tconv.c ./src/debug.c ./test/dtypes.c ./test/istore.c ./test/theap.c ./test/tohdr.c ./test/tstab.c Removed some atom functions from the API and made them library-scope. Also changed some names by removing the redundant `atom' from the name and by adding a `_' after the `H5A'.
* [svn-r157] Reformatted code with indent...Quincey Koziol1998-01-161-17/+17
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* [svn-r155] Changes since 19980114Robb Matzke1998-01-161-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./html/Datasets.html Removed some archaic comments about data spaces. Fixed example code. ./MANIFEST ./html/H5.format.html ./src/H5O.c ./src/H5Oprivate.h ./src/H5Ocstore.c [DELETED] ./src/H5Oistore.c [DELETED] ./src/H5Olayout.c [NEW] ./src/Makefile.in ./test/istore.c Replaced H5O_CSTORE and H5O_ISTORE messages with a more general H5O_LAYOUT message. ./src/H5D.c ./src/H5Dprivate.h ./src/H5Dpublic.h A little more work on the pipeline. Access to the file data is through the new H5F_arr_read() and H5F_arr_write() which do I/O on hyperslabs of byte arrays and don't depend on data layout. This should simplify the I/O pipeline quite a bit. I also added another argument to H5Dread() and H5Dwrite() to describe the hyerslab of the file array on which I/O is occuring. We discussed this at last week's meeting. ./src/H5Farray.c [NEW] Added functions that sit on top of H5F_block_read() and H5F_istore_read() and implement a common set of functions between all layouts. This means I/O of hyperslabs of byte-arrays in the file to arrays of bytes in memory. When operating on arrays of elements (>1byte) then we just add another dimension. That is, a 10x20 array of int32 becomes a 10x20x4 array of bytes. [This is the area I'll be working on most of next week to implement partial I/O for contiguous data and to improve performance for chunked data.] ./src/H5Fistore.c ./src/H5Fprivate.h Replaced the H5F_istore_t data type with the layout message H5O_layout_t which looks almost the same. Eventually I'd like to rename `istore' to `chunked' everywhere and use `istore' for 1-d storage where the chunks are all different sizes like in the small object heap where each object is a chunk. ./src/H5V.c Changed ISTORE to LAYOUT in one place. ./test/dsets.c Fixed for extra argument to H5Dread() and H5Dwrite().
* [svn-r151] Changes since 19980105Robb Matzke1998-01-071-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./config/freebsd2.2.1 ./config/linux Added -UH5O_DEBUG to the debug flags. Turn this on to get lots of lines on stderr to show what objects are opened and closed. ./src/H5C.o ./src/H5Cpublic.h ./test/dsets.c ./test/tfile.c Split H5Cget_prop() and H5Cset_prop() into functions for each property. ./src/H5D.c ./src/H5Dpublic.h ./src/H5Gstab.c ./src/H5O.c ./src/H5Ocont.c ./src/H5Ocstore.c ./src/H5Odtype.c ./src/H5Oefl.c ./src/H5Oistore.c ./src/H5Oname.c ./src/H5Onull.c ./src/H5Oprivate.h ./src/H5Osdspace.c ./src/H5Ostab.c ./src/H5P.c ./src/istore.c ./test/tohdr.c Object header functions now understand constant vs. non-constant messages. ./src/H5F.c ./src/H5Fprivate.h The file OID can be closed before other OID's. ./src/H5Flow.c H5F_addr_defined() is a macro in this file. ./src/H5G.c ./src/H5Gpublic.h ./test/tstab.c A current working group cannot be deleted. ./src/H5Gent.c ./src/H5Gpkg.h Removed unused functionality. ./src/H5public.h Includes <sys/types.h> for size_t.
* [svn-r139] ./src/*.[ch]Robb Matzke1997-12-101-6/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Removed the interface initialization argument from FUNC_ENTER() and made it a locally-defined preprocessor symbol, INTERFACE_INIT. Changed `offset' to `address' and `length' to `size' in documentation so it's more consistent. `Offset' still appears occassionally when it refers to a byte offset within some other data structure. Moved interface termination function prototypes from public header files to .c files and made them static. ./src/H5.c ./src/H5public.h Added H5init() because it's possible that the predefined data types are not initialized. This happens only if the first call to the hdf5 library passes a predefined data type symbol as an argument. There should be some way to fix this... ./src/H5A.c ./src/H5Aprivate.h ./src/H5Apublic.h The free_func returns SUCCEED or FAIL, although the return value is ignored by H5A. This is so we can use the various H5*_close() functions to free things. H5Ainc_ref() and H5Adec_ref() are no longer public. Many of the other atom functions should also be made private, but I'll save that for later... Added additional template groups called H5_TEMPLATE_0 through H5_TEMPLATE_7 that are used by the various template subclasses. Increased the number of bits used for atom groups to prevent negative atoms. ./src/H5AC.c ./src/H5ACprivate.h Changed H5AC_new() to H5AC_create() to make names more consistent. ./src/H5B.c ./src/H5Bprivate.h Changed H5B_new() to H5B_create() to make names more consistent. ./src/H5C.c ./src/H5Cprivate.h ./src/H5Cpublic.h Now supports multiple subclasses of templates, although it's done with big switch statements. The default values for templates are defined in the source file to which that template belongs. This got rid of lots of needless preprocessor constants. Added H5Ccreate() to create a new template. Changed H5C_release() to H5Cclose() to make the naming more consistent. ./src/H5D.c ./src/H5Dprivate.h ./src/H5Dpublic.h Enhanced to use the new dataset interface, and uses the enhanced data type and data space interfaces, which haven't been completely implemented. The dataset interface doesn't handle non-contiguous storage, compression, or data type and space conversions yet. ./src/H5F.c ./src/H5Fprivate.h ./src/H5Fpublic.h Removed H5Fflush() since just calls H5F_flush(), which doesn't do what the user would probably think it does, namely, flush everything. It only flushes those things sitting in the H5AC cache and the boot block. Changed the `file_create_parms' field of H5F_low_t to just `create_parms' since the `file' part is obvious. ./src/H5Fistore.c Added some support for external files. Mostly just in the file format and not supported much by the library yet. I need to finish some dataset functions first. Changed H5F_istore_new() to H5F_istore_create() to make names more uniform across packages. ./src/H5Flow.c Flushing a file causes the file to be physically extended to the logical eof. This prevents H5F_open() from thinking a file has been truncated. Most of the time the file will already be that large, and when it isn't Unix will often just allocate the final block anyway. ./src/H5G.c ./src/H5Gent.c ./src/H5Gnode.c ./src/H5Gpkg.h ./src/H5Gprivate.h ./src/H5Gstab.c Removed H5G_basename() Removed (temporarily) data type information from symbol table entries and renamed H5G_CACHED_SDATA to H5G_CACHED_SDSPACE to reflect that it's a simple data space and has nothing to do with raw data. Changed H5G_node_new() to H5G_node_create() and H5G_stab_new() to H5G_stab_create() to make names more uniform across packages. Fixed an undefined address bug that happens when H5G_node_debug() program doesn't pass enough info to H5G_node_load(). ./src/H5H.c ./src/H5Hprivate.h Changed H5H_new() to H5H_create() to make the names more uniform across packages. ./src/H5M.c ./src/H5Mprivate.h ./src/H5Mpublic.h Nulled all the create functions. Most of the other callbacks are to public functions. Removed H5Mcreate(). Changed hobjtype_t to group_t since it has to be the same thing anyway. ./src/H5O.c ./src/H5Oprivate.h ./src/H5Osdim.c ./src/H5Osdtyp.c Changed H5O_SIM_DIM to H5O_SDSPACE (simple data space) since `simple data space' is its official name, not `simple dimensions'. Will eventually add H5O_CDSPACE for comples data spaces. Changed _sim_dim_ to _dspace_. Replaced H5O_SIM_DTYPE and the compound data type messages with a single H5O_DTYPE message. Changed _sim_dtype_ to _dtype_. Changed H5O_STD_STORE to H5O_CSTORE (contiguous storage) since contiguous storage is not necessarily standard. Changed _std_store_ to _cstore_ in H5Ocstore.c Added the H5O_EFL (external file list) message. Changed H5O_new() to H5O_create() to make names more uniform across packages. ./src/H5Oefl.c NEW External file list message for specifying which non-hdf5 files contain raw data for a dataset. ./src/H5P.c ./src/H5Pprivate.h ./src/H5Ppublic.h Renamed and moved data structures to make the names conform to our naming scheme. ./src/H5T.c ./src/H5Tprivate.h ./src/H5Tpublic.h ./src/H5Tpkg.h NEW Data structures redesigned to be more flexible. The interface was redesigned to make it more regular and to make some names more uniform across packages. ./src/H5detect.c Output was changed to produce a file that conforms to the hdf5 coding standard. ./src/Makefile.in Generates H5Tinit.c by running H5detect. ./src/debug.c Moved command argument processing.
* [svn-r108] Changed all hatom_t types to hid_t. (Isn't 'sed' nifty.. :-)Quincey Koziol1997-09-241-4/+4
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* [svn-r96] Added "atexit" routines to each interface to free buffers ↵Quincey Koziol1997-09-181-0/+1
| | | | | | allocated during runtime. Isolated but can't figure out how to fix bug reported with purify.
* [svn-r78] Checkpointing dataset code. Everything is currently working, ↵Quincey Koziol1997-09-151-0/+1
| | | | | | except writing a second dataset out to the file seems to loose the first one.
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