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* [svn-r1572] Changes since 19990810Robb Matzke1999-08-171-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./MANIFEST ./src/H5FDmulti.c [NEW] ./src/H5FDmulti.h [NEW] ./src/Makefile.in ./src/hdf5.h The split driver was reimplemented as a more general "multi" driver which is capable of splitting data into multiple files like the family driver except the partioning is done by memory usage type instead of address. The H5Pset_fapl_split() function just calls H5Pset_fapl_multi() with arguments which prepare to split the address space into two files: meta and raw data. This is the first version. I plan to allow the open() call to relax a bit which would allow one to open an hdf5 file when only the meta-data file is present. This would allow a very large file to be split and stored on tape and the relatively small meta file to be mirrored on disk to allow limited browsing of the file (any request for raw data would fail). ./src/H5private.h ./src/H5F.c ./src/H5FD.c ./src/H5FDprivate.h ./src/H5FDpublic.h ./src/H5FDcore.c ./src/H5FDfamily.c ./src/H5FDmpio.c ./src/H5FDsec2.c Added the ability for a file driver to store information in the superblock which would be needed if the file were opened again later for reading. The format is driver-defined which allows users to extend it however they like. ./doc/html/H5.format.html Added information about the new driver information block of the superblock. This is where file drivers store information they need in order to reopen the file later. ./src/H5F.c ./src/H5Fprivate.h ./src/H5FD.c ./src/H5FDprivate.h ./src/H5FDpublic.h ./src/H5FDcore.c ./src/H5FDfamily.c ./src/H5FDmpio.c ./src/H5FDsec2.c ./src/H5Fistore.c ./src/H5R.c The file access properties and the file access property list were decoupled, which allows the property list to more cleanly contain properties for various levels of the file and which allows the property list to be modified more cleanly when opening files. ./src/H5.c ./src/H5FDpublic.h Removed H5FD_MEM_META and H5FD_MEM_GROUP since they're never used. ./src/H5D.c Changed the way we detect the MPIO driver in all these special cases. ./src/H5F.c ./src/H5Rpublic.h ./test/tfile.c The default file sizeof(offset) was changed to be a function of haddr_t instead of hsize_t. THE H5RPUBLIC.H DEFINITIONS WILL HAVE PROBLEMS IF THE USER CREATES A FILE WITH NON-DEFAULT OFFSET AND SIZE SIZES! ./src/H5F.c Fixed an uninitialized memory access bug in file closing related to the VFL. ./src/H5T.c ./src/H5Tpublic.h Added an H5T_NATIVE_HADDR predefined datatype which corresponds to the `haddr_t' type. ./test/Makefile.in Reformatted long lines. ./test/big.c ./test/cmpd_dset.c ./test/dsets.c ./test/dtypes.c ./test/extend.c ./test/external.c Removed the H5F_ACC_DEBUG flag from file creation/open calls. ./test/big.c Plugged a memory leak. ./test/h5test.c Added support for the `multi' driver. Removed #warning about not having the stdio driver. Plans are to not implement it since the sec2 driver serves the same purpose and testing didn't show any difference in execution times between the two.
* [svn-r1568] Changes since 19990730Robb Matzke1999-08-101-1/+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-r1548] Changes since 19990727Robb Matzke1999-07-281-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./src/H5.c [1.3] ./src/H5AC.c [1.3] ./src/H5ACprivate.h [1.3] ./src/H5B.c [1.3] ./src/H5Bprivate.h [1.3] ./src/H5D.c [1.3] ./src/H5F.c [1.3] ./src/H5Farray.c [1.3] ./src/H5Fcore.c [1.3] ./src/H5Ffamily.c [1.3] ./src/H5Fistore.c [1.3] ./src/H5Flow.c [1.3] ./src/H5Fmpio.c [1.3] ./src/H5Fprivate.h [1.3] ./src/H5Fsec2.c [1.3] ./src/H5Fsplit.c [1.3] ./src/H5Fstdio.c [1.3] ./src/H5G.c [1.3] ./src/H5Gent.c [1.3] ./src/H5Gnode.c [1.3] ./src/H5Gprivate.h [1.3] ./src/H5Gstab.c [1.3] ./src/H5HG.c [1.3] ./src/H5HGprivate.h [1.3] ./src/H5HL.c [1.3] ./src/H5HLprivate.h [1.3] ./src/H5MF.c [1.3] ./src/H5MFprivate.h [1.3] ./src/H5O.c [1.3] ./src/H5Oattr.c [1.3] ./src/H5Ocont.c [1.3] ./src/H5Odtype.c [1.3] ./src/H5Oefl.c [1.3] ./src/H5Olayout.c [1.3] ./src/H5Oprivate.h [1.3] ./src/H5Oshared.c [1.3] ./src/H5Ostab.c [1.3] ./src/H5P.c [1.3] ./src/H5R.c [1.3] ./src/H5Smpio.c [1.3] ./src/H5T.c [1.3] ./src/H5Tvlen.c [1.3] ./src/H5private.h [1.3] ./test/dtypes.c [1.3] ./test/gheap.c [1.3] ./test/istore.c [1.3] ./test/lheap.c [1.3] ./test/ohdr.c [1.3] ./tools/h5debug.c [1.3] File addresses (the `haddr_t' type) are passed by value instead of by reference. The type is no longer a struct. This is one of the preliminary changes needed for the Virtual File Layer stuff. ./src/H5Fprivate.h [1.3] ./src/H5Flow.c [1.3] Some address functions were rewritten as macros.
* [svn-r1385] Updated H5Rdereference, H5Rget_object_type and H5Rget_region ↵Quincey Koziol1999-06-251-39/+72
| | | | | | | | | | | to accept a location ID (i.e. a file or group ID) as well as the dataset ID. This should allow Dave to get the palettes stored in the file correctly and also enable Bob and/or Bruce's indexing stuff. This change should be folded into the documentation for these three functions for the release. Also, I fixed a number of bugs in the hyperslab and point selection iterators for H5Diterate and they are working correctly now.
* [svn-r1332] Fixes to get the VL datatypes working. The only function ↵Quincey Koziol1999-06-111-0/+1
| | | | | | currently working is H5Tvlen_create().
* [svn-r1306] Changes since 19990602Robb Matzke1999-06-071-2/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./doc/html/Datatypes.html ./test/dtypes.c Added documentation and tests for opaque types. ./tools/h5ls.c Added a `-x' or `--hexdump' argument which is not fully implemented (because I want to synchronize h5tools.c first) but which will eventually print raw data in hexadecimal format without any translation from disk. This would be useful for debugging references and VL types. ./tools/h5tools.c Added support for references (not quite finished yet, but compiles -- I wanted to sync up this file before Patrick and I got too far apart...) ./src/H5R.c Checked for error return value from H5R_get_object_type() ./src/H5A.c ./src/H5D.c Changed error return values from NULL to FAIL ./test/Makefile.in ./test/trefer.c Creates trefer1.h5 and trefer2.h5 so that the second test doesn't clobber the first file since the files might be useful for debugging.
* [svn-r1224] Changes since 19990426Robb Matzke1999-04-271-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./tools/h5tools.c ./tools/h5tools.h Finally fixed a long-standing bug that caused core dumps if a compound datum rendered to more than some number of characters (we kept bumping up the limit at the risk of violating stack size limits on some machines). The fix works only on systems that have the vsnprintf() function (otherwise a 4kB limit is imposed, which if violated probably dumps core). If vsnprintf() is present then the library dynamically allocates space for the output string. Also made it possible to control how compound data is rendered across multiple lines of output by allowing the caller to specify where optional line-breaks get inserted. The output functions split up the value at one or more optional line-breaks to prevent it from wrapping around the screen. If a datum doesn't fit on the current line but would fit on the next line then it is printed on the next line regardless of whether optional line-breaks would have prevent wrapping around the screen. This makes it easier to find the beginnings of compound data values. This feature is disabled by default but can be enabled by the application. If a datum doesn't fit on the current line and the previous datum also occupied more than one line then we move to the next line before printing. This makes it easier to find the beginnings of compound data values but prevents the output from looking fragmented if there are only a few long values among mostly short values. This feature is disabled by default but can be enabled by the application. The application can control the printf() formats used for all the native data types. The defaults are what the library used to use: %g, %ld, %lu, %d, and %u ./tools/h5ls.c Compound datatype values can now be split across multiple lines of output instead of just wrapping. Also, when lots of compound values are too long they all start at the beginning of a line. This only required about 10 lines of changes in the setup for tools library calls (I didn't modify the h5dump program because it uses its own version of the tools library that forked off long ago). Added code for Win32 which is unable to cast `unsigned long long' to `double'. If the dataset size exceeds (2^63)-1 then the percent utilization is not displayed (this is easily possible with chunked datasets). This is untested yet. ./configure.in ./src/H5config.h.in ./src/H5.c ./src/H5private.h Check for vsnprintf() and provide a simple, stupid definition if it isn't available. The stupid definition just calls vsprintf() and ignores the second argument. This can result in buffer overflows in h5ls and h5dump since vsprintf() is an unsafe function (and anyone can create an hdf5 file that runs an arbitrary command from h5ls and h5dump in that case)! ./config/conclude.in Remove more *.o files for `make clean' ./src/H5A.c ./src/H5D.c ./src/H5F.c ./src/H5I.c ./src/H5Iprivate.h ./src/H5P.c ./src/H5R.c ./src/H5RA.c ./src/H5S.c ./src/H5T.c ./src/H5TB.c Cleaned up a memory leak during H5_term_library() by allowing H5I_clear_group() to skip items that couldn't be freed. This allows the item to remain in the group until we can free it later. ./src/H5F.c The H5F_close_all() function fails if a file cannot be closed.
* [svn-r1217] Changes since 19990426Robb Matzke1999-04-261-6/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./config/commence.in ./examples/Makefile.in ./test/Makefile.in ./testpar/Makefile.in ./tools/Makefile.in Fixed some dependency problems in Makefiles. If the library version is updated then everything gets recompiled. ./src/H5G.c ./src/H5R.c Failure return value for object type functions is now H5G_UNKNOWN as documented. ./src/H5Shyper.c ./src/H5Spoint.c Fixed an unused argument warning. ./tools/h5debug.c Fixed a call to H5F_block_read() since the 4th argument is different now. ./tools/h5ls.c Added a space between the object name and class to make the output readable when the object name is longer than 24 characters. C
* [svn-r1184] Changes since 19990402Robb Matzke1999-04-151-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./config/commence.in ./config/conclude.in ./test/Makefile.in ./tools/Makefile.in Fixed so private libraries are not installed publicly. The installation directories `bin', `include', and `lib' are created mode 755. ./src/H5.c ./src/H5A.c ./src/H5F.c ./src/H5Fcore.c ./src/H5Fistore.c ./src/H5Flow.c ./src/H5Fmpio.c ./src/H5Fsec2.c ./src/H5Fstdio.c ./src/H5G.c ./src/H5Gent.c ./src/H5Gnode.c ./src/H5HG.c ./src/H5HL.c ./src/H5O.c ./src/H5Oattr.c ./src/H5Ocomp.c ./src/H5Ocont.c ./src/H5Odtype.c ./src/H5Oefl.c ./src/H5Ofill.c ./src/H5Olayout.c ./src/H5Omtime.c ./src/H5Oname.c ./src/H5Osdspace.c ./src/H5Oshared.c ./src/H5Ostab.c ./src/H5R.c ./src/H5Sall.c ./src/H5Shyper.c ./src/H5Smpio.c ./src/H5Snone.c ./src/H5Spoint.c ./src/H5T.c ./src/H5Tconv.c ./src/H5Vprivate.h ./src/H5Z.c ./src/H5detect.c ./src/H5private.h ./test/chunk.c ./test/dsets.c ./test/dtypes.c ./test/h5test.c ./test/overhead.c ./test/ragged.c ./test/tattr.c ./tools/h5dump.c ./tools/h5findshd.c ./tools/h5ls.c Changed `__unused__' to `UNUSED' to fix a conflict with GNU header files. ./src/H5Tpkg.h ./test/h5test.h Removed __unused__ from forward function declarations. ./src/H5P.c Removed a comment about restrictions for the type conversion temporary buffers. Thanks to Quincey, the comment no longer applied. ./src/H5T.c Relaxed the H5Tpack() a little so it would pack compound data structures that had non-transient atomic members. ./tools/h5ls.c Added a `-g' (or `--group') flag that causes information to be printed about the specified group instead of the group's contents. (sort of like Unix's `ls -d'). The `-g' can be used in combination with `-r' to print information about the group and its contents.
* [svn-r1169] ./configure.inRobb Matzke1999-03-301-6/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ./configure [REGENERATED] ./src/H5D.c ./src/H5O.c Removed H5AC, H5B, and H5T from the default list of packages to debug (because they're pretty expensive debugging), and added H5O. Also fixed a bug for undefined variable in H5D when H5S debugging is turned on but H5T debugging is turned off. ./config/conclude.in Fixed installation of header files for building in a directory other than the source directory. This fixes a bug where H5config.h wasn't being installed. ./src/H5.c ./src/H5A.c ./src/H5D.c ./src/H5F.c ./src/H5G.c ./src/H5I.c ./src/H5Iprivate.h ./src/H5P.c ./src/H5R.c ./src/H5RA.c ./src/H5S.c ./src/H5T.c ./src/H5TB.c ./src/H5Tprivate.h ./src/H5Z.c ./src/H5detect.c ./src/H5private.h Changed the way the library shuts down again. Now it handles cycles between packages and isn't so sensitive to dependencies between packages. A package might shut down only to be restarted to process a request from some other package being shut down. Loops are detected after 100 iteractions and the shutdown is aborted with a message on standard error. This also makes it a lot easier to debug. ./src/H5A.c Fixed H5A_write() and H5A_read() so they pass a non-null background buffer to the conversion functions. This is necessary when an attribute has a compound data type. ./src/H5Flow.c ./src/H5Fprivate.h ./src/H5Fsec2.c Reindented new Win32 stuff. ./src/H5Odtype.c Fixed a bug when enumeration types are used in a compound data type. The byte pointer wasn't incremented after the type information was written. ./tools/h5ls.c Compound data types display their total size because it's not always obvious from looking at the members. Scalar attributes show their space as `scalar' instead of `{}'. The index value is not printed for attributes that have only a few values. Instead the word `Data:' is printed on the first line of attribute data. Named types display their data type only if verbose output was requested.
* [svn-r1151] Changes since 19990318Robb Matzke1999-03-191-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./Makefile.in ./configure.in ./configure [REGENERATED] ./src/H5config.h.in [REGENERATED] ./config/commence.in ./config/conclude.in ./config/dec-osf4.x ./config/depend.in ./config/freebsd ./config/linux-gnu ./config/linux-gnulibc1 ./config/linux-gnulibc2 ./config/solaris2.x ./examples/Makefile.in ./src/Makefile.in ./test/Makefile.in ./testpar/Makefile.in ./tools/Makefile.in ./tools/testh5dump.sh Changes that allow hdf5 to be configured and compiled in a directory other than the source directory. This is especially useful if you want to concurrently compile with different compilers and/or compile flags, or if the hdf5 source is on read-only media like a CDROM. The changes were surprisingly easy ;-) Here's what you can do now... $ mkdir /tmp/build1 # or something $ cd /tmp/build1 $ /cdrom/hdf5/configure # where ever the source is $ make Paul, you'll have to change the testh5toh4 script similar to the way I changed testh5dump.sh. I started working on it but then gave up because of a number of problems: (1) I had to comment out all the tests that let h5toh4 choose the output file name because it always tried to put the output file in the same directory as the input file, (2) if path names are used during the h4 dump then they interfere with the diff. The test works fine when run in the source directory, but try this instead: $ gunzip <hdf5-1.1.67.tar.gz |tar xf - $ chmod -R ugo-w hdf5-1.1.67 $ mkdir build $ cd build $ ../hdf5-1.1.67/configure $ make check Dan, I didn't modify the pablo/Makefile.in because I have no way to test it. I think all you need to do is add a couple lines before the @COMMENCE@ line and add a couple search directories for header files. Anyway, it seems like almost an exact duplicate of the src/Makefile.in, so it shouldn't be a problem... ./Makefile.in Removes a few more temporary files during make clean and distclean. ./configure.in I fixed the creation of the time-stamp files so that the initial make doesn't have to regenerated all the makefiles (only GNU make users will see any change). ./src/H5R.c Changed a return type from `intn' to `int' for an API function. ./src/H5detect.c Added the volatile qualifier to a couple more variables. ./tools/h5tools.c Fixed a compiler warning about an unused local. ./tools/h5toh4.c Initialized `optind' to 1 because it's zero on my system. It should always be one on a unix system. ./tools/testh5toh4 Redirected "broken pipe" messages to /dev/null so outut is formatted correctly.
* [svn-r1146] Added support for object references to named datatypes.Quincey Koziol1999-03-181-0/+12
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* [svn-r1144] Added support for object references to groups.Quincey Koziol1999-03-181-0/+11
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* [svn-r1139] Added code for H5Rget_object_typeQuincey Koziol1999-03-121-0/+95
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* [svn-r1135] Expanded API for reading lists blocks/points to allow for just a ↵Quincey Koziol1999-03-111-9/+26
| | | | | | portion of the block/point-list to be read at a time.
* [svn-r1132] Dataset region references are now finished and working ↵Quincey Koziol1999-03-101-6/+8
| | | | | | | | | | | | | | | | | | | | correctly. Also, there are five new API functions for querying selections: H5Sget_select_hyper_nblocks - retrieves the number of hyperslab blocks in current hyperslab selection for a dataspace H5Sget_select_elem_npoints - retrieves the number of element points in current element selection for a dataspace H5Sget_select_hyper_blocklist - retrieves a list of the hyperslab blocks in current hyperslab selection for a dataspace H5Sget_select_elem_pointlist - retrieves a list of the element points in current element selection for a dataspace H5Sget_select_bounds - retrieves a n-dimensional bounding box containing current selection.
* [svn-r1101] Changes since 19990219Robb Matzke1999-02-251-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./config/irix64 The old (-32) compiler is now supported by setting envrionment CC='cc -32'. The -64 compiler is the default or you can set CC='cc -64'. ./src/H5A.c ./src/H5D.c ./src/H5F.c ./src/H5Fistore.c ./src/H5Flow.c ./src/H5G.c ./src/H5I.c ./src/H5Ocomp.c ./src/H5P.c ./src/H5R.c ./src/H5RA.c ./src/H5T.c ./src/H5Tbit.c ./src/H5Tconv.c ./src/H5Z.c ./src/H5detect.c ./test/big.c ./test/cmpd_dset.c ./test/dsets.c ./test/dtypes.c ./test/enum.c ./test/mtime.c ./test/ohdr.c ./tools/h5ls.c Fixed lots of warnings on Irix64. Mailed a few remaining warnings in H5S to Quincey and a few in the dumper to Ruey-Hsia.
* [svn-r1087] Changes since 19990218Robb Matzke1999-02-201-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./src/H5F.c ./src/H5private.h ./src/H5Ipublic.h ./src/H5O.c Fixed a rather nasty bug with file closing that caused the file boot block to be updated incorrectly, effectively truncating the file. The bug I fixed was triggered by: 1. Create a file, F 2. Open an object, X 3. Close file F 4. Reopen file F for read/write. 5. Create and close some objects 6. Close file F 7. Close library (exit). Step 3 pended the close because object X is still open, but the file ID was removed from the H5I_FILE ID group. Step 4 created a new file because it didn't see any matching file on the H5I_FILE ID group. Step 5 extends the file. Step 6 writes the new file boot block to disk. Step 7 closes object X and completes the close from step 3, writing the old boot block information to disk. The new behavior is that step 3 moves the file from the H5I_FILE group to the H5I_FILE_CLOSING group. Step 4 searches both groups and finds the file. Step 5 extends the file using the same H5F_file_t struct as step 3. Step 6 closes the H5F_t struct opened in step 3 but not the H5F_file_t struct shared by steps 1 and 3. Step 7 closes object X which closes the H5F_file_t from step 1, flushing the boot block which was shared by all steps. ./src/H5F.c Added some bulletproofing to file reference counting and removed comments which no longer apply. Added H5F_flush_all() and H5F_close_all() which apply to all files. ./src/H5A.c ./src/H5D.c ./src/H5F.c ./src/H5G.c ./src/H5I.c ./src/H5Iprivate.h ./src/H5R.c ./src/H5RA.c ./src/H5S.c ./src/H5T.c Added the new H5I_free_t data type to describe the function type to be passed as the `free_func' argument to H5I_init_group(). ./src/H5I.c Bulletproofed the object removal functions. Removed comments which no longer apply. Changed global variable names so they don't violate the naming scheme. Added H5I_debug() that prints the contents of an ID group. Removed H5I_inc_ref() because it isn't used. Reindented a couple of functions. ./src/H5.c ./src/H5G.c ./src/H5Ipublic.h Changed H5I_MAXID to H5I_NGROUPS to better relect the fact that it's the total number of valid ID groups. ./src/H5Shyper.c Changed hyperslab offset arrays to signed quantities to get rid of warnings on DEC cluster. ./src/H5Flow.c ./src/H5Fprivate.h Changed the objno argument of H5F_addr_pack() to be unsigned to get rid of warnings on DEC cluster.
* [svn-r956] Fixes for dataset region code.Quincey Koziol1998-11-301-0/+3
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* [svn-r947] Lots of patches to enable dataset region references. The testing ↵Quincey Koziol1998-11-251-30/+159
| | | | | | for these need to be finished and checked in still.
* [svn-r936] Changes since 19981119Robb Matzke1998-11-211-14/+16
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./src/H5.c ./src/H5A.c ./src/H5AC.c ./src/H5B.c ./src/H5D.c ./src/H5E.c ./src/H5F.c ./src/H5Farray.c ./src/H5Fcore.c ./src/H5Ffamily.c ./src/H5Fistore.c ./src/H5Flow.c ./src/H5Fmpio.c ./src/H5Fsec2.c ./src/H5Fsplit.c ./src/H5Fstdio.c ./src/H5G.c ./src/H5Gent.c ./src/H5Gnode.c ./src/H5Gstab.c ./src/H5HG.c ./src/H5HL.c ./src/H5I.c ./src/H5Iprivate.h ./src/H5MF.c ./src/H5MM.c ./src/H5O.c ./src/H5Oattr.c ./src/H5Ocomp.c ./src/H5Ocont.c ./src/H5Odtype.c ./src/H5Oefl.c ./src/H5Ofill.c ./src/H5Olayout.c ./src/H5Omtime.c ./src/H5Oname.c ./src/H5Osdspace.c ./src/H5Oshared.c ./src/H5Ostab.c ./src/H5P.c ./src/H5R.c ./src/H5RA.c ./src/H5S.c ./src/H5Sall.c ./src/H5Shyper.c ./src/H5Smpio.c ./src/H5Snone.c ./src/H5Spoint.c ./src/H5Sselect.c ./src/H5T.c ./src/H5TB.c ./src/H5Tbit.c ./src/H5Tconv.c ./src/H5V.c ./src/H5Z.c ./src/H5detect.c ./src/H5private.h Most of these changes are because the `interface_initialize_g' variable change from hbool_t to int. It's a one line change. Changed the way the library is closed so we have more control over the order the interfaces are shut down. Instead of registering an atexit() function for every interface in some haphazard order we just register one: H5_term_library() which then calls the H5*_term_interface() functions in a well-defined order. If the library is closed and then reopened repeatedly by calling H5close() and H5open() in a loop we only add one copy of the library termination functions with atexit(). Termination is a two-step process in order to help detect programming errors that would cause an infinite loop caused by the termination of one interface waking up some other previously terminated interface. The first step terminates the interface and *marks it as unusable*. After all interfaces are terminated then we mark them all as usable again. The FUNC_ENTER() macro has been modified to return failure or to dump core (depending on whether NDEBUG is defined) if we try to call an interface while it's shutting down. ./src/H5.c The H5dont_atexit() function returns failure if it's called more than once or if it's called too late. However, the error stack is not automatically printed on failure because the library might not be initialized yet ./test/chunk.c ./test/flush1.c ./test/flush2.c ./test/iopipe.c ./test/overhead.c ./test/ragged.c Changed the extra cast for Win32 so we do floating point division again -- it was just confusion about precedence and associativity of casting and the C coercion rules. Removed extra carriage returns inserted by broken operating system. ./src/H5Ffamily.c Fixed an bug where H5F_fam_write() lowered the EOF marker for one of the family members causing H5F_fam_read() to read zeros. ./test/h5test.h [NEW] ./test/h5test.c [NEW] ./test/Makefile.in ./test/bittests.c ./test/cmpd_dset.c ./test/dsets.c ./test/dtypes.c ./test/extend.c ./test/external.c Support library for test files. This isn't done yet but Katie's contractions are ~10 minutes apart so I figured I better back this stuff up just in case I'm not here next week... Eventually all test files will understand HDF5_DRIVER to name the low level file driver and parameters so we can easily test various drivers. They will also understand HDF5_PREFIX to prepend to the beginning of file names which is necessary for testing ROMIO with various drivers. Also, the cleanup function will know how to use the file name prefix and will understand different file driver naming schemes like file families. I'm not sure they'll understand the `gsf:' type prefixes yet. Note, the external test is completely commented out because I'm in the middle of modifying it. It will still compile and run but it doesn't test anything at the moment.
* [svn-r925] Changes since 19981116Robb Matzke1998-11-181-8/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./INSTALL.parallel [NEW] We're beginning to unify some of the parallel installation steps. This file will contain general information for installing the parallel library. It's not complete yet. ./configure.in ./configure [REGENERATED] ./src/H5config.h.in [REGENERATED] Check for xdr_int() in libnsl required on Solaris when linking with hdf4. It's found on the Irix system I tested which complains that `-lnsl' didn't resolve any symbols. Oh well. Fixed the order of searching for libdf and libmfhdf for hdf4 linking. ./configure.in ./configure [REGENERATED] ./src/H5config.h.in [REGENERATED] ./src/H5Z.c Check for compress() in libz in order to find older versions of the library that will still work for hdf4. Added a separate check for compress2() that hdf5 will use. ./configure.in ./configure [REGENERATED] ./src/H5config.h.in [REGENERATED] ./src/H5.c ./src/H5private.h ./src/H5A.c ./src/H5B.c ./src/H5Bprivate.h ./src/H5D.c ./src/H5F.c ./src/H5Farray.c ./src/H5Fcore.c ./src/H5Ffamily.c ./src/H5Fistore.c ./src/H5Flow.c ./src/H5Fmpio.c ./src/H5Fprivate.h ./src/H5Fsec2.c ./src/H5Fsplit.c ./src/H5Fstdio.c ./src/H5Gent.c ./src/H5Gnode.c ./src/H5Gpkg.h ./src/H5Gprivate.h ./src/H5HG.c ./src/H5HL.c ./src/H5O.c ./src/H5Oattr.c ./src/H5Ocomp.c ./src/H5Ocont.c ./src/H5Odtype.c ./src/H5Oefl.c ./src/H5Ofill.c ./src/H5Olayout.c ./src/H5Omtime.c ./src/H5Oname.c ./src/H5Oprivate.h ./src/H5Osdspace.c ./src/H5Oshared.c ./src/H5Ostab.c ./src/H5R.c ./src/H5RA.c ./src/H5Sall.c ./src/H5Shyper.c ./src/H5Snone.c ./src/H5Spoint.c ./src/H5Sprivate.h ./src/H5Sselect.c ./src/H5T.c ./src/H5Tbit.c ./src/H5Tconv.c ./src/H5Tpkg.h ./src/H5V.c ./test/bittests.c ./test/gheap.c ./test/hyperslab.c ./test/istore.c ./test/tmeta.c ./test/trefer.c ./test/tselect.c ./tools/h5debug.c ./tools/h5tols.c Added checks for Posix.1g types like `int8_t'. If not defined then H5private.h defines them. Changed all `int8' etc. to `int8_t'. ./src/H5A.c ./src/H5D.c ./src/H5F.c ./src/H5G.c ./src/H5I.c ./src/H5P.c ./src/H5R.c ./src/H5RA.c ./src/H5S.c ./src/H5T.c ./src/H5TB.c ./src/H5Z.c Calling H5*_term_interface() resets interface_initialize_g to FALSE so a subsequent call to H5open() (implied or explicit) reinitializes global variables properly. ./src/H5private.h ./src/H5Oefl.c ./src/H5S.c Changed MAX_SIZET, MAX_SSIZET, MAX_HSIZET, and MAX_HSSIZET to SIZET_MAX, SSIZET_MAX, HSIZET_MAX, and HSSIZE_MAX to they match the Posix.1 constants in <limits.h>. ./src/H5T.c ./src/H5Tconv.c ./src/H5Tpkg.h ./src/H5Tprivate.h ./src/H5detect.c Added 36 more integer hardware conversion functions to the type conversion table for conversions to/from `long long' and `unsigned long long'. The `long long' names will be changed shortly to make them portable to Win32. Changed H5T_init() to H5T_native_open() and added an H5T_native_close() to open and close the predefined native data types. Increased the initial size of the type conversion table from 64 to 128 entries. Reordered the 90 new integer conversion functions so the names that are printed favor `int' over `short' or `long' when two of them are the same. ./test/dtypes.c Added hardware and software integer conversion tests for the 56 functions I added recently but not the additional 36 checked in this time. That will come next. Call H5close() after each test so type conversion statistics are easier to follow. Try this: $ HDF5_DEBUG=t ./dtypes Added more debugging output for when things go wrong. ./src/H5private.h Removed trailing carriage-returns inserted by broken operating system ;-)
* [svn-r904] Fixed bug in H5dont_atexit.Quincey Koziol1998-11-131-2/+37
| | | | | | | Plugged a memory leak in the union of hyperslabs code. Checkpointing dataset region references, which are working, but not stored in file yet.
* [svn-r816] Fixed bug with references on certain platforms.Quincey Koziol1998-10-281-1/+3
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* [svn-r797] Changed comments from returning "SUCCEED/FAIL" to ↵Quincey Koziol1998-10-261-7/+7
| | | | | | "non-negative/negative" and also fixed a few more explicit checks against FAIL.
* [svn-r795] Changes since 19981026Robb Matzke1998-10-261-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./MANIFEST ./test/th5s.h5 [NEW] ./test/th5s.c Added a test to make sure that creating a data space with too large a rank fails. Added a test to make sure that reading a file that has a dataset with a space with too large a rank fails. Actually, this one is a little weird: the code that reads the data space message assumes the space is scalar if the message cannot be read. Fortunately the layout message fails also, preventing the dataset from being opened. However, since the data type message is still visible h5ls will report that the object is a named data type. ./test/space_overflow.c [NEW] This is the little program that makes the th5s.h5 file. ./src/H5A.c ./src/H5R.c ./src/H5Sselect.c Updated trace info. ./src/H5Olayout.c ./src/H5Osdspace.c Added code to fail if the dimensionality is too large when decoding a layout or simple data space message. ./src/H5Oprivate.h Redefined H5O_LAYOUT_NDIMS in terms of H5S_MAX_RANK. ./src/H5P.c ./src/H5S.c Check for ndims>H5S_MAX_RANK in API function calls, added assert to internal functions. ./src/H5V.c Changed a `<' to an `<=' in an assert. ./test/flush2.c Includes stdlib.h for getenv(). ./tools/h5tools.c Able to handle up to H5S_MAX_RANK dimensions during output.
* [svn-r791] Internal API tweaks to H5D_open_oidQuincey Koziol1998-10-261-7/+1
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* [svn-r790] Updated parameters for H5R API and changed constants from ↵Quincey Koziol1998-10-261-13/+12
| | | | pointers to references
* [svn-r789] Changes since 19981023Robb Matzke1998-10-261-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./MANIFEST ./test/Makefile.in ./test/flush1.c [NEW] ./test/flush2.c [NEW] Test to see if calling H5Fflush() results in a consistent file. ./src/H5.c ./src/H5A.c ./src/H5D.c ./src/H5Fistore.c ./src/H5I.c ./src/H5S.c ./src/H5Shyper.c ./src/H5Sselect.c ./src/H5TB.c Changed comparisons against SUCCEED and FAIL to >=0 and <0 in about 15 places. ./src/H5.c ./src/H5V.c ./src/H5detect.c ./src/H5private.h ./src/H5public.h ./test/big.c ./test/chunk.c ./test/cmpd_dset.c ./test/dsets.c ./test/dtypes.c ./test/external.c ./test/fillval.c ./test/iopipe.c ./test/links.c ./test/mount.c ./test/mtime.c ./test/ragged.c ./test/shtype.c ./test/unlink.c Removed ^M from the end of lines inserted on broken OS's ;-) ./src/H5private.h Changed c++ comments to c comments. ./src/H5R.c Added tracing macros.
* [svn-r776] Fixed references, object references should be working now.Quincey Koziol1998-10-221-26/+53
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* [svn-r766] Checkpointing the reference code.Quincey Koziol1998-10-191-89/+16
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* [svn-r761] Changes since 19981013Robb Matzke1998-10-141-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./src/H5.c Fixed a signed vs. unsigned comparison. ./src/H5D.c Setting a fill value of all zeros will cause the fill value to be written to the dataset instead of relying on the low-level file driver initializing unwritten areas with zero. ./src/H5D.c ./src/H5F.c ./src/H5Fprivate.h ./src/H5G.c ./src/H5Gpkg.h ./src/H5Gprivate.h ./src/H5O.c ./src/H5T.c More file mounting stuff. ./src/H5I.c Fixed a bug where trying to close an invalid object id caused a core dump. For instance, H5Gclose(-1). ./MANIFEST ./test/Makefile.in ./test/mount.c [NEW] Mounting tests. ./src/H5R.c Fixed a couple (herr_t)NULL casts.
* [svn-r757] Added code for object references.Quincey Koziol1998-10-131-5/+395
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* [svn-r743] Added H5I_type_t type to H5_trace and added H5Iget_type function ↵Quincey Koziol1998-10-071-0/+83
| | | | | | call. Also checked in H5R skeleton files.
* [svn-r739] Switched ragged array "H5R" API to "H5RA" to make room for the ↵Quincey Koziol1998-10-061-1189/+0
| | | | reference API.
* [svn-r737] Changed H5I groups to have a H5I_ prefix before them, to better ↵Quincey Koziol1998-10-051-10/+10
| | | | | | align with the library.
* [svn-r654] Fixed last bug (hah! ;-) for beta release, changed H5Gget_stat to ↵Quincey Koziol1998-09-021-6/+6
| | | | | | H5Gget_objinfo and renamed internal functions to match up with the renamed API functions.
* [svn-r633] Changes since 19980828Robb Matzke1998-08-311-32/+44
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./RELEASE Updated with important changes I made since the second beta. ./src/H5A.c ./src/H5D.c ./src/H5Dprivate.h ./src/H5G.c ./src/H5Gprivate.h ./src/H5R.c ./src/H5Rprivate.h ./src/H5T.c ./src/H5Tprivate.h Any API function that used to take an `hid_t loc_id' followed by a `const char *name' can now take any type of object for the loc_id as long as the object is somehow associated with a file. Internally, H5G_loc() was modified to return an H5G_entry_t* instead of an H5G_t* so it's more general. Among other things, this allows one to retrieve information about an object like a named type or dataset without knowing the name of the type or dataset: int get_nlinks (hid_t obj) { H5G_stat_t sb; if (H5Gstat(obj, ".", TRUE, &sb)<0) return -1; return sb.nlink; } ./test/gheap.c ./test/istore.c These files needed a couple of changes because they call some of the internal functions whose H5G_t arguments changed to H5G_entry_t. ./src/H5A.c Got rid of all the switch statements for getting symbol table entries for varous objects and replaced them with a call to H5G_loc() allowing attributes to automatically apply to any type of object that belongs to a file. ./test/Makefile.in Moved the ragged array tests from the normal list of tests to the `make timings' target. ./test/ragged.c Added rewrite tests -- rewrite the rows of a dataset changing the number of rows and the length of each row. ./test/mtime.c Added a test that checks that H5Gstat() can be called with a dataset as the first argument. ./src/H5S.c Added #ifdef HAVE_PARALLEL around code to check for the HDF5_MPI_OPT_TYPES environment variable because the global variable that gets set is #ifdef'd. ./bin/release bzip2 uses .bz2 as the file extension.
* [svn-r627] Changes since 19980827Robb Matzke1998-08-281-13/+115
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./src/H5G.c Fixed a link count on groups. Groups were always created with a link count of zero instead of one. ./src/H5Gpublic.h Added H5G_NTYPES so applications can easily declare arrays which are indexed by object type. ./src/H5O.c Calling `H5O_link(&ent,0)' will succeed when the file is open for read only because it's the only way to get the object's current link count. ./tools/h5ls.c Can take non-group object names on the command line (and multiple objects). Reorganized to be more extendible. The link count is displayed for `-v'. ./src/H5F.c Dumping of cache statistics is controlled by only the HDF5_DEBUG environment variable and not the H5F_ACC_DEBUG flag for H5Fopen() and H5Fcreate() since this makes it similar to the other debugging options. ./src/H5R.c ./test/ragged.c ./test/Makefile.in Tests pass but still a little work left to be done.
* [svn-r620] Changes since 19980825Robb Matzke1998-08-271-0/+1075
---------------------- ./MANIFEST ./src/H5R.c [NEW] ./src/H5Rprivate.h [NEW] ./src/H5Rpublic.h [NEW] ./src/Makefile.in ./src/hdf5.h ./test/ragged.c [NEW] Preliminary support for 2d ragged arrays for Mark Miller and Jim Reus. Not fully implemented yet. The test is not actually part of `make test' because we still have some memory problems. ./src/H5E.c ./src/H5Epublic.h Added H5E_RAGGED as a major error number. ./bin/release Checks the MANIFEST file against `svf ls' on systems that have it. ./bin/trace Fixed a bug that caused arguments of type `void *x[]' to not be handled. ./src/H5.c Removed unused variables and changed a couple types to fix compiler warnings. Added tracing support for ragged array object ID's and arrays of pointers. ./src/H5D.c H5Dcreate() will complain if either of the property lists are invalid (instead of using the default). ./src/H5D.c ./src/H5Dprivate.h Split H5Dget_space() into an API and internal function so it can be called from the new ragged array layer. ./src/H5Fistore.c Fixed warnings about unsigned vs. signed comparisons. ./src/H5Flow.c Fixed a warning about a variable being shadowed in the MPI-IO stuff. ./src/H5Iprivate.h ./src/H5Ipublic.h Added the H5_RAGGED atom group. ./src/H5Shyper.c Fixed some freeing-free-memory errors that resulted when certain arrays were freed but the pointers were left in the data structures. I simply set the pointers to null after they were freed. ./src/H5Sprivate.h ./src/H5Sselect.c Split the H5Sselect_hyperslab() function into an API and a private function so it could be called from the ragged array layer. Added H5S_SEL_ERROR and H5S_SEL_N to the switch statements to get rid or compiler warnings. ./src/H5Tconv.c Removed a misleading comment. ./test/bittests.c Fixed a warning about a printf(). ./test/cmpd_dset.c Fixed warnings about unused variables because of test #11 being commented out. ./bin/trace Shortened the right margin for the output to allow room for the `);' at the end of the TRACE() macros.
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