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* [svn-r770] H5B.c:Albert Cheng1998-10-211-1/+1
| | | | | | | | | | | | | | | | | | Replaced FAIL with H5B_INS_ERROR in routine H5B_remove_helper. Updated code that calls H5B_remove_helper with the proper code. H5Fmpio.c: Removed a typo. H5Gnode.c: Replaced FAIL with H5B_INS_ERROR in routine H5G_node_remove. H5Odtype.c: Put in proper casting to remove compiler warnings. H5S.c: Replaced FAIL with H5S_NO_CLASS in routine H5Sget_simple_extent_type. H5Sselect.c: Fixed couple typos to remove compiler warnings. Platform tested: O2K.
* [svn-r750] Put the MPIO header file inside the ifdef HAVE_PABLODan Wells1998-10-081-0/+2
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* [svn-r749] Changes for Pablo Tracing.Dan Wells1998-10-081-0/+1
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* [svn-r735] Changes since 19981002Robb Matzke1998-10-051-5/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./src/H5D.c Fill values are working for contiguous datasets now except there are two things that need more support from the data space layer, specifically the ability to form a selection from the difference of two selections. They are (1) extending an external contiguous dataset, (2) optimization by delaying the fill until after the first H5Dwrite(). Renamed H5D_allocate() to H5D_init_storage() since allocation is only part of the story. Added a data space argument so it doesn't have to query the space from the object header -- the space is always available in the caller anyway. Removed `#ifdef HAVE_PARALLEL' from a few places where it wasn't necessary. We don't need it around code that doesn't compile anything from mpi.h or mpio.h. ./src/H5Fistore.c Uncommented H5F_istore_alloc() for non-parallel and moved the `#ifdef HAVE_PARALLEL' just around Kim's barrier. ./src/H5Fmpio.c Wrapped a couple long lines. Got rid of two signed vs. unsigned comparison warnings. ./MANIFEST ./test/Makefile.in ./test/fillval.c [NEW] Added tests for fill values. The contiguous dataset extend test is disabled until H5S_SELECT_DIFF is implemented. ./tools/Makefile.in Fixed a bug where `make test' didn't build the executables first. This should cause the snapshots to start up again. ./Makefile.in Changed to build in `test' directory before `tools' directory. We want the library tests to pass before we even start considering the tools. You can still build and/or test the tools independent of the library tests passing.
* [svn-r707] Made correction to reading zeroes at end of file, in H5F_mpio_read.Robert Kim Yates1998-09-181-9/+7
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* [svn-r637] Added include H5Fmpioprivate.hRobert Kim Yates1998-08-311-0/+1
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* [svn-r632] Extended comment about elimination of redundant metadata writes.Robert Kim Yates1998-08-291-0/+7
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* [svn-r630] Added code to eliminate redundant writes of metadata,Robert Kim Yates1998-08-281-1/+80
| | | | | | so only proc 0 writes it to disk. The elimination is activated only when the environment variable HDF5_MPI_1_METAWRITE is nonzero; otherwise all processes that opened the file will write the metadata to disk.
* [svn-r623] Cosmetic change: H5F_mpio_read uses local var use_types_this_time ↵Robert Kim Yates1998-08-271-1/+1
| | | | in condition.
* [svn-r596] Added conversion to MPI datatypes.Robert Kim Yates1998-08-171-52/+210
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* [svn-r435] ./INSTALLRobb Matzke1998-06-231-1/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ./INSTALL_MAINT ./README ./RELEASE Partially updated for second alpha, but haven't updated version numbers yet. ./src/H5.c ./src/H5A.c ./src/H5AC.c ./src/H5B.c ./src/H5D.c ./src/H5F.c ./src/H5Fcore.c ./src/H5Ffamily.c ./src/H5Fistore.c ./src/H5Fmpio.c ./src/H5Fsec2.c ./src/H5Fsplit.c ./src/H5Fstdio.c ./src/H5G.c ./src/H5Gnode.c ./src/H5HG.c ./src/H5HL.c ./src/H5I.c ./src/H5MM.c ./src/H5MMprivate.h ./src/H5O.c ./src/H5Oattr.c ./src/H5Ocomp.c ./src/H5Ocont.c ./src/H5Odtype.c ./src/H5Oefl.c ./src/H5Olayout.c ./src/H5Oname.c ./src/H5Osdspace.c ./src/H5Oshared.c ./src/H5Ostab.c ./src/H5P.c ./src/H5S.c ./src/H5T.c ./src/H5Tconv.c ./src/H5detect.c ./test/hyperslab.c ./test/istore.c Changed memory allocation functions so they fail instead of dumping core. The `x' was removed from the name to remind us of that: H5MM_xmalloc() -> H5MM_malloc(), etc. H5MM_calloc() takes one argument like H5MM_malloc() instead of two like calloc() because we almost always called it with `1' for one of the arguments anyway. The only difference between the two functions is that H5MM_calloc() returns memory which is initialized to zero. ./src/H5Gent.c ./src/H5Gprivate.h Removed H5G_ent_calloc() since it wasn't used. ./src/H5Fistore.c Fixed a bug found by Albert. Thanks, Albert! This fix combined with the changes to memory allocation prevent the library from failing an assertion if the application uses an unreasonable size for chunks (like Alberts 10000x10000x4). ./src/H5MF.c ./src/H5MFprivate.h Changed H5MF_free() to H5MF_xfree() since calling it with an undefined address is allowed.
* [svn-r426] Fixed processing of debug string gotten from MPI_Info_get in ↵Robert Kim Yates1998-06-121-4/+9
| | | | H5F_mpio_open.
* [svn-r422] Added runtime debug flags for H5Fmpio routines,Robert Kim Yates1998-06-111-47/+103
| | | | | | which can be set by passing to H5Fcreate and H5Fopen a string of characters (one character for each flag to turn on) as the value of MPI_Info with key H5F_MPIO_DEBUG_KEY.
* [svn-r418] ./html/Files.htmlRobb Matzke1998-06-101-14/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ./src/H5F.c ./src/HFcore.c ./src/H5Ffamily.c ./src/H5Flow.c ./src/H5Fmpio.c ./src/H5Fprivate.h ./src/H5Fsec2.c ./src/H5Fsplit.c ./src/H5Fstdio.c ./src/H5MF.c ./src/H5P.c ./src/H5Ppublic.h Added H5Pset_alignment() so that it is now possible to align file allocation requests on application-specified boundaries. Any request >= the specified threshold will begin on an address which is a multiple of the specified alignment. Defaults are one for threshold and alignment. The alignment is done on relative addresses, so the size of the user block can affect the location of the data in the file. ./src/H5D.c ./src/dsets.c Added a test for, and fixed the data space caching bug in datasets. Extending a dataset through one handle will cause all other handles to the same dataset to get the new dataset size. ./src/H5S.c ./src/H5Sprivate.h Removed an unused argument from H5S_read() which duplicated information from the other argument. ./config/linux Made `--enable-parallel' the default on my system. It used to be that way before but then I accidently turned it off and forgot about it. ./src/H5Fmpio.c Qualified some function arguments with __unused__. Changed a couple places where NULL was returned on error for herr_t functions. ./src/H5P.c Removed unused autos from H5Pset_mpi().
* [svn-r415] Problem:Albert Cheng1998-06-101-3/+17
| | | | | | | | | | | | | H5Fmpio.c was not part of the serial distribution. The auto- dependence configuration runs for serail distribution only, thus H5Fmpio.c has no dependence. It ended up not recompiled even when header files it depends on are changed. Solution: Changed configuration to always include this file. Enclosed the whole code in a big #ifdef HAVE_PARALLEL macro so that they would be compiled for parallel distribution only. Platform tested: O2K
* [svn-r414] Problem:Albert Cheng1998-06-101-14/+25
| | | | | | | | | | | | | | Parallel File open has a racing condition if file already exists. Some processes see file exists, then truncate it (some system by remove and create). Some processes does not see the file exist, then attempt to just create it. Inconsistency. Solution: Instead of opening the file with COMM_SELF (which results in racing condition in routine that calls it), open it with the communicator in access_parms. (This assumes this access call must be called collectively.) Platform tested: O2K.
* [svn-r411] Added data-transfer-mode to various function to specify whichAlbert Cheng1998-06-071-18/+23
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r372] Removed redundant write from H5F_mpio_write.Robert Kim Yates1998-04-241-2/+3
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* [svn-r365] Problems:Albert Cheng1998-04-231-8/+0
| | | | | | | | | | | | When data is read or written out, some layers did an immediate return(SUCCEED) if number of elements to be accessed is zero. This caused problems when collective access is used. In a collective call, all processes in a communicator must call the lowest layer of MPIO routines even if some of them happen to access no date. Solutions: Eliminated all those pre-mature return if #element==0;
* [svn-r351] Removed the access_mode argument from H5Pset_mpi which was laterAlbert Cheng1998-04-171-7/+7
| | | | | | | | | | | | | | | | | used to open an HDF5 file with MPIO access. The design has changed to provide access-mode controll (independent or collective access) as an argument in the H5D read/write calls. Also removed the macros H5FACC_INDEPENDENT and H5FACC_COLLECTIVE. The original thinking was to define how a file is independent or collective access. They are replaced by the enum H5D_transfer_t with values of H5D_XFER_INDEPENDENT and H5D_XFER_COLLECTIVE. These values are used in the H5Pset_xfer to setup a data transfer property list to be used during the H5D read/write calls. The original access_mode field in the File access structure is still there. It would be removed soon once the transfer control can be passed down to the low level I/O routines.
* [svn-r342] H5F_mpio_write and H5F_mpio_read now do collective versions of MPI-IORobert Kim Yates1998-04-101-7/+40
| | | | write and read based on the value of the access_parms.
* [svn-r312] MPI_File_open now uses the comm and info as specificied inAlbert Cheng1998-03-081-3/+1
| | | | | the access_template, instead of COMM_WORLD and INFO_NULL as before.
* [svn-r290] Changes since 19980206Robb Matzke1998-02-191-36/+76
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./configure.in ./src/H5Fprivate.h ./src/H5Fsec2.c We now detect and use lseek64() on systems that have it (e.g., Irix64) and are able to generate >2GB files on Irix XFS file systems (and anything else that supports large files). This change also removed some warning messages from the Irix `-64' compiler. > $ ls -l istore.h5 > -rw-r--r-- 1 matzke meshtv 8605436856 Feb 17 14:03 istore.h5 ./configure.in ./src/H5Fprivate.h ./src/H5Fstdio.h We now detect and use fseek64() on systems that have it (e.g., Irix64) and are able to generate >2GB files on Irix XFS file systems (and anything else that supports large files). This change also removed some warning messages from the Iris `-64' compiler. ./src/H5E.c ./src/H5Epublic.h Added the H5E_OVERFLOW error to signal file address overflow. ./src/H5Fpublic.h ./examples/h5_chunk_read.c ./examples/h5_compound.c ./examples/h5_extend_write.c ./examples/h5_group.c ./examples/h5_read.c ./examples/h5_write.c ./html/Datasets.html ./html/Files.html ./html/H5.api.html ./html/H5.intro.html ./html/H5.sample_code.html ./html/ph5example.c ./html/review1.html ./test/cmpd_dset.c ./test/dsets.c ./test/extend.c ./test/tfile.c ./test/th5p.c ./test/theap.c ./test/tohdr.c ./test/tstab.c ./testpar/phdf5.c Renamed file access constants to follow the naming scheme. Also changed the base names a little to be more accurate as to what they do. The old names H5ACC_WRITE and H5ACC_OVERWRITE will temporarily work. H5ACC_DEFAULT --> H5F_ACC_RDONLY for H5Fopen() H5ACC_DEFAULT --> H5F_ACC_EXCL for H5Fcreate() H5ACC_WRITE --> H5F_ACC_RDWR H5ACC_OVERWRITE --> H5F_ACC_TRUNC Albert or Kim: The H5ACC_INDEPENDENT and H5ACC_COLLECTIVE macros in H5Fpublic.h should be an enum typedef and have names more like H5F_MPIO_INDEPENDENT and H5F_MPIO_COLLECTIVE. Also change the access_mode argument of H5Cset_mpio(). H5Fcreate() and H5Fopen() are more strict now about which flags are acceptable for the operation. ./src/H5Fprivate.h ./src/H5F.c ./src/H5C.c Changed the file access template to make it more general. A union contains a struct for each type of low-level driver and the default template is initialized at run-time. ./src/H5Fpublic.h ./src/H5F.c Added H5Fget_access_template() and cleaned up H5Fget_create_template(). ./src/H5C.c The H5Cset_mpi() no longer trashes the file access template when an error is detected. We check for errors and *then* update the file access template. Added H5C_close() so Albert and Kim have a place to release the MPI communicator and info from the file access property list. Kim or Albert: I notice in H5Cset_mpi() you copy the MPI communicator. Do you need to do something similar in H5C_copy()? ./src/H5F.c Added more error checking for the file creation and access property lists because it used to be possible to make the library dump core by swapping the creation and access property list ID numbers of H5Fcreate(). ./test/istore.c ./test/tfile.c ./test/th5p.c ./test/theap.c ./test/tohdr.c ./test/tstab.c ./testpar/testphdf5.c One must pass H5C_DEFAULT as the file creation or access property list in order to get the default property list. It is no longer possible to pass zero or any other arbitrary bad object ID. ./src/H5Fcore.c ./src/H5Ffamly.c ./src/H5Flow.c ./src/H5Fmpio.c ./src/H5Fsec2.c ./src/H5Fsplit.c ./src/H5Fstdio.c ./src/H5MF.c The file access property list is passed to all H5F_low_...() functions and to the drivers. ./src/H5Fcore.c The block size can be set at run time on a per-file basis instead of at compile time across all files. The "5000 items in a group test" now takes 1.6 seconds. ./src/H5private.h Removed inclusion of mpi.h and mpio.h since they're included from H5public.h. ./src/H5Cpublic.h ./src/H5C.c Added H5Cset_stdio(), H5Cset_sec2(), H5Cset_core(), H5Cset_split(), and H5Cset_family() in addition to the H5Cset_mpio() that Kim and Albert already wrote. We still need the H5Cget_driver() and an H5Cget...() counterpart for each of those functions. The split and family drivers still need a little work but I'm checking this in anyway.
* [svn-r234] Cleaned up conversion between MPIOffset and haddr_t in H5Fmpio.c.Robert Kim Yates1998-02-101-34/+54
| | | | In H5Fprivate.h made MPI-IO the default low-level I/O module when HAVE_PARALLEL.
* [svn-r224] Initial implementation of the upper levels of PHDF5. TheAlbert Cheng1998-02-061-8/+10
| | | | | MPIO lower interface layer (H5Fmpio.c) has been commited by Kim already. All PHDF5 codes are "bracket'ed" by #ifdef HAVE_PARALLEL macro.
* [svn-r221] In H5F_mpio_open, if truncation was requested, all processes must ↵Robert Kim Yates1998-02-051-21/+24
| | | | | | | call MPI_File_set_size (a collective operation). Also changed/added some error messages.
* [svn-r212] Fixed H5F_mpio_read's handling of number of bytes read,Robert Kim Yates1998-02-031-8/+33
| | | | | and removed MPI_Init and MPI_Finalize from H5.c (these should be done in the user program).
* [svn-r211] Added hooks for MPI-IO low-level I/O module.Robert Kim Yates1998-02-021-0/+549