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* [svn-r12820] Added fragmental copy buffer to H5FD_direct_write. This buffer ↵Raymond Lu2006-10-274-97/+141
| | | | | | | size is set through H5Pset_fapl_direct. It's been added to H5FD_direct_read in the previous checkin. Still, a test is needed at later checkin.
* [svn-r12819] Pedro Vicente Nunes2006-10-268-36/+812
| | | | | | | h5diff: print a message of "not comparable" in a case where the relative error compare is not possible, due to the denominator being zero. Modified the test file generator program to include a example for this and a new test on the shell script
* [svn-r12817] Purpose: Minor fixBinh-Minh Ribler2006-10-261-2/+1
| | | | | | | | | Description: Added (long) to a verify_val call. Platforms tested: Linux 2.6 (kagiso) - very minor, and Kent will test it on Windows, because that was where it was complained about.
* [svn-r12816] Update batch files to reflect h5diff and h5repack's changes on ↵MuQun Yang2006-10-262-3/+20
| | | | windows.
* [svn-r12815] Pedro Vicente Nunes2006-10-2585-1464/+2650
| | | | | | | | | | | | | | 1) added a new parameter to the h5diff function diff_array that contains the beginning position of the hyperslab, so that the total position in the array is printed correctly when reading by hyperslabs. 2) added a new test to h5diff that reads and diffs by hyperslabs. The test reads a 1GB dataset, from which a 1KB hyperslab was written with differences . 3) added the generation of 2 files to the generator program to test the h5diff hyperslab read. 4) changed the h5diff binary pre-generated file names to be more descriptive (e.g, instead of file1.h5, made it h5diff_basic1.h5) 5) changed the name of the h5repack options text file to info.h5repack
* [svn-r12814] MuQun Yang2006-10-251-0/+1
| | | | Add a new batch file copytest.BAT to test h5copy on windows.
* [svn-r12813] Update C++ project files to reflect the recent changes although ↵MuQun Yang2006-10-252-1/+9
| | | | compiling errors have been found.
* [svn-r12812] Add h5copy tool tests for windows.MuQun Yang2006-10-253-4/+216
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* [svn-r12811] Purpose:Albert Cheng2006-10-251-10/+44
| | | | | | | | | | | | | | | | | | | Bug fix. Description: AIX complained if some files are still open when MPI_Finalize is called, so code called _exit without calling MPI_Finalize. But in Linux hosts with MPICH, the MPI processes terminated but the launch processes got stuck waiting for those processes to end properly and they would hang on forever. As more tests ran, more processes got stuck. Solution: In order to please both AIX and MPICH, the MPI file handles are retrieved and closed outside of the HDF5 library, then call MPI_Finalize and then _exit. Tested: in heping and copper.
* [svn-r12809] Purpose:Albert Cheng2006-10-251-2/+4
| | | | | | | | | | | | | | Bug fix. Description: H5FD_get_vfd_handle() would return okay even if an VFD did not have the get_vfd_handle callback function defined. Solution: Return failure if get_vfd_handle function is not defined. Tested: in heping and copper.
* [svn-r12808] Fixed a few typos in the recent changes to support g95 that ↵Elena Pourmal2006-10-242-4/+4
| | | | | | | were exposed on Windows. Platforms tested: Those were changes to the Windows related code only; will be tested by windows daily tests.
* [svn-r12807] Need to add another dependency for windows.MuQun Yang2006-10-241-2/+2
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* [svn-r12806] Description:Quincey Koziol2006-10-246-156/+251
| | | | | | | | | | Reduce memory usage for common cases of I/O pipeline filter memory usage. Also, clean up some more code... Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12805] Description:Quincey Koziol2006-10-231-2/+2
| | | | | | | | Fix off-by-one memory error when retrieving I/O pipeline filter's name. Tested on: Linux/64 2.4 (mir) FreeBSD/32 4.11 (sleipnir)
* [svn-r12804] Missing an argument(fapl) for a routine that tests the ↵MuQun Yang2006-10-231-1/+1
| | | | | | existence of szip encoder. Windows picked this up. Tested with VS 6.0 with szip enabled.
* [svn-r12803] Description:Quincey Koziol2006-10-2329-800/+985
| | | | | | | | | | | | | | Finish new version of the I/O pipeline message, which is much smaller than the previous version. This version is used with the "use the latest version of the format" flag. Closed several memory leaks/overruns (found with valgrind). Also, lots of compiler & formatting cleanups. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12802] Description:Quincey Koziol2006-10-232-23/+27
| | | | | | | | | | Clean up code in passing... Tested on: Linux/32 2.4 (heping) Linux/64 2.4 (mir) FreeBSD/32 4.11(sleipnir) Mac OS/32 10.4.8 (amazon)
* [svn-r12801] Description:Quincey Koziol2006-10-234-340/+483
| | | | | | | | | | | | Fix several errors in the "latest version" of the object header format changes and enable the new version when requested now. Clean up several confusing or duplicated sections of code. Tested on: Linux/32 2.4 (heping) Linux/64 2.4 (mir) FreeBSD/32 4.11 (sleipnir)
* [svn-r12799] Purpose: Fixed typoBinh-Minh Ribler2006-10-221-3/+0
| | | | | | | | Description: Removed a leftover prototype. Platform tested: Linux 2.6 (kagiso) - very minor
* [svn-r12797] Purpose: Adding testBinh-Minh Ribler2006-10-221-0/+1
| | | | | | | | Description: Added trefer.cpp to c++/test. Platform tested: ran bin/chkmanifest
* [svn-r12796] Purpose: Adding testBinh-Minh Ribler2006-10-224-6/+328
| | | | | | | | | | | Description: Wrappers of H5Rcreate had incorrect prototypes. Fixed and added object reference tests. Platform tested: Linux 2.4 (heping) AIX 5.1 (copper) SunOS 5.8 64-bit (sol)
* [svn-r12795] Purpose: Fixing bugBinh-Minh Ribler2006-10-2213-142/+281
| | | | | | | | | | | | | | | | | | | | | | | | | Description: Wrappers of H5Rcreate had incorrect prototypes. Solution: Added these overloaded functions for H5Rcreate wrapper to IdComponent: void reference(void* ref, const char* name, DataSpace& dataspace, H5R_type_t ref_type = H5R_DATASET_REGION) const; void reference(void* ref, const char* name) const; void reference(void* ref, const H5std_string& name) const; Added these overloaded functions for H5Rdereference: void dereference(IdComponent& obj, void* ref); DataSet(IdComponent& obj, void* ref); Group(IdComponent& obj, void* ref); DataType(IdComponent& obj, void* ref); The incorrect wrappers will be removed after announcing. Platform tested: Linux 2.4 (heping) AIX 5.1 (copper) SunOS 5.8 64-bit (sol)
* [svn-r12794] Pedro Vicente Nunes2006-10-201-16/+4
| | | | | 1. bug fix. the h5_cleanup file names were not build properly on the h5repacktest call 2. added only a call to test_bigout.h5 to be clean, because the other files are generated anyway by the shell script. test_bigout.h5 is only made on the C program part (h5repacktst)
* [svn-r12793] 1. fix a compiling error in atlantiaPedro Vicente Nunes2006-10-206-38/+65
| | | | | 2. added the test library delete framework to delete output .h5 files 3. cleaned warnings
* [svn-r12792] Fixed a Makefile.am to clean up a test file generated by the ↵James Laird2006-10-208-892/+894
| | | | | | | | | | | Packet Table compression test. Tested that the file is removed on juniper and heping. Running reconfigure also regenerated the H5E* files (I think this means somebody updated these files but didn't run reconfigure).
* [svn-r12791] Change stattest.bat to stattest.BAT. MuQun Yang2006-10-201-1/+1
| | | | Windows is not case sensitive but Unix is.
* [svn-r12790] Add a new batch file to test h5stat.MuQun Yang2006-10-203-7/+167
| | | | | Update repacktest.bat for the new h5repack test. Update tooltest.bat to include h5stat test.
* [svn-r12789] Add a new windows test batch file(stattest.bat) to test h5stat ↵MuQun Yang2006-10-201-0/+1
| | | | on windows.
* [svn-r12788] Enable the algorithm of Direct driver to read data in fragment ↵Raymond Lu2006-10-191-36/+76
| | | | | | | | from file. If the application requests large data from file, to avoid using too much of memory for copying data from library's own aligned buffer to application's (unaligned) buffer, this step is done in fragment. The next step checkin is to handle writing data in fragment.
* [svn-r12787] Fix some references to Variable-length packet table functions.James Laird2006-10-192-0/+22
| | | | | | | For some reason, only Visual Studio DLLs complained about these. Current code compiles for me under Visual Studio and generates no related warnings on juniper.
* [svn-r12786] Pedro Vicente Nunes2006-10-191-85/+89
| | | | | a more improved usage message, specially on the filter and layout information
* [svn-r12785] Pedro Vicente Nunes2006-10-191-14/+20
| | | | added a new much more readable usage message
* [svn-r12784] Pedro Vicente Nunes2006-10-1913-291/+710
| | | | | | | | | | | | | | | | | Fixes for bugs 676, 228 676: both h5repack and h5diff use H5Dread. In the case of a "big" dataset, use read/write by hyperslabs the same way h5dump uses. An arbitrary value of 1GB was defined for "big", i.e, if the dataset is greater than 1GB, then read/write by hyperslabs 228: use the file type in read/write by default. A new switch -n was introduced if the user wants to use a native type, which was the previous use by default. Added a new test for h5repack that repacks a 1GB dataset Tested: heping (serial, parallel), sol, copper
* [svn-r12783] Took out the function H5FD_direct_alloc that was added ↵Raymond Lu2006-10-191-47/+1
| | | | | | | yesterday. This function would be redundant because the allocation function in H5FD.c H5FD_real_alloc actually has handled the aligned allocation.
* [svn-r12778] Multi file driver test fails. Elena Pourmal2006-10-191-8/+4
| | | | | | | | | | | | | | | | | Skipped until fix is found. Tested on heping with pgf90. Note: Logic was wrong; as a result, the test was bypassed for all compilers except those (like Intel) that understand !DEC compiler directive. I confirmed that the test fails on heping with pgf90. The symptoms are the same: 1.6.5 h5dump can read multi files created by fortran test, but built h5dump fails with internal error. --This line, and those below, will be ignored-- M test/fortranlib_test.f90
* [svn-r12777] Added support to aligned file space allocation. The alignment ↵Raymond Lu2006-10-181-1/+47
| | | | | | should be set through H5Pset_alignment.
* [svn-r12776] The internal change is to make the 3 parameters of ↵Raymond Lu2006-10-183-25/+213
| | | | | | | | H5Pset_fapl_direct be a structure and passed through driver info functions in H5FD_direct_open, H5FD_direct_read, and H5FD_direct_write. The external change is to add a new API function H5Pget_fapl_direct to query 3 control values, the memory boundary, file system block size, and the maximal buffer size for copying data.
* [svn-r12775] Fixed HL C++ errors from removing VL packet table. Silly me forJames Laird2006-10-183-0/+10
| | | | | | omitting the C++ test in the first place! Tested on heping (with --enable-cxx!).
* [svn-r12774] Modified flush code in the metadata cache to allow it toJohn Mainzer2006-10-1815-232/+7496
| | | | | | | | | | | | | | | | | handle flush callbacks which can dirty other entries, and resize and/or rename the target entry. This feature is needed by the fractal heap code. Also added associated test code. H5Commit tested. Test failed on heping, but the error appears to be a syntax error in an un-related file. Tests on copper & sol passed, along with tests on phoenix.
* [svn-r12773] Removed Variable-length packet tables from the HL libraries.James Laird2006-10-176-0/+18
| | | | | | | This is a quick change to make sure nothing breaks; VL functions in the header files have been #ifdef'd out. Tested on mir.
* [svn-r12772] Pedro Vicente Nunes2006-10-173-24/+173
| | | | added more tests for h5copy (compressed datasets, vl named datatypes )
* [svn-r12771] Description:Quincey Koziol2006-10-174-151/+453
| | | | | | | | | | | | | | | | | More fixes to make the I/O & memory operations more efficient when loading & flushing object header chunks. Add in concept of a chunk having a "gap" at the end - unused space that is not large enough to hold a full null message that describes it. Clean up formatting a bit. Latest version of object header format not enabled yet, still working on a few bugs... Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12770] Description:Quincey Koziol2006-10-164-375/+367
| | | | | | | | | | | | | | | Overhaul usage of object header chunks to reduce I/O operations and memory allocations. The object header prefix is now stored in the first object header chunk's "image" in memory. Also, lots of formatting cleanups. Taught h5debug tool about new object header format (which isn't enabled just yet). Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12769] Description:Quincey Koziol2006-10-161-53/+50
| | | | | | | | | | | Move object header creation past several internal possibilities for errors, making the routine more resistant to errors encountered. Also, various formatting/compiler warning cleanups. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12768] Description:Quincey Koziol2006-10-167-36/+36
| | | | | | | | | | Add 'initval' parameter to "lookup3" checksum routine (and implicitly to the metadata checksum routine), to allow chaining several checksums together easily (which isn't used by these modules, but will be used in my next checkin) Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12767] Description:Quincey Koziol2006-10-165-17/+19
| | | | | | | | Code cleanup to improve formatting & reduce compiler warnings. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12766] Made two changes to Direct I/O VFD: first added 3 parameters to ↵Raymond Lu2006-10-164-128/+176
| | | | | | | | H5Pset_fapl_direct to control memory boundary, file block size, and maximal copy buffer size; second in H5FD_direct_write and H5FD_direct_read, the library checks whether data buffer is aligned. If it is, then write and read the data directly instead of making a copy buffer.
* [svn-r12765] Description:Elena Pourmal2006-10-163-30/+30
| | | | | | | | | | Daily tests failed for Absoft f95 compiler Solution: Failure was due to several typos in H5f90prpto.h file; fixed I also removed redundant flags from the configration files. Platforms tested: heping with f95, g95, pgf90; pommier with f95
* [svn-r12764] Pedro Vicente Nunes2006-10-162-88/+134
| | | | | | | | put the H5LTcreate_compound_type function inside the #ifdef NOT_YET macro meaning that the function is not used by us
* [svn-r12763] Pedro Vicente Nunes2006-10-162-52/+8
| | | | | | | | | | | removed the function H5LTcreate_compound_type from the source directory. this function was not being used. when it was written, it was meant to be an auxiliary function to be used on the table api, but it never had an usage commented the H5LTrepack function with the #ifdef NOT_YET macro it is also not being used
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