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* [svn-r15007] Purpose: configure cleanupMike McGreevy2008-05-1511-11/+0
| | | | | | | Description: cleaning up configure related to removal of --disable-hsizet flag, which we no longer support. Tested: kagiso
* [svn-r15003] Purpose:Albert Cheng2008-05-1511-0/+165
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Improvement. Description: src/libhdf5.settings was the initial configure summary and is installed. Then configure is changed to dump a summary of the configure settings to the output and also append it to src/libhdf5.settings. That created two different output formats and duplicated information. This is the initial attempt to clean up this confusion and unify the output format. It is decided to use the src/libhdf5.settings template as the unified means. This requires more macros symbols be defined. The following symbols are all related to generating the src/libhdf5.settings file. AC_SUBST(EXTERNAL_FILTERS) AC_SUBST(MPE) MPE=no AC_SUBST(STATIC_EXEC) STATIC_EXEC=no AC_SUBST(HDF_FORTRAN) HDF_FORTRAN=no AC_SUBST(FC) HDF_FORTRAN=no AC_SUBST(HDF_CXX) HDF_CXX=no AC_SUBST(CXX) HDF_CXX=no AC_SUBST(HDF5_HL) HDF5_HL=yes AC_SUBST(GPFS) GPFS=no AC_SUBST(LINUX_LFS) LINUX_LFS=no AC_SUBST(INSTRUMENT) INSTRUMENT=no AC_SUBST(CODESTACK) CODESTACK=no AC_SUBST(HAVE_DMALLOC) HAVE_DMALLOC=no AC_SUBST(DIRECT_VFD) DIRECT_VFD=no AC_SUBST(THREADSAFE) THREADSAFE=no AC_SUBST(STATIC_SHARED) AC_SUBST(enable_shared) AC_SUBST(enable_static) AC_SUBST(UNAME_INFO) UNAME_INFO=`uname -a` The src/libhdf5.settings.in has CONDITIONAL's added to it too. The untrue conditions turned into a "#" and these lines are cleaned by the post processing script. Platform tested: h5committest on kagiso, smirom and linew.
* [svn-r14977] update comments, formattingPedro Vicente Nunes2008-05-121-5/+9
| | | | tested: windows, linux
* [svn-r14976] Support for external links follow up. The format is to print ↵Pedro Vicente Nunes2008-05-125-35/+184
| | | | | | | | | | | | | | | | | | | | | | | | | | | | the target object as part of TARGETPATH, noted with some extra indentation The previous printing of LINKCLASS 64 was removed HDF5 "textlinksrc.h5" { GROUP "/" { EXTERNAL_LINK "ext_link1" { TARGETFILE "textlinktar.h5" TARGETPATH "dset" DATASET "dset" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE { ( 6 ) / ( 6 ) } DATA { (0): 1, 2, 3, 4, 5, 6 } } } } } There is no script test for this behavior so far, because test script uses complete paths that vary from test to test, making not possible to define a valid TARGETFILE in the file tested: windows, linux, solaris
* [svn-r14937] fix typo in commentPedro Vicente Nunes2008-05-061-2/+2
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* [svn-r14935] correct an error in the usage textPedro Vicente Nunes2008-05-052-2/+2
| | | | tested: windows, linux, solaris
* [svn-r14934] Add a test for the floating point user defined printf formatPedro Vicente Nunes2008-05-056-3/+93
| | | | | | | | | | | | | | | | Usage is -m T, --format=T Where T - is a string containing the floating point format, e.g '%.3f' The test consists of writing a number with 7 fractional digits (default precision display of %f is 6 digits) and have the 7 digits displayed with -m %.7f fpformat.h5 Tested: windows, linux, solaris Note: the output file was generated in linux, it may be possible that platforms other than the ones tested have a different representation of the number
* [svn-r14933] Purpose: Updating HDF5 to use automake 1.10.1 and libtool 2.2.2Mike McGreevy2008-05-0511-171/+215
| | | | | | | | | | | | | | | | | | Description: Applying update to autotools that was applied to 1.8 a couple of weeks ago to the trunk. Updated bin/reconfigure script to reflect the new versions of libtool and automake in the /home1/packages/ directory. Rearranged configure.in script. When using libtool 2.2.2, the libtool script doesn't generate until later in the configuration process, so I had to move a test that parsed through the libtool script to a point after where it was actually being generated. Ran libtoolize on the project, and ran bin/reconfigure to regenerate configure and Makefile.in's throughout. Tested: kagiso, smirom, linew (h5committest)
* [svn-r14913] Introduced a compression ratio = uncompressed size / ↵Pedro Vicente Nunes2008-05-011-13/+15
| | | | | | | | compressed size in the printing of the compression with 3 digits of precision per hdf-forum NASA developers suggestion tested: windows, linux
* [svn-r14905] Introduced a ratio formula compression ratio = uncompressed ↵Pedro Vicente Nunes2008-05-016-12/+12
| | | | | | | | size / compressed size in the printing of the compression with 3 digits of precision per hdf-forum NASA developers suggestion tested: windows, linux, solaris
* [svn-r14903] Undoing change committed in r14902.Scot Breitenfeld2008-04-3069-1424/+2094
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* [svn-r14902] Merged fortran_1_8 branch changes r14505:14901 into the trunk. ↵Scot Breitenfeld2008-04-3069-2094/+1424
| | | | New fortran wrappers added.
* [svn-r14893] fix typo in commentPedro Vicente Nunes2008-04-291-1/+1
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* [svn-r14892] RFC display compression ratio in h5dumpPedro Vicente Nunes2008-04-296-11/+82
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Here's the current behavior of h5dump regarding the printing of the dataset creation property list For example ./h5dump -H -p -d filters HDF5 "tfilters.h5" { DATASET "deflate" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE { ( 20, 10 ) / ( 20, 10 ) } STORAGE_LAYOUT { CHUNKED ( 10, 5 ) SIZE 385 } FILTERS { COMPRESSION DEFLATE { LEVEL 9 } } FILLVALUE { FILL_TIME H5D_FILL_TIME_IFSET VALUE 0 } ALLOCATION_TIME { H5D_ALLOC_TIME_INCR } } } The proposed behavior is to add this information after SIZE SIZE 385 (51.9%COMPRESSION) That percentage is obtained trough Per = (b-a) / a Where a = theoretical size obtained by multiplying datum size times number of elements b = size obtained with H5Dget_storage_size The final print would look like HDF5 "tfilters.h5" { DATASET "deflate" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE { ( 20, 10 ) / ( 20, 10 ) } STORAGE_LAYOUT { CHUNKED ( 10, 5 ) SIZE 385 (51.9%COMPRESSION) } FILTERS { COMPRESSION DEFLATE { LEVEL 9 } } FILLVALUE { FILL_TIME H5D_FILL_TIME_IFSET VALUE 0 } ALLOCATION_TIME { H5D_ALLOC_TIME_INCR } } } tested: windows, linux, solaris
* [svn-r14792] bug fix: #1106 h5dump -b will dump ASCII values for datasets ↵Pedro Vicente Nunes2008-04-034-32/+9
| | | | | | after the first one. One variable that controls the binary output was incorrectly reset to zero after a binary output was done a first time. The effect was that on cases of several datasets, the ones after the first were not binary written. Eliminated the resetting of that variable and tested a file with several datasets. Modified the test file so that it is easier to test with the tool binread, that reads the binary output of h5dump. tested: windows, linux
* [svn-r14735] make 1.8 and 1.6 code equal or similarPedro Vicente Nunes2008-03-131-19/+22
| | | | | formatted code tested: windows, linux
* [svn-r14733] make 1.8 and 1.6 code equal or similarPedro Vicente Nunes2008-03-131-134/+134
| | | | | | formatted code bug fix: the 1.6 branch did not have a test for the existence of long double type on print_type (print name of datatype) tested: windows, linux
* [svn-r14730] make 1.8 and 1.6 code equal or similarPedro Vicente Nunes2008-03-121-678/+691
| | | | Tested: windows, linux
* [svn-r14728] make 1.8 and 1.6 code look equal or similarPedro Vicente Nunes2008-03-121-92/+125
| | | | Tested: windows, linux
* [svn-r14726] Removed unused code and make 1.8 and 1.6 code look equal or similarPedro Vicente Nunes2008-03-121-28/+37
| | | | Tested: windows, linux
* [svn-r14725] Removed unused code and make 1.8 and 1.6 code look equal or similarPedro Vicente Nunes2008-03-121-43/+1
| | | | Tested: windows, linux
* [svn-r14716] remove a commented test call that was calling for an invalid ↵Pedro Vicente Nunes2008-03-101-2/+1
| | | | | | block selection tested: linux
* [svn-r14702] 1. H5HFiblock.c: fixed problem for uninitialized "u" for bug ↵Vailin Choi2008-03-043-11/+11
| | | | | | | | | | | | #1072 in H5HF_man_iblock_size(). 2. H5HFstat.c: Since H5HF_space_size() zeroed out fs_size, add "meta_size" to store free-space size before adding to "heap_size". 3. h5stat_gentest.c: increase # of groups to get "h5stat_newgrat.h5" that contains indirect block entries in fractal heap. This is for testing the recursive part of the code in H5HF_man_iblock_size(). 4. h5stat_newgrat.h5: the new .h5 file generated by h5stat_gentest.c. 5. h5stat_newgrat.ddl: expected output from new "h5stat_newgrat.h5".
* [svn-r14700] bug fix: the function equal_double that compares double type ↵Pedro Vicente Nunes2008-03-041-69/+119
| | | | | | did not had nan logic for the cases of options -d and -p tested: windows, linux
* [svn-r14690] Description:Quincey Koziol2008-02-2810-91/+460
| | | | | | | Handle comparing datasets & attributes w/variable-length strings properly. Tested on: Linux/64 2.6.9 (chicago)
* [svn-r14671] fix typo in comments and remove unused header mentionPedro Vicente Nunes2008-02-252-11/+5
| | | | tested: linux
* [svn-r14615] this one escaped the purgePedro Vicente Nunes2008-02-191-12/+0
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* [svn-r14613] 971 (B2) h5import bug on Windows w/binary datasets. CLOSED. ↵Pedro Vicente Nunes2008-02-1939-191/+397
| | | | | | | | | | | | | | | | | | fread in windows needs a binary file to be open with "rb" instead of "r" otherwise it terminates execution if an end of file character is found on the input file. Besides that the binary file generated needs to be open with "wb" , otherwise an end of line character is read twice. DONE NOW for 1.8, already done previously for 1.6 renamed the h5import test files to have the extensions text input files = .txt binary input files = .bin configuration files = .conf hdf5 files = .h5 besides that in very test the files have the same name except extension. For example TOOLTEST txtin16.txt -c $srcdir/testfiles/txtin16.conf -o txtin16.h5 The convention for the test name is for example, for "txtin16" "txt" for text then "in16" means integer 16 size Tested: linux, solaris
* [svn-r14470] Purpose: Fixing configure problem on IRIX64.Mike McGreevy2008-01-302-4/+4
| | | | | | | | | | | | | | | Description: IRIX64 failed to build tools/h5import, as well as c++/test with szip. This is because IRIX is very picky when it comes to linking libraries, and must be done in specific order. (other UNIXes are not as such, and thus the problem wasn't present). Solution: Rearrange the order in which the libraries are linked on the compiler line by sorting the line that assigns libraries into the LDADD variable in the Makefile.am's of the two respective directories. Tested: IRIX64, kagiso, smirom
* [svn-r14437] bug fix for h5dump subsetting (deal with blocks)and new test runsPedro Vicente Nunes2008-01-167-79/+166
| | | | | | | | | | | | | | | | | | | | | | | | | add a check for block overlap after the command line parsing * Algorithm * * In a inner loop, the parameters from SSET are translated into temporary * variables so that 1 row is printed at a time (getting the coordinate indices * at each row). * We define the stride, count and block to be 1 in the row dimension to achieve * this and advance until all points are printed. * An outer loop for cases where dimensionality is greater than 2D is made. * In each iteration, the 2D block is displayed in the inner loop. The remaining * slower dimensions above the first 2 are incremented one at a time in the outer loop * * The element position is obtained from the matrix according to: * Given an index I(z,y,x) its position from the beginning of an array * of sizes A(size_z, size_y,size_x) is given by * Position of I(z,y,x) = index_z * size_y * size_x * + index_y * size_x * + index_x * tested: windows, linux
* [svn-r14420] Description:Quincey Koziol2008-01-152-2/+2
| | | | | | | | Correct the prototype for H5Sselect_elements() to take an 'hsize_t *' for the coordinates, instead of 'hsize_t **'. Tested on: Mac OS X/32 10.5.1 (amazon)
* [svn-r14414] revert the subsetting calls of h5dump to 1 size block, still a ↵Pedro Vicente Nunes2008-01-154-27/+15
| | | | | | bug with size > 1 tested: linux
* [svn-r14413] Description:Quincey Koziol2008-01-143-3/+3
| | | | | | | | | | | | | | | | | | | Change H5P[gs]et_format_bounds() => H5P[gs]et_libver_bounds() and also enumerated values H5F_FORMAT_{EARLIEST, LATEST} => H5F_LIBVER_{EARLIEST, LATEST} Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14412] more progress on the block hyperslab bug, clean code Pedro Vicente Nunes2008-01-142-18/+10
| | | | | | modified the 3D test case for subsetting with block and stride factors tested: windows, linux
* [svn-r14411] more progress on the block hyperslab bug, clean code Pedro Vicente Nunes2008-01-142-12/+10
| | | | | | | modified the 2D test case for subsetting with block and stride factors tested: windows, linux
* [svn-r14410] code cleaningPedro Vicente Nunes2008-01-141-8/+6
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* [svn-r14409] more progress on the block hyperslab bug, clean code Pedro Vicente Nunes2008-01-143-14/+28
| | | | | | modified the 1D test case for subsetting with block and stride factors tested: windows, linux
* [svn-r14408] Pedro Vicente Nunes2008-01-141-2/+9
| | | | | | | more progress on the block hyperslab bug, clean code tested: windows, linux
* [svn-r14407] more progress on the block hyperslab bug, clean code Pedro Vicente Nunes2008-01-141-10/+6
| | | | tested: windows, linux
* [svn-r14402] Description:Quincey Koziol2008-01-1311-0/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add work-around to allow reading files that were produced with a buggy earlier version of the library, which could create objects with the wrong object header message count. There is now a configure flag "--enable-strict-format-checks" which triggers a failure on reading a file with this sort of corruption (when enabled) and allows the object to be read (when disabled). The default value for the "strict-format-checks" flag is yes when the "debug" flag is enabled and no when the "debug" flag is disabled. Note that if strict format checks are disabled (allowing objects with this particular kind of corruption to be read) and the file is opened with write access, the library will re-write the object header for the corrupt object with the correct # of object header messages. This closes bugzilla bug #1010. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14397] partial fix for the block selection subsetting bug (2D case ok)Pedro Vicente Nunes2008-01-101-3/+49
| | | | tested: windows, linux
* [svn-r14384] new file with output regarding the new binary filePedro Vicente Nunes2008-01-081-0/+2
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* [svn-r14383] new binary file: with double dataset with NaN valuesPedro Vicente Nunes2008-01-081-0/+0
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* [svn-r14382] bug fix: enable NaN detection for double typePedro Vicente Nunes2008-01-082-1953/+2249
| | | | | | note: RFC at http://www.hdfgroup.uiuc.edu/RFC/HDF5/NaNs_and_HDF5/ tested: windows, linux, solaris
* [svn-r14381] comment typo fixPedro Vicente Nunes2008-01-071-1/+1
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* [svn-r14380] Eliminate old code not used and that was replaced (command line)Pedro Vicente Nunes2008-01-071-308/+73
| | | | tested: windows, linux
* [svn-r14379] add check of some values for the nbit and scale offest filters ↵Pedro Vicente Nunes2008-01-071-10/+15
| | | | | | | | on the h5repack verify function note: some sybols were made public tested: windows, linux
* [svn-r14376] moved a couple more private filter symbols to the public side, ↵Pedro Vicente Nunes2008-01-041-1/+5
| | | | | | needed by h5repack tested: windows, linux
* [svn-r14368] clean code and reshufle functions between modules, remove ↵Pedro Vicente Nunes2008-01-034-198/+141
| | | | | | unused functions tested: windows, linux
* [svn-r14366] comments grammar correctionPedro Vicente Nunes2008-01-031-6/+1
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