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* [svn-r16324] Purpose:Mike McGreevy2009-01-151-102/+77
| | | | | | | | | | | | | | | Code Cleanup Description: - Pulled out repetitive cache stats code into its own new macro. - Converted HDasserts in cache stats macros to if / HGOTO_ERROR statments in order to keep code consistent. Tested: jam, smirom, liberty
* [svn-r16321] Purpose:Albert Cheng2009-01-141-0/+2
| | | | | | | | | | | Improvement Description: Modified the warning messages from the Version mismatch checking to suggest the users to try recompiling or checking the shared lib setting. Platforms tested: Tested in Jam only since it was just a simple text string changes.
* [svn-r16316] Added support for OpenVMS pathname for external links.Raymond Lu2009-01-143-5/+42
| | | | Tested on jam. Tested v1.8 on OpenVMS.
* [svn-r16308] Purpose: Fix problem with H5TpackNeil Fortner2009-01-141-2/+7
| | | | | | | | | Description: If a compound type was packed except for some extra space at the end, H5Tpack would not modify the type and the extra space would remain. Changed H5T_is_packed to fix this behaviour. Tested: jam, smirom (h5committest - linew down)
* [svn-r16306] Description:Quincey Koziol2009-01-149-16/+109
| | | | | | | | | | | | | | Bring r16305 back from revise_chunks branch: Add detection of C99 "designated initializers" to configure script and use new H5_HAVE_C99_DESIGNATED_INITIALIZER macro to conditionally compile default layout variables in src/H5Pdcpl.c Also, minor code cleanups, etc. Tested on: FreeBSD/32 6.3 (duty) in debug mode (Other platforms tested on branch)
* [svn-r16290] Purpose: Mike McGreevy2009-01-093-187/+702
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Adding code to maintain a min_clean_fraction in the cache in serial mode. Description: The metadata cache now has the ability to maintain a min_clean_fraction when in serial mode. The default initial cache size has been changed from 1MB to 2MB, and the default min_clean_fraction has been set at 30%. This check-in includes modifications to H5C.c to support maintaining a min_clean_size, including the addition of clean_index_size and dirty_index_size trackers, modifications to the H5C_make_space_in_cache algorithm, as well as associated test code and additional statistics tracking variables. Maintaining the min_clean_fraction addresses the possibility of experiencing a "metadata blizzard" when the cache gets completely full with dirty entries. Upon having to make space, the cache would previously need to flush every single entry in the cache before coming across a clean entry which could be evicted. This resulted in unnecessary flushing of oftentimes hot entries in the cache. Maintaining the min_clean_fraction ensures that, when space is needed, clean entries are more readily available to evict. Tested: jam, smirom, linew (h5committest)
* [svn-r16281] Purpose: Add functions to allow more flexible traversal of ↵Neil Fortner2009-01-0813-22/+318
| | | | | | | | | | | external links. Description: Added H5Pset/get_elink_cb to allow the user to specify a callback function to be called whenever an external link is traversed. Added H5Pset/get_elink_acc_flags to allow the user to specify the file access flags to use to open the target file of an external link. All these properties are set on a LAPL. Tested: jam, linew, smirom (h5committest)
* [svn-r16279] Description:Quincey Koziol2009-01-0831-494/+582
| | | | | | | | | | | | | | Bring revision 16278 back from revise_chunks branch: Update layout information in DCPL to unify all information in one underlying property and switch to using H5O_layout_t for storing it, which simplifies things considerably. Also, fix many compiler warnings. Tested on: FreeBSD/32 6.3 (duty) in debug mode (Original patch tested on many machines)
* [svn-r16223] Modified H5Dset_extent so that it fails when called for compact ↵Pedro Vicente Nunes2008-12-291-0/+14
| | | | | | | | datasets and contiguous with no external storage new test program: It adds tests for several ranks, use of fill value or not, compression, different fill value allocation times, use of different storage layouts, and external files tested: windows, linux
* [svn-r16220] Snapshot version 1.9 release 26HDF Tester2008-12-282-11/+11
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* [svn-r16214] Added HDlseek to the H5FD_core_truncate function in H5FDcore.c ↵Raymond Lu2008-12-222-1/+8
| | | | | | | | | to rewind the file pointer to the beginning of the file. Otherwise, the file might be re-extended later on Open VMS. Also updated the return value for the HDlseek to be more appropriate. Tested 1.8 on Open VMS.
* [svn-r16209] Purpose:Choonghwan Lee2008-12-193-6/+10
| | | | | | | | | | | | | | Bug fix (#1357) Description: Three filters have not assigned correct value to one value-result argument, "buf_size". N-bit, szip, and scale offset filter have had this problem. However, I don't think this problem has been making buffer overrun because those filters were informing the caller that the "buf", another value-result argument, is smaller than it actually is. If there was actual buffer overrun, I believe another problem exists although I don't know. Tested: jam, smirom, linew Although all test were passed, I'm concerned about valgrind memcheck error. There can be another miscommunication between filter and the caller.
* [svn-r16204] Description:Quincey Koziol2008-12-185-258/+301
| | | | | | | | | | | | | | | | | | | | | Moved v1 B-tree debugging routines into separate module and thinned out header files a bit. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r16202] Added HDlseek in front of the truncate function in ↵Raymond Lu2008-12-151-1/+7
| | | | | | | | | H5FD_sec2_truncate for VMS only. On Open VMS, if the last read or write put the file pointer beyond the current file size (it happens when an object is deleted), the file can be extended when it's truncated. Tested v1.8 on VMS.
* [svn-r16194] Purpose:Mike McGreevy2008-12-151-26/+4
| | | | | | | | | | | | | | | | | | | | | | | Bug Fix Description: Resolved issues with broken sanity checks that were failing when the 'b2' debugging package was enabled (v2 b-tree debugging): - Fixed outdated assertions that would not compile. They now compile and function correctly. - Removed too far outdated assertions that would require too much unnecessary refactoring of code in order to satisfy their initial purpose. - Re-enabled b2 debugging package when "--enable-debug=all" is specified on the configure line. Tested: jam, smirom, linew
* [svn-r16187] Description:Quincey Koziol2008-12-113-4/+4
| | | | | | | Change a few more "istore" references in comments to "chunk" or "btree". Tested on: None, just comments
* [svn-r16182] Description:Quincey Koziol2008-12-1114-399/+394
| | | | | | | | | | | | | | | | | | | | | | Rename internal routines, variables, macros, typedefs, etc. for chunked dataset storage from "istore" to some variant of "chunk" or "btree". Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r16180] Description:Quincey Koziol2008-12-113-5/+5
| | | | | | | | | | Rename the current chunk indexing routines module for B-tree indices to better reflect their purpose, and to make the upcoming extensible array index module fit in better. Tested: FreeBSD/32 6.3 Too minor to require h5committest
* [svn-r16179] Description:Quincey Koziol2008-12-111-2/+2
| | | | | | | | Use the H5F_KVALUE macro in a couple more places, to make the code easier to read. Tested on: Mac OS X only (very minor)
* [svn-r16176] Remove terminal whitespace in links.c, H5Lexternal.c, H5Pfapl.cNeil Fortner2008-12-092-7/+7
| | | | Tested: jam
* [svn-r16150] Change a call to H5FL_fac_free to H5FL_FAC_FREE so it works ↵Neil Fortner2008-12-021-1/+1
| | | | | | | | correctly when free lists are disabled. Tested: jam
* [svn-r16144] Removed the check of H5Dset_extent for the space to be ↵Pedro Vicente Nunes2008-12-011-4/+1
| | | | | | chunked, since external datasets can be extended Tested: windows, linux
* [svn-r16142] Added a check to H5Dset_extent for the space to be chunked, ↵Pedro Vicente Nunes2008-12-011-8/+11
| | | | | | | | exit with error otherwise A call to H5Dset_extent in the external test was removed Tested: windows, linux
* [svn-r16138] Snapshot version 1.9 release 25HDF Tester2008-11-302-3/+3
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* [svn-r16137] Description:Quincey Koziol2008-11-2816-144/+1089
| | | | | | | | | | | | | | | | | | | | | | | | | | Add support for paging large data blocks to extensible arrays Clean up allocation/destroy code for extensible array index, super and data blocks Add a couple of routines to set/get bit values in memory buffers Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r16132] some chunks were not deleted for some cases, the comparison to ↵Pedro Vicente Nunes2008-11-251-1/+1
| | | | | | | | | | check for chunk offsets outside of the new dimensions was chunk_offset[ i ] > dimension [ i ] and it must be chunk_offset[ i ] >= dimension [ i ] tested: windows, linux
* [svn-r16121] Snapshot version 1.9 release 24HDF Tester2008-11-232-3/+3
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* [svn-r16094] Description:Quincey Koziol2008-11-185-47/+121
| | | | | | | | | | | | | | | | | | | | | | Add initial support for data block 'page init' bitmasks to super blocks. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r16093] Description:Quincey Koziol2008-11-186-12/+42
| | | | | | | | | | | | | | | | | | | | | | | | Initial changes to allow data blocks to be paged in, instead of loaded completely. Also, refactored test code to be smaller and more maintainable. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r16082] Purpose: Fix a problem in the file unmounting codeNeil Fortner2008-11-171-5/+13
| | | | | | | | | Description: Fixes a problem in H5F_close_mounts where it wouldn't correctly reshape the "child" array when unmounting files. Test added for this case. Also fixed a potential bug in H5F_unmount where that routine reshapes the child array. Tested: kagiso linew smirom (h5committest)
* [svn-r16078] Snapshot version 1.9 release 23HDF Tester2008-11-163-3/+5
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* [svn-r16062] Purpose: Allow per-dataset rdcc configurationNeil Fortner2008-11-1227-117/+514
| | | | | | | | Description: Adds 3 new public functions: H5Pset_chunk_cache, H5Pget_chunk_cache, and H5Dget_access_list. First implementation of dataset access properties. See RFC_chunk_cache_functions for details. Tested: kagiso, linew, smirom (h5committest)
* [svn-r16061] Description:Quincey Koziol2008-11-116-4/+71
| | | | | | | | | | | | | | | | | | | | | | | Store extra information about each block in the metadata for the block, in the hope that a corrupted file will be easier to recover. (Similar to the information stored for fractal heaps) Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r16060] Description:Quincey Koziol2008-11-115-8/+2
| | | | | | | | | | | | | | | | | | | | | Remove unused field from direct block struct. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r16044] Snapshot version 1.9 release 22HDF Tester2008-11-093-3/+4
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* [svn-r16036] Purpose: add H5Iis_valid functionNeil Fortner2008-11-052-0/+48
| | | | | | | | | Description: H5Iis_valid function added. This function checks if the id is valid (i.e. it is currently registered and visible to the application), and returns TRUE if it is valid, or FALSE otherwise. It should never return an error. Tested: kagiso, linew, smirom (h5committest)
* [svn-r16020] Purpose: Fix behaviour of H5OvisitNeil Fortner2008-11-031-0/+4
| | | | | | | Description: H5Ovisit and H5Ovisit by name will now check for a positive return value from the first callback. Test added for this case. Tested: kagiso
* [svn-r16018] Snapshot version 1.9 release 21HDF Tester2008-11-022-3/+3
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* [svn-r16006] Modify the commit of r15943 for H5_USE_16_API. Let H5version.h ↵Raymond Lu2008-10-302-5/+9
| | | | | | check if H5_USE_16_API_DEFAULT is defined by the configure. Then define H5_USE_16_API and use it throughout. Tested on kagiso - supposed to be simple.
* [svn-r15997] Merge from 1.8Pedro Vicente Nunes2008-10-301-0/+6
| | | | | | Added a definition of HDftruncate for windows to compile with VC6 and later versions Tested: windows
* [svn-r15983] Description:Quincey Koziol2008-10-281-2/+2
| | | | | | | Remove redundant check for 1.6 default API. Tested on: Eyeballed - very trivial
* [svn-r15968] Correct some minor syntax errors in the checkin #15943.Raymond Lu2008-10-271-3/+3
| | | | Tested with h5committest.
* [svn-r15953] Snapshot version 1.9 release 20HDF Tester2008-10-263-6/+6
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* [svn-r15952] Fix Bug 1300.Albert Cheng2008-10-261-26/+21
| | | | | | | Removed duplicated information due to previous incompleted changes. Also rearranged the entries to a more logical combinations. Tested: h5committest.
* [svn-r15943] Changed the library's macros H5_USE_16_API to ↵Raymond Lu2008-10-243-8/+8
| | | | | | | | | H5_USE_16_API_DEFAULT avoid possible conflict wi th user's definition of H5_USE_16_API. The H5_USE_16_API_DEFAULT is defined through configure with the flag --with-default-api-version=v16. Tested with h5committest.
* [svn-r15942] Purpose: Bug Fixes and Libtool UpgradeMike McGreevy2008-10-241-6/+6
| | | | | | | | | | | | | | | | | | Description: - Remove need to set LD_LIBRARY_PATH when using shared szip library. - Libtool 2.2.6a is now used to generate libraries. - 'make check install' dependency bug is fixed, and should no longer break the build. - removed hard coding of shell in config/commence.am, as this causes problems on Solaris with the new version of libtool. - RELEASE.txt with appropriate changes. Tested: - kagiso, smirom, linew (merged from 1.8, pretty quick tests)
* [svn-r15941] Purpose: Close bug 1305.Neil Fortner2008-10-241-4/+182
| | | | | | | | | Description: Added a new function, H5O_alloc_shrink_chunk, which removes all null messages from a chunk and shrinks the chunk appropriately. Modified H5O_merge_null to call this function when a null message is created with a size >= 64k. Tests added for this functionality. Tested: kagiso (h5committest on 1.8 version)
* [svn-r15937] Description:Quincey Koziol2008-10-231-45/+46
| | | | | | | | | | | | | | | | | | | | | | Correct error in metadata accumulator code which wasn't expanding the metadata accumulator when adjoining (but not overlapping) I/O writes occurred. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (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/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15868] Description:Quincey Koziol2008-10-152-2/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | Correct a minor error in file free space allocation which was affecting the 'multi' VFD and preventing some tests from fully working with it. Wholesale revisitation of all the places where tests were disabled with various VFDs and remove or correct all these so that _only_ the tests which _really_ can't work with particular VFDs are skipped during a 'make check-vfd' test. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (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/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15861] Description:Quincey Koziol2008-10-1417-176/+296
| | | | | | | | | | | | | | | | | | | | | | | | Various bug fixes & cleanups with VFDs and file free space changes, along with cleaning up compiler warnings. Enable more VFDs (for 'make check-vfd' testing) for many tests. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (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/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
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