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* [svn-r15549] Description:Quincey Koziol2008-08-281-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | Initial checkin of extensible array data structure prototype code and regression tests. Initial definitions for revised FUNC_ENTER/LEAVE and error reporting macros, which are being vetted in the extensible array code. Minor warning and formatting cleanups in other sections of code. Tested on: Mac OS X/32 10.5.4 (amazon) in debug mode Mac OS X/32 10.5.4 (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-r15485] Purpose: Allow library to shut down properly when objects have ↵Neil Fortner2008-08-191-3/+3
| | | | | | | | | | | | | | | | reference count > 1. Description: Added a new field 'app_count' to H5I_id_info_t struct, to track the reference count on an id due to the application. the old 'count' field tracks the total. Generally any id visible to the application gets placed in app_count. Added app_ref boolean parameter to H5I_inc_ref, H5I_dec_ref, H5I_register, H5I_clear_type, and a few other functions, to specify whether the operation(s) being performed on the id(s) are due to the application (TRUE) or not (FALSE). Test added for this case. Tested: kagiso, smirom, linew (h5committest)
* [svn-r15015] Description:Quincey Koziol2008-05-161-1/+1
| | | | | | | | | | | | | | | | | Detect chunks that are >4GB before dataset gets created and return error to application. Tweak lots of internal variables that hold the chunk size/dimensions to use an 'uint32_t', instead of a 'size_t', so that the integer size is constant. Correct a number of our tests which were creating datasets with chunks that were >4GB and add some specific tests for >4GB chunk size detection. Minor whitespace & other code cleanups. Tested on: Mac OS X/32 10.5.2 (amazon) Forthcoming testing on other platforms...
* [svn-r14916] Description:Quincey Koziol2008-05-011-2/+4
| | | | | | | | Clean up files created & cleaned up for dataset tests. Tested on: Max OS X/32 10.5.2 (amazon) Too minor to require h5committest
* [svn-r14903] Undoing change committed in r14902.Scot Breitenfeld2008-04-301-1/+2
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* [svn-r14902] Merged fortran_1_8 branch changes r14505:14901 into the trunk. ↵Scot Breitenfeld2008-04-301-2/+1
| | | | New fortran wrappers added.
* [svn-r14847] 1. test/links.c: add tests specific for windowsVailin Choi2008-04-161-1/+1
| | | | | | | | | remove HDputenv() from external_link_env() test (will add script later to set HDF5_EXT_PREFIX for running the test) modify and add more comments 2. src/H5private.h: remove #define for HDputenv() Tested on kagiso, linew and smirom.
* [svn-r14789] Add handling for external link:Vailin Choi2008-04-021-1/+2
| | | | | | | 1. src/H5F.c, src/H5system.c: formulate path for mainfile 2. src/H5Lexternal.c: add search for target file 3. configure.in: add H5_HAVE_WINDOW_PATH 4. test/links.c: add tests for external link
* [svn-r14402] Description:Quincey Koziol2008-01-131-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r14385] This checkin completely modified the test for the coordinate ↵Raymond Lu2008-01-091-2/+2
| | | | | | | | calculation of dataspace selection. It covers many cases. Tested on smirom, kagiso, and linew.
* [svn-r14354] Bug fix for #956 where the element coordinates went wrong for ↵Raymond Lu2007-12-201-1/+1
| | | | | | | | dataspace selection. Added a test for it, too. This round of checkin isn't well tarnished yet. I'll come back to work on Jan. 8. I'll revise it then. Tested it on kagiso, smirom, linew.
* [svn-r14285] Description:Quincey Koziol2007-11-241-1/+1
| | | | | | | | | | | | | | | | | | | | | | | Add H5Lvisit() API routine. Add explicit regression tests for H5Lvisit_by_name(). Correct error with visiting links when links contain loop to group already encountered. 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-r14270] Description:Albert Cheng2007-11-201-1/+1
| | | | | | | | | | Removed the stream-vfd from the basic library code. (The stream-vfd source files are not removed yet but the MANIFEST has been updated to NOT release those stream-vfd source files.) Platforms tested: Kagiso and smirom. Then test the release tar ball in kagiso.
* [svn-r14199] Description:Quincey Koziol2007-10-111-3/+3
| | | | | | | | | | | | | | | | | | | | | Add H5Dcreate to API versioned routines, replacing internal usage with H5Dcreate2 Fix thread-safe error stack initialization for API versioned error stack printing routines. 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
* [svn-r14193] Description:Quincey Koziol2007-10-081-3/+3
| | | | | | | | | | | | | | | | | | | Make H5Dopen versioned and change all internal usage to use H5Dopen2 Add simple regression test for H5Dopen1 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
* [svn-r14097] Description:Quincey Koziol2007-08-211-1/+4
| | | | | | | | | | | | | First real use of API versioning code, H5E routines switched to use new API versioning scheme. Tested on: Mac OS X/32 10.4.10 (amazon) FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (kagiso) Linux/64 2.6 (smirom) Solaris/32 5.10 (linew)
* [svn-r13858] Added sec2.h5 to the list of the files to be deleted.Raymond Lu2007-06-121-2/+2
| | | | | It's output file from big.c. Tested on smirom because it's a simple change.
* [svn-r13846] Purpose: To remove changes from version #13839 (regarding ↵Mike McGreevy2007-06-081-2/+0
| | | | | | | | DEFAULT_VFD). Description: Changes made during this checkin need to be greatly modified, so I'm removing them now rather than leaving them in and fixing them later.
* [svn-r13839] Purpose: creation of a DEFAULT_VFD macro in the ↵Mike McGreevy2007-06-071-0/+2
| | | | | | | | | | | test/Makefile. Description: a new configure flag has been created that will now set a macro in the test/Makefile. The flag is with-default-vfd=. When set to a virtual file driver (e.g. "--with-default-vfd=sec2"), the macro DEFAULT_VFD will hold this value. Tested: kagiso, smirom, linew
* [svn-r13721] Description:Quincey Koziol2007-05-011-1/+1
| | | | | | | | | | | | | Add "fail if unknown" and "mark if unknown" flags to object header messages. This gives the library a clean way to tell older libraries that a message should not be just ignored if it's unknown, but that other actions should occur. Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13588] A support of files bigger than 2GB for STDIO driver. Configure ↵Raymond Lu2007-04-041-3/+3
| | | | | | | | will check if fseeko is available. Using it instead of fseek can support big files because the offset is of type off_t not long int. Also added the test for STDIO in big.c.
* [svn-r13264] Updated Makefile.am with new THG copyright notice.Albert Cheng2007-02-071-2/+3
| | | | Ran reconfigure to generate the Makefile.in files.
* [svn-r12942] Description:Quincey Koziol2006-11-181-3/+2
| | | | | | | | | | | Fix H5Rget_name() routine with dataset region references and merge tests into getname test. Tested on: FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) AIX/32 5.? (copper)
* [svn-r12930] Description:Elena Pourmal2006-11-161-2/+3
| | | | | | | | Added new refreg_name.c file to test H5Rget_name and H5Iget_name for region references. H5Rget_name tests are skipped for now since they do not work (at least for me :-) Platforms tested: heping and copper
* [svn-r12902] Checkin of Shared Object Header Message work.James Laird2006-11-131-1/+1
| | | | | | | | | | | | This feature is still in progress; Shared Object Header Messages are not complete as a feature and are not thoroughly tested. There are still "TODO" comments in the code (comments with the word "JAMES" in them, so as not to be confused with other TODO comments). Hopefully this checkin will reduce the liklihood of conflicts as I finish implementing this feature. All current tests pass on juniper, copper (parallel), heping, kagiso, and mir.
* [svn-r12875] Description:Quincey Koziol2006-11-071-2/+2
| | | | | | | | | | Fix retrieving name for references to root group. Also, move 'ref' test earlier in testing, right after 'getname' test Tested on: Linux/64 2.6 (chicago2)
* [svn-r12850] Purpose: FeatureLeon Arber2006-11-021-2/+2
| | | | | | | Description: Test the ability to determine a path name given an object reference Tested: kagiso, sol
* [svn-r12741] Added support for direct I/O to check-vfd. The direct VFD is ↵James Laird2006-10-101-1/+5
| | | | | | | | | | only tested if it is enabled. Added Direct VFD status to the configure summary. Removed a line left over from pablo support. Oops!
* [svn-r12700] Alert:Quincey Koziol2006-10-021-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | File format is not stable, don't keep files produced! Description: First stage of checkins modifying the format of groups to support creation order. Implement "dense" storage for links in groups. Try to clarify some of the symbols for the H5L API. Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest file format options (including "dense" link storage in groups) Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation order tracking in groups (although no index on creation order yet). Remove --enable-group-revision configure flag, as file format issues are now handled in a backwardly/forwardly compatible way. Clean up lots of compiler warnings and other minor formatting issues. Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/FORTRAN & C++ Linux/64 2.4 (mir) w/enable-v1.6 compa Mac OSX/32 10.4.8 (amazon) AIX 5.3 (copper) w/parallel & FORTRAN
* [svn-r12630] Description:Quincey Koziol2006-08-261-1/+1
| | | | | | | | | | | Re-order the fheap & btree2 tests so that the btree2 test runs first, because the fractal heaps use v2 B-trees for tracking huge objects. Tested on: FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) Solaris/64 2.9 (shanti)
* [svn-r12605] Description:Quincey Koziol2006-08-211-3/+4
| | | | | | | | | | | | | Break out a bunch of the misc. routines that were in src/H5.c into more specific modules. Add optimized fletcher32 checksum routine, for checksumming metadata as well as raw data. Tested On: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2) Will test further after checkin...
* [svn-r12528] Added User-Defined links to the library.James Laird2006-08-021-8/+6
| | | | | | | | | | | | | | Users can create external links using H5L_create_external(). These links point to an object in another HDF5 file. Users can alter the behavior of external links or create new kinds of links by registering callbacks using the H5L interface. Added tests, tools support, etc. Also a number of other, minor changes have been made (some restructuring of the H5L interface, for instance). Additional documentation and examples are forthcoming.
* [svn-r12519] Fixed "make check-vfd"James Laird2006-07-311-0/+2
| | | | | | | | | | "make check-vfd" will now run all tests in the test directory with different file drivers (at least, all of those tests that use the testing framework's FAPL). Tests that fail will be skipped. This is not a perfect fix, but is better than nothing. Along with this change, check-vfd should be added to the Daily Tests.
* [svn-r12455] Purpose:Albert Cheng2006-07-061-2/+6
| | | | | | | | | | | | adjustment Description: These tests (fheap, btree2) are under development and are not used by the library yet. Move them to the end so that their failure do not block other current library code tests. Platforms tested: heping.
* [svn-r12440] Purpose:Quincey Koziol2006-06-271-1/+1
| | | | | | | | | | | Code cleanup Description: Trim trailing whitespace in Makefile.am and C/C++ source files to make diffing changes easier. Platforms tested: None necessary, whitespace only change
* [svn-r12431] Purpose:James Laird2006-06-211-1/+1
| | | | | | | | | | | | | | Configuration feature Description: 'make install' now tests both static and shared libraries if both are installed. Solution: Previously, shared libraries were only tested when static libraries were not installed. Also cleaned up line in commence.am that was including HL library in all Makefiles. Platforms tested: mir (Makefile change only)
* [svn-r12229] Purpose:Pedro Vicente Nunes2006-04-121-1/+1
| | | | | | | | | | | | | | | | | | | | | new feature Description: 1) separated the HL library into "public" and "private" header files, with the same caracteristics as the basic library 2) added the public headers to hdf5.h (with a conditional include macro, defined in configure.in) 3) added the path to HL in all Makefile.am 's , because of the inclusion in hdf5.h Solution: Platforms tested: linux 32, 64 AIX solaris with fortran and c++ (one packet table example fails) Misc. update:
* [svn-r12151] Purpose: New testRaymond Lu2006-03-241-2/+2
| | | | | | | | | | | | | Description: cross_read.c is a new program to test reading data created on an OpenVMS, a little-endian, and a big-endian machine. The three data files are vms_data.h5, be_data.h5, and le_data.h5. To generate these data files, run gen_cross.c on these machines and change the file names. Platforms tested: fuss and h5committest Misc. update: MANIFEST
* [svn-r11967] Purpose:Quincey Koziol2006-02-271-2/+2
| | | | | | | | | | | | | | | New feature Description: Check in initial "fractal heap" code, for supporting the group redesign. Also, remove some remnants of the segmented heap/block tracker/B+tree code which I didn't find during the last pass. Platforms tested: FreeBSD 4.11 (sleipnir) Mac OSX (amazon) Linux 2.4
* [svn-r11965] Purpose:Quincey Koziol2006-02-241-2/+2
| | | | | | | | | | | | Maintenance Description: Remove half-built (half-baked? :-) implementation of B+tree, block tracker and segmented heaps. (In preparation for starting the new heap coding) Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (heping)
* [svn-r11897] Purpose:John Mainzer2006-01-271-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 1) Add parallel test for metadata cache 2) Split serial test for metadata cache into two parts 3) Fix bug in which cache was flushed needlessly when the cache wasn't full. 4) Performance improvements 5) Update API for parallel cache coherency bug fix. Description: See above. Solution: See above. Platforms tested: h5committest Misc. update:
* [svn-r11712] Purpose:Quincey Koziol2005-11-151-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | New feature Description: Check in baseline for compact group revisions, which radically revises the source code for managing groups and object headers. WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! This initiates the "unstable" phase of the 1.7.x branch, leading up to the 1.8.0 release. Please test this code, but do _NOT_ keep files created with it - the format will change again before the release and you will not be able to read your old files!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! Solution: There's too many changes to really describe them all, but some of them include: - Stop abusing the H5G_entry_t structure and split it into two separate structures for non-symbol table node use within the library: H5O_loc_t for object locations in a file and H5G_name_t to store the path to an opened object. H5G_entry_t is now only used for storing symbol table entries on disk. - Retire H5G_namei() in favor of a more general mechanism for traversing group paths and issuing callbacks on objects located. This gets us out of the business of hacking H5G_namei() for new features, generally. - Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t - Lots more... Platforms tested: h5committested and maybe another dozen configurations.... :-)
* [svn-r11686] Purpose:Quincey Koziol2005-11-071-2/+3
| | | | | | | | | | | | | | | | | | | New feature Description: Add in baseline "object copy" code from Peter [in the form of a new API routine: H5Gcopy()]. There's still some work to do (like handling variable- length datatypes and possibly support for references) and it hasn't been tested on mounted files yet, but the core functionality is there and working correctly. I've also got a set of patches to update the 1.6 branch with tweaks to keep the branches mostly in sync, but Elena will kill me if I import them before the 1.6.5 release is out... :-) Platforms tested: FreeBSD 4.11 (sleipnir) h5committested
* [svn-r11601] Purpose:James Laird2005-10-241-1/+2
| | | | | | | | | | | | | | | | | Added additional targets to build-all Description: Surveyed files to find out which ones are not built. Added test/space_overflow and perform/benchpar to programs built with --enable-build-all. Discovered that tools/misc/pdb2hdf5 and tools/misc/h5import were obsolete and deleted them. Platforms tested: mir, modi4, sol Misc. update: Update of release file and removal of --enable-pdb2hdf5 to follow.
* [svn-r11590] Purpose:James Laird2005-10-201-2/+3
| | | | | | | | | | | | | | Bug fix Description: test/gen_new_fill.c used some old APIs that didn't compile with the current library. Brought it up-to-date. Some other files (test/gen_old_*) are designed to be compiled only with older versions of the library. Removed rules to try to build them in the current Makefiles. Platforms tested: mir
* [svn-r11566] Purpose:James Laird2005-10-141-0/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | Makefile bug fix Description: Previously, automake didn't output rules to build perform/mpi-perf or the test/gen_* programs. Now these can be built by typing 'make mpi-perf' (or 'make foo') or by configuring with --enable-build-all. Solution: Automake doesn't like having rules for programs it doesn't build. Tricked it by having these programs built "sometimes"--whenever the user enables --build-all. This should be used mostly for testing and to ensure that these helper programs compile. ***IMPORTANT*** These programs do *not* currently compile. When --enable-build-all is used (not the default), gen_new_fill fails because it uses an old API. This is an existing "bug" that has simply been exposed by this checkin. Platforms tested: sleipnir, modi4, sol Misc. update:
* [svn-r11411] Purpose:James Laird2005-09-131-7/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix Description: Building with --disable-static seems to have been broken on several platforms. Fixed this. Configure will now disable shared libraries automatically when using pgf90 or when building on Cygwin. Solution: To avoid errors when using shared libraries with pgf90 (which I had not realized were compiler-specific), I had manually set convenience libraries to use the -static linking flag. Apparently, this is not necessary, and caused these libraries to be created as empty archives when --disable-static was used. Also, some libraries were including other libraries, which was not necessary. I also fixed code in configure.in to correctly detect whether shared or static libraries are enabled, and moved code that disables shared libraries to before libtool is created (rather than editing libtool after the fact). Despite repeated warnings that only one shared library can be linked at a time, I have yet to have shared libraries break the linking of tests on any system. We'll see if the Daily Tests turn up anything. Platforms tested: mir (fortran, C++), sleipnir (C++), modi4 (fortran, C++, parallel), sol (fortran, C++), cygwin
* [svn-r11319] Purpose:James Laird2005-08-301-0/+1
| | | | | | | | | | | | | | | | | | | | | | | Bug fixes Description: This checkin fixes an occasional error on kelgia on sol during distclean. It also causes test scripts to depend properly on the programs they're supposed to be testing. Solution: The kelgia bug was due to some files being cleaned by automake and manually. Removed the manual cleaning in src/Makefile.am. Test script dependencies now need to be specified manually, since the makefile can't guess what they test from their name. Currently all test scripts in a given directory have a single list of dependencies--this was easy and seems to be sufficient. These dependencies are listed in the SCRIPT_DEPEND variable in the Makefile.am. Platforms tested: heping, mir, modi4, sol Misc. update:
* [svn-r11185] Purpose:James Laird2005-08-021-2/+2
| | | | | | | | | | | | | | | Makefile feature Description: 'make check-clean' now cleans *.h5 files created by tests as well as .log and .chkexe files. Solution: check-clean is now a separate target in its own right, which cleans less than mostlyclean (check-clean < mostlyclean < clean < distclean). Platforms tested: mir, heping, modi4 (serial and parallel)
* [svn-r11095] Purpose:James Laird2005-07-211-1/+3
| | | | | | | | | | | | | | | | | | | | | | Configuration feature Description: Serial test output is now stored in log files and printed when all tests in a directory complete, or when a test fails. This should make test output more readable and useful. Also made changes to clean up ii_files directories that are created by some C++ compilers/linkers. Also fixed a few minor Makefile bugs. Solution: When serial tests run, their output is saved in *.log or *.logsh. While running, tests only print when they begin and when they complete; their more specific output (from the log file) is printed if the test fails or when all tests have completed. Comments welcome. Platforms tested: mir, modi4 (parallel and serial), copper, shanti
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