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* [svn-r18678] Just mopped up some looseends by using the macro HDxyz instead ↵Albert Cheng2010-04-291-7/+7
| | | | | | | | the xyz function names. Tested: Jam only since this is trivial.
* [svn-r18661] Description:Quincey Koziol2010-04-282-122/+105
| | | | | | | | | Tweak H5detect to be even more careful about its actions, to allow gcc 4.5 to use '-O3'. Also, minor code cleanups in H5Tfloat.c Tested on: FreeBSD/64 6.3 (liberty) w/gcc 4.5 & production mode (h5committest not necessary/appropriate)
* [svn-r18658] Bug: 1764Albert Cheng2010-04-282-65/+203
| | | | | | | | | | | | | | | | | | | | | | | | Description: longjmp do not necessary restore signal that is blocked during the signal handling. This caused the Alignment test to fail quietly, resulting in wrong alignment information which will cause failures later. Solution: One can use sigsetjmp/siglongjmp to restore signal handling but not all systems such as Cray XT or VMS supports sigsetjmp. Backup solution is to use sigprocmask to reset the signal. Again, some systems may not support it either. Added code to try the first and then the second solution. Also added tests to verify if the signal_handler routines are working properly. Finally, added code to print results of the verification (in form of comments) to H5Tinit.c for inspection in case of failure. (Note that many platforms do not have alignment limits at all and ALIGNMNET code never raise the SIGBUS or SIGSEGV errors. In those cases, it does not matter whether the signal handlers work or not. Again, this can be deduced from the results comments near the end of the H5Tinit.c. If the sum of signal handlers called equals the total of verify, it means ALIGNMENT does not raise any signals.) Tested: htcommittested (linew is not accessible), jam(serial), Redstorm.
* [svn-r18656] I added some more comments. No test is needed.Raymond Lu2010-04-281-2/+18
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* [svn-r18653] Bug 1741:Allen Byrne2010-04-281-1/+3
| | | | | | | | Added check in H5Rcreate for space_id = -1 and is region reference type. Added test of H5R package API parameters to testhdf5 test, these test only the public API parameter checks. Tested: local linux
* [svn-r18652] Description:Quincey Koziol2010-04-2723-41/+78
| | | | | | | | | | | | Bring r18650 from trunk to 1.8 branch: Bring back various minor tweaks & cleanups from the revise_chunks branch. Tested on: FreeBSD/32 6.3 (duty) in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode (h5committested on trunk)
* [svn-r18646] In H5T_get_native_type of H5Tnative.c, I changed the way that ↵Raymond Lu2010-04-272-7/+11
| | | | | | | | | the offset, alignment, and size of nested compound type are calculated by using H5T_cmp_offset. The old way had a bug in it (see bug #1850). Tested on amani, linew, and jam.
* [svn-r18635] Description:Quincey Koziol2010-04-2711-43/+352
| | | | | | | | | | | Bring r18634 from trunk to 1.8 branch: Clean up compiler warnings. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode (h5committested on trunk)
* [svn-r18631] Description:Quincey Koziol2010-04-271-336/+419
| | | | | | | | | | | | | Bring r18630 from trunk to 1.8 branch: Fix remaining aliasing problems and enable optimizations w/gcc now. This addresses the remaining issues for Bug#1398. Tested on: Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode (h5committested on trunk)
* [svn-r18628] Description:Quincey Koziol2010-04-251-16/+8
| | | | | | | | | | | | Bring r18627 from trunk to 1.8 branch: More progress toward addressing Bz#1398: add 'volatile' keyword to floating- point types when detecting their properties. Also, minor code formatting cleanups. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug) (h5committested on trunk)
* [svn-r18626] Description:Quincey Koziol2010-04-233-602/+610
| | | | | | | | | | | Bring r18625 from trunk to 1.8 branch: Checkpoint progress on Bz#1398 - strict aliasing issues. (Lots of compiler warnings & code cleanups also) Tested on: Mac OS X/32 10.6.3 (amazon) in debug mode (h5committested on trunk)
* [svn-r18622] Description:Quincey Koziol2010-04-237-62/+336
| | | | | | | | | | Bring r18621 from trunk to 1.8 branch: Clean up compiler warnings. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor to require h5committest)
* [svn-r18619] Description:Quincey Koziol2010-04-229-219/+401
| | | | | | | | | | | | | | | | | Bring r18618 from trunk to 1.8 branch: Add new internal object header routines to query the header chunk that a message is in, and to lock/unlock a message into a chunk (so it doesn't get moved into another chunk during allocation/free events). Also, move dataspace message to beginning of object header messages added to a dataset's object header, so it can be locked into chunk #0 (when performing SWMR operations). Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode (h5committested on trunk)
* [svn-r18617] Description:Quincey Koziol2010-04-2223-50/+122
| | | | | | | | | | Bring r18616 from trunk to 1.8 branch: Clean up compiler warnings. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor to require h5committest)
* [svn-r18613] Description:Quincey Koziol2010-04-223-1886/+2079
| | | | | | | | | | Bring r18612 from trunk to 1.8 branch: Clean up compiler warnings & code formatting Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor to require h5committest)
* [svn-r18611] Description:Quincey Koziol2010-04-222-119/+121
| | | | | | | | | | Bring r18610 from trunk to 1.8 branch: Clean up compiler warnings & code formatting issues. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug) (too minor to require h5committest)
* [svn-r18609] Description:Quincey Koziol2010-04-224-54/+65
| | | | | | | | | | | Bring r18608 from trunk to 1.8 branch: Simplify object header allocation routines, and clean up some compiler warnings. Tested on: FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode (h5committested on trunk)
* [svn-r18602] Description:Quincey Koziol2010-04-206-31/+37
| | | | | | | | | | | | Bring r18600 from trunk to 1.8 branch: Increment reference count on object header when "fake" object header chunk proxy is returned from H5O_chunk_protect(). Also, clean up the interface to H5O_chunk_unprotect by removing the unnecessary 'oh' parameter. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (h5committested on trunk)
* [svn-r18598] Description:Quincey Koziol2010-04-201-2/+2
| | | | | | | | Fix missing NULL initialization of pointers. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (h5committested on trunk)
* [svn-r18596] Description:Quincey Koziol2010-04-2047-326/+596
| | | | | | | | | | Bring r18595 from trunk to 1.8 branch: Clean up compiler warnings Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor to require h5committest)
* [svn-r18591] Snapshot version 1.8 release 4 (snap19)HDF Tester2010-04-191-2/+2
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* [svn-r18580] Purpose:Mike McGreevy2010-04-152-20/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Autotool Upgrade / Libtool Bug Fix Description: Updated autotools referenced in bin/reconfigure as follows: Autoconf 2.64 --> Autoconf 2.65 Automake 1.11 --> Automake 1.11.1 Libtool 2.2.6a --> Libtool 2.2.6b-mcg The referenced libtool version is a custom version of 2.2.6b. It has been tweaked to fix a bug in libtool that occurs when using PGI 10.0 compilers. A check incorrectly categorizes the C++ compiler as version 1.0 instead of 10.0, and the link line is subsequently set up incorrectly and fails to compile. A patch has been made available and will be included in the next release of libtool, but in the meantime I've applied the patch to a custom installation as indicated above. This bin/reconfigure now references the custom installation, and the resulting configure script will correctly categorize the PGI 10.0 C++ compiler. Ran bin/reconfigure to regenerate configure and makefiles. Tested: jam and amani with PGI 10.0 compilers. h5committest
* [svn-r18574] Description:Quincey Koziol2010-04-1529-1063/+2604
| | | | | | | | | | | | | | | | | | | | | | | Bring r18571 from trunk to 1.8 branch: Bring r18542 from metadata journaling "merging" branch to trunk: Bring new object header pin/unpin & protect/unprotect routines and split-out object header chunk proxy changes from metadata_journaling branch to "merging" branch, along with some other minor tweaks to clean up compiler warnings, etc. Also: clean up chunk protect/unprotect calls when allocating or freeing space in a chunk, optimize metadata accumulator code to avoid some re-reading of information from the file, refactor H5O_pin/H5O_unpin from way they are done on the merging branch back to way they were previously done on trunk, other minor code cleanups, etc. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode (h5committested on trunk)
* [svn-r18568] Purpose: Fix error in call to memmove() in H5B_remove_helper. ↵Neil Fortner2010-04-151-1/+1
| | | | | | | | This error was only reproducible through the use of electric fence. Tested: Fedora (too minor for h5committest)
* [svn-r18566] Description:Quincey Koziol2010-04-158-64/+116
| | | | | | | | | Bring r18564 & r18565 from trunk to 1.8 branch: clean up compiler warnings and whitespace issues. Tested on: Mac OS X/32 10.6.3 (amazon) (too minor to require h5committest)
* [svn-r18550] Description:Quincey Koziol2010-04-131-1/+1
| | | | | | | | | | Bring r18548 from trunk to 1.8 branch: Minor cleanups to compile with PGI C compiler 10.x. Tested on: Mac OS X/32 10.6.3 (amazon) (tested on trunk)
* [svn-r18546] Snapshot version 1.8 release 4 (snap18)HDF Tester2010-04-121-2/+2
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* [svn-r18544] Description:Mike McGreevy2010-04-101-2/+13
| | | | | | | | Allow 'save returned ID structures' mechanism to be toggled per ID type. Also added initialization of new fields omitted in a previous commit. Tested: h5committest, and full check-vfd on linew, amani, and jam.
* [svn-r18536] Purpose: Fix bug 1815Neil Fortner2010-04-082-37/+48
| | | | | | | | | | | Description: Attempting to copy an object with NULL references (all bytes zero) with the H5O_COPY_EXPAND_REFERENCE_FLAG flag set would cause a failure or an assertion (depending on whether it was in debug mode). Changed copy routine to detect NULL references (object and region) and avoid attempting to expand the reference in this case. Tested: jam, linew, amani (h5committest)
* [svn-r18526] Description:Quincey Koziol2010-04-064-56/+80
| | | | | | | | | | | | | | Bring r18525 from trunk to 1.8 branch: Bring r18523 from metadata journaling "merging" branch to trunk: Bring metadata journaling branch into closer correspondence with trunk: extract data structure freeing routines from metadata cache client 'destroy' callbacks. Tested on: FreeBSD/32 6.3 (duty) in debug mode (h5committested on trunk)
* [svn-r18521] Description:Quincey Koziol2010-04-065-37/+83
| | | | | | | | | | | | | Bring r18520 from trunk to 1.8 branch: Bring r18519 from metadata journaling "merging" branch to trunk: Converge metadata_journaling branch and trunk: separate destroy routines for data structures from cache callbacks. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode (h5committested on trunk)
* [svn-r18515] Bug:Albert Cheng2010-04-051-1/+1
| | | | | | | | | | | | | | | | PGI v10.2 in Red Storm Qual complained about the H5_IS_API macro with the following message when -Mbounds is used: PGC-S-0053-Illegal use of void type The compiler did not like to treat the literal strings as arrays. The -Mbounds option is used when --disable-production is used. Solution: Casted all the literal to (char *). Tested: h5committest passed. Red Storm Qual passed with the fixed H5_IS_API macro though it has other failures later. Will be fixed in another batch.
* [svn-r18507] Purpose:Mike McGreevy2010-04-021-10/+66
| | | | | | | | | | | | | | | | | | | | Fix Bug 1730 (in 1.8) Description: This is a fix for Bug 1730. Note that this fix is only going into 1.8, as there is a more desired fix prepared for the trunk, but we don't want that one in 1.8 for compatibility reasons. This change adds a mechanism to the H5I interface to save returned ID structures for immediate re-use if needed. This addresses a potential performance issue by delaying the case when the next ID to be registered has grown so large that it wraps around and needs to be checked to see if it is available for distribution again. Tested: h5committest, and manually on jam, amani, liberty, others.
* [svn-r18506] Description:Quincey Koziol2010-04-023-8/+42
| | | | | | | | | | | Bring r18505 from trunk to 1.8 branch: Move code to free superblock data structure into separate routine, in preparation for upcoming metadata journaling -> trunk merging. Tested on: FreeBD/32 6.3 (duty) w/debug (h5committested on trunk)
* [svn-r18503] Description:Quincey Koziol2010-04-025-55/+88
| | | | | | | | | | | | | Bring r18502 from trunk to 1.8 branch: Bring r18501 from metadata journaling "merging" branch to trunk: Extract data structure 'destroy' routines from metadata cache client 'destroy' callbacks. Tested on: FreeBSD/32 6.3 (duty) w/debug (h5committested on trunk)
* [svn-r18499] Description:Quincey Koziol2010-04-028-58/+167
| | | | | | | | | | | | | Bring r18498 from trunk to 1.8 branch: Bring r18497 from metadata journaling "merging" branch to trunk: Extract data structure 'destroy' routines from metadata cache client 'destroy' callbacks. Tested on: FreeBSD/32 6.3 (duty) w/debug (h5committested on trunk)
* [svn-r18495] Description:Quincey Koziol2010-04-0212-218/+372
| | | | | | | | | | | | | Bring r18494 from trunk to 1.8 branch: Bring r18491 from metadata journaling "merging" branch to trunk: Extract data structure 'destroy' routines from metadata cache client 'destroy' callbacks. Tested on: FreeBSD/32 6.3 (duty) w/debug (h5committested on trunk)
* [svn-r18493] Bug fix:Albert Cheng2010-04-015-89/+102
| | | | | | | | | | | | | | | | | Testlibinfo.sh failed again. Solution: Removed the const from H5libhdf5_settings definition, again. Revamp the whole setting so that H5lib_settings.c is compiled individually, just like H5Tinit.c. Hope this will take care of the problem once for all. Tested: Amani using --disable-shared with --enable and --disable-embedded-libinfo. Will test this on the AIX platform after commit (cannot run bin/reconfigure in the AIX platform and it is too clumsy to try to ssh files back and forth and incurred "svn merge inconsistency" later too. Pretty confident this fix should work in all other platforms.
* [svn-r18485] Description:Quincey Koziol2010-04-015-24/+1
| | | | | | | | | | | | Bring r18484 from trunk to 1.8 branch: Bring r18483 from metadata journaling 'merging' branch to trunk: Remove unused symbol table entry dirty flag Tested on: FreeBSD/32 6.3 (duty) w/debug (h5committested on trunk)
* [svn-r18470] bug fix:Albert Cheng2010-03-305-11/+15
| | | | | | | | | | | | | recent changes to the embedded library generation code does not quite work for the AIX system. The strings command of AIX does not display the embedded library information be default. Solution: Changed the H5libhhdf5_setting[] to be an extern variable. Also removed the const qualifier so that strings can see the variable data. Tested: Blue-print (with embedded-libinfo enabled and disabled).
* [svn-r18467] Snapshot version 1.8 release 4 (snap17)HDF Tester2010-03-291-2/+2
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* [svn-r18461] Description:Quincey Koziol2010-03-2622-628/+548
| | | | | | | | | | | | | | | | | | | | | Bring r18460 from trunk to 1.8 branch: Fold metadata journaling changes into the trunk: mostly tweaky small stuff, also removed the H5F_t* field from the H5G_entry_t struct. Tested on: 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/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) 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 debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r18446] Purpose: Fix bug 1637Neil Fortner2010-03-248-133/+197
| | | | | | | | | | Description: Modified algorithm for extending a dataset with early allocation so it only deals with the new chunks. Formerly, it would loop over all chunks, checking to see if each existed in cache and on disk, causing major performance issues with large numbers of chunks. Tested: jam, linew, amani (h5committest)
* [svn-r18434] Snapshot version 1.8 release 4 (snap16)HDF Tester2010-03-221-2/+2
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* [svn-r18422] Description:Quincey Koziol2010-03-186-106/+323
| | | | | | | | | | | | | | | | | | | | | | | Bring r18413:18420 from trunk to 1.8 branch: - unify srcdir query, etc. - Move libhdf5.settings string out of H5Tinit.c Tested on: 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/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) 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 debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r18408] Snapshot version 1.8 release 4 (snap15)HDF Tester2010-03-151-2/+2
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* [svn-r18396] Purpose: Fix links.c failureNeil Fortner2010-03-091-18/+107
| | | | | | | | | | | | | | | | Description: The core file driver previously matched files only based on the name used to open them, even when a backing store is used. This caused problems in the failing test when it traversed an external link to itself, and did not recognize that it was the same file. Similar tests in links.c were skipped when the core file driver was used. The failure was previously masked by inappropriate file flushes caused by external link traversal. Added code to the core file driver to keep track of low level file information of the backings store to allow for accurate recognition of duplicate files. Also re-enabled all links.c tests for the core file driver. Tested: Fedora (core and sec2 drivers; no time for full commit test, will monitor daily tests)
* [svn-r18389] Description:Quincey Koziol2010-03-064-71/+88
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r18388 from trunk back to 1.8 branch: Bring changes from Coverity session from branch into trunk: r18378: Fixed coverity issues 207 and 322. Pointer hdr was checked for NULL after being asserted and dereferenced. Check was removed. r18379: Fix coverity issues # 88 and # 435. r18380: Fixed Coverity issue # 85. Added check of returned pointer for NULL before use. r18381: Resolve coverity issues # 214 and # 215 r18382: Issue 131: Add null checks to allocations and check for free in error handling r18383: Issue 421: Reorganized code to make intention clearer. Also, set local variable fl to NULL after transfer to tail. Heap->freelist will take care of all allocations r18384: Coverity #249 and #250 - STRING_ATT_CHECK wasn't allocated before being used and freed in function test_write_vl_string_attribute and test_read_vl_string_attribute. Tested on: Mac OS X/32 10.6.2 (amazon) w/debug & prod (h5committested in daily tests)
* [svn-r18386] Description:Quincey Koziol2010-03-061-11/+17
| | | | | | | | | | Bring r18385 from trunk to 1.8 branch: Tweak fix in r18372 to reset other messages read in also. Tested on: Mac OS X/32 10.6.2 (amazon) w/debug & production (too minor to require h5committest)
* [svn-r18377] Purpose: Fix bug 1733Neil Fortner2010-03-054-44/+79
| | | | | | | | | Description: Support for expanding external links was not implemented in H5Ocopy, even though a flag existed for H5Pset_copy_object to enable this. This patch implements this feature. Tested: jam, amani, linew (h5committest); Fedora
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