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* [svn-r18029] Description:Quincey Koziol2009-12-171-1/+1
| | | | | | | | Code cleanups & tweaks to converge branch toward trunk. Tested on: Mac OS X/32 10.6.2 (amazon) debug & production (h5committest not required on this branch)
* [svn-r17028] Added binary journal file support and related tests.John Mainzer2009-06-115-656/+3768
| | | | | | | | | Removed a bunch of debug code. Other minor changes. Did only limited testing -- just build and test on Phoenix (AMD64 linux with debug).
* [svn-r16726] Fix for the source dir build bug that Quincey discovered.John Mainzer2009-04-101-2/+2
| | | | Tested only on Phoenix -- serial source dir and in place builds.
* [svn-r16714] Description:Quincey Koziol2009-04-082-7/+5
| | | | | | | | | | Clean up code, remove unused variables, remove "naked" printf()s, make h5recover test script work in 'srcdir' build, etc. (The h5recover tests are failing still and the script prints "PASSED" when it doesn't, but we'll work on that more next) Tested on: Mac OS X/32 10.5.6 (amazon)
* [svn-r16670] Interrim checkin of journal file modifications supporting ↵John Mainzer2009-04-04159-37/+8253
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | recognition and rejection of attempts to apply the wrong journal file to a corrupt HDF5 file. Specifically, I made the following changes: 1) Moved all journaling data into the journaling in progress superblock extension message. 2) Added a "magic number" to the journaling in progress message, with the same "magic number being added to the header of the associated journal file. 3) Modifications to library test code to support the above. 4) Modified h5recover to examine the supplied hdf5 file, determine if it is in fact a HDF5 file, if so determine if it is marked as having journaling in progress, and if it does, extract the contents of the journaling in progress super block extension message. 5) Modified h5recover to examine the supplied journal file, determine if it is in fact a HDF5 journal file, and if so, extract the data from its header. 6) Modified h5recover to refuse to apply the supplied journal file to the supplied HDF5 file unless the "magic numbers" obtained from these files matches. 7) Added an examine option to h5recover that causes it to examine and report on the supplied files, but do nothing. This option exists primarily to facilitate testing, but I expect that some users will find it useful as well. 8) Added test code to exercise items 4-7. Note that while I have tried to cover the more likely cases, this test code is extremely cursory. In particular, the code to examine the supplied HDF5 file is barely tested at all. Need a library of HDF5 files exibiting the full range of possible super block and super block extension message structures to test this properly. 9) In passing, tighened up the code that controls dumps of "possibly significant" differences between the contents of the control and recovered data sets in the h5recover. It should now ignore one integer matches in what appears to be garbage raw data. Tested: serial and parallel on Phoenix serial and parallel on Jam serial on Linew serial on Liberty All tests were done in debug mode.
* [svn-r16193] Two items:John Mainzer2008-12-131-0/+682
| | | | | | | | | | | 1) Fix for assertion failure mentioned in my last checkin. Thanks to Quincey for the fix. 2) Added tools/h5recover/trecover_verifier.c -- forgot to do this in the last checkin. Tested on Phoenix (serial), Linew (serial) and Jam (parallel).
* [svn-r16184] Several Items:John Mainzer2008-12-116-91/+384
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1) In H5F.c, modified several metadata cache related routines to talk to the new cache, not the pre-journaling cache. 2) Enabled the API smoke check in cache2_journal. 3) Wrote a example of use of the journaling API and included it as a test in cache2_journal.c. Some re-factoring of the cache2 test code to move supporting macros and functions out of cache2_api.c and into cache2_common.c & .h. 4) Modified tools/h5recover/trecover to include a new verify option, which is intended to verify that a file has been correctly recovered via h5recover. The basic idea of this feature is to look at the data sets in the architype and recovered files, and verify that the metadata in the versions in the recovered file (if they appear at all), agree with the architype versions where it must, and contain plausible values where it is possible that changes were lost. The test also looks at the raw data, and dumps the architype and recovered versions to stdout if anything looks "odd". At present, my addition only works with the integer chunked data set -- not with the other data set types that can be created by trecover. The code for the verify function is in the new file trecover_verifier.c. Updated Makefile.am and the manifest accordingly. 5) Modified the synchronous crash test in tools/h5recover to to function when return codes are not passed back to the calling script, and to use the above modifications to trecover to examine the recovered file, instead of comparing the output of dumps of the architype and recovered files. 6) Commented out the asynchronous crash test in tools/h5recover, as the functionality of that test is now handled in the "walking crash" test. 7) Modified the "walking crash" test to use the trecover modifications to verify each recovery. 8) Modified the journaling file marking tests to function when the the return code is not passed back to the calling script. 9) Commented out the "tgroup-1.ls 1 -w80 -r -g tgroup.h5" in tools/h5ls. I am given to understand that this test was failing on redstorm due to yod's failure to pass back return codes. I have not investigated this personally. 10) Updated bin/reconfigure to deal with recent changes in the file system structure on jam. Testing: Tested (serial) on Phoenix, Linew, and RSQ -- all pass. Note that on the "walking crash" test in tools/h5recover, I was unable to set the asynchronous crash delay small enough to get the crash to occur before trecover completed (I got down to 1 usec). This was not a problem on on redstorm the last time we tried testing there, so I'm not too worried about it. I also did a parallel test on jam -- this test failed with an assertion failure in dtypes -- output follows: ============================ dtypes Test Log ============================ Testing non-aligned conversions (ALIGNMENT=1).... Testing H5Tget_class() PASSED Testing H5Tcopy() PASSED Testing H5Tdetect_class() PASSED Testing compound datatypes PASSED Testing query functions of compound and enumeration types PASSED Testing transient datatypes PASSED Testing named datatypes PASSED Testing functions of encoding and decoding datatypes PASSED Testing encoding datatypes with the 'use the latest format' flag PASSED Testing exceptions for int <-> float conversions PASSED Testing deprected API routines for datatypes PASSED Testing string conversions PASSED Testing random string conversion speed PASSED Testing some type functions for string PASSED Testing compound element reordering PASSED Testing compound subset conversions PASSED Testing compound element shrinking & reordering PASSED Testing optimized struct converter PASSED Testing compound element growing PASSED Testing compound element insertion PASSED Testing packing compound datatypes PASSED Testing compound datatype with VL string dtypes: H5FD.c:2150: H5FD_write: Assertion `1==H5P_isa_class(dxpl_id,(H5P_CLS_DATASET_XFER_g))' failed. Command terminated by signal 6 0.20user 0.10system 0:00.39elapsed 75%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (4major+10263minor)pagefaults 0swaps I'm checking in anyway, as this looks unrelated to any of my recent changes. Quincey and I should get together about this one.
* [svn-r16136] Several changes:John Mainzer2008-11-272-7/+258
| | | | | | | | | | | | | | | | | | | | | | | | | | | Modified H5C2_journal_post_flush() write the super block and flush the file before truncating the journal. Failure to do this opened a window in which the application could crash leaving the HDF5 file in a state that was un-recoverable. The hope is that this will fix the file recovery bug observed on RSQ -- but I have not been able to test there. However, I was able to generate a similar bug on Linew, and this fix seems to deal with the Linew bug. Added a third test to the h5recovery tests. This is really a test for the library, but it was easier to use existing test code there to construct the new test. The new test runs the same application repeatedly, but setting a timer to crash the application at progressively later times. The object is to search for windows in which the application leaves the HDF5 file in an un-recoverable state. Also, updated H5recover.c to use HDstrtoll() instead of HDstrtod() to read some addresses and such from the journal file. Tested serial (debug) on Phoenix and Linew, and parallel (debug) on Jam.
* [svn-r15935] added a comment cautioning the the async test is highly machine ↵Albert Cheng2008-10-231-0/+3
| | | | dependent.
* [svn-r15934] Now that h5recover has been fixed, updated the expected output ↵Albert Cheng2008-10-231-1/+41
| | | | | | | | for the async test. Tested: kagiso.
* [svn-r15922] Description:Quincey Koziol2008-10-2148-223465/+422
| | | | | | | | | | | | | | | | | | | Bring revisions 15289:15457 from trunk into metadata journaling branch. 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 10.5.2 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r15897] Purpose: Bug fixMike McGreevy2008-10-171-1/+1
| | | | | | | | Description: Correcting a typo which was causing the wrong value to get pulled in for journal entry size, occasionally causing entries to become truncated and only partially journaled. Tested: kagiso
* [svn-r15867] Fixed the trecover test by updating it to match the new ↵Albert Cheng2008-10-153-3217/+51
| | | | | | | | | expected output. But the async test still fails as h5recover fails to recover the file to a legal state that is acceptable by h5dump. The rest of the other tests passed.
* [svn-r15857] Purpose: Bug fixMike McGreevy2008-10-131-3/+1
| | | | | | | | | | Description: The pre-parse of the journal file to determine maximum entry size (to determine proper memory allocation amount) didn't take into account incomplete entries at the end of the file. Modified to only parse up through the last complete entry, rather than the entire file. Tested: kagiso
* [svn-r15575] README file showing the instruction of using the Metadata ↵Albert Cheng2008-09-021-0/+47
| | | | Journaling feature.
* [svn-r15568] trecover and enable_journaling were installed by mistake. ↵Albert Cheng2008-09-012-4/+4
| | | | | | | Moved them from $bin_PROGRAMS which are installed to $check_PROGRAMS which are built always but not necessary tested automatically.
* [svn-r15554] Modified it to be able to read the previous recorded time step ↵Albert Cheng2008-08-291-12/+29
| | | | | | counter value and continue adding more rows from there.
* [svn-r15519] Grouped all the just changed statments to turn on journal toAlbert Cheng2008-08-221-44/+42
| | | | | | | | | | | | a separated function for easier identification. Removed the redundent call of H5Pset_libver_bounds(). Changed return(-1) to return(1) since main can't return negative value, at least not in Unix systems. -This line, and those below, will be ignored-- M enable_journaling.c
* [svn-r15518] A variety of changes:John Mainzer2008-08-222-8/+65
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1) Removed references to H5AC2__CURR_JNL_CONFIG_VER from H5Fget_jnl_config() and H5Pget_jnl_config(), and also references to H5AC__CURR_CACHE_CONFIG_VERSION from H5Fget_mdc_config() and H5Pget_mdc_config(). 2) Removed H5Pset_journal() from H5C2journal.c, and modified test code to use H5F/Pget/set_mdj_config() instead. 3) Implemented support for callbacks on metadata journaling status change along with the associated registration / deregistration calls and associated test code. 4) Fixed bug in journaling shutdown exposed by 3 above. Tested and passed on Phoenix (serial), Linew (serial), and Kagiso (parallel). However, while I was testing there were a couple of checkins, forcing an update and second round of testing. On the second round, tested and passed on Phoenix (serial) and Kagiso (parallel), but failed on Linew (serial). As best I can tell, this was caused by Mike M's checkin -- which broke the smoke checks in cache2_journal on Linew but not Phoenix or Kagiso. A typical delta in the architype files follows: linew.hdfgroup.uiuc.edu% diff -ctw cache2_journal_sc00_000.jnl tmp/cache2_journal_sc00_000.jnl *** cache2_journal_sc00_000.jnl Fri Aug 22 08:28:49 2008 --- tmp/cache2_journal_sc00_000.jnl Fri Aug 22 05:08:41 2008 *************** *** 1,5 **** ! 0 ver_num 1 target_file_name cache_journal_test.h5 creation_date Fri Aug 22 human_readable 1 ! E eoa_value 0x0 C comment Begin transaction on transaction 1.0. 1 bgn_trans 1 2 trans_num 1 length 1 base_addr 0x401 body 01 --- 1,5 ---- ! 0 ver_num 1 target_file_name cache_journal_test.h5 creation_date Wed Aug 20 human_readable 1 ! E eoa_value 0x772a9c01 C comment Begin transaction on transaction 1.0. 1 bgn_trans 1 2 trans_num 1 length 1 base_addr 0x401 body 01 As you can see, it looks like garbage is getting into the first eoa write on Linew. I'm checking in anyway, as Quincey needs my changes, and I will not have time to work on this for several days. Mike: Let me know if you are tackling this one -- if not, I'll deal with it.
* [svn-r15517] Put a pause of 2 seconds after dataset write but before file ↵Albert Cheng2008-08-221-16/+47
| | | | | | | | flush to allow manual abort of the application, thus simulate a crash. If program is NOT aborted, it will complete successfully. Previously, it would abort itself for -w but that is removed.
* [svn-r15514] Purpose:Mike McGreevy2008-08-211-236/+523
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - EOA logging update Description: - EOA values will now be written to the journal file in their own transaction when the EOA changes. - The EOA will be udpated in the HDF5 file's superblock before the recovery process begins. This should prevent some loss of raw data as the file won't be getting truncated upon file open as it will read the correct EOA value from the superblock. - Removed storing of EOA in journal entry messages since they're in their own transaction. - Updated tests to reflect change of transaction formats. Regenerated smoke test files to account for new entry types, and tweaked transaction number tests to reflect change in size of journal entries. - Large testfiles (in test/testfiles) should now unzip when ./configure is run. - When journal file is supplied but contains no complete transactions, instead of reporting an error, h5recover now informs the user of said nonexistant transactions, and opens/closes the hdf5 file with the journal recovered flag set. - Other various organizational changes to h5recover, included a bit more added to verbose output. Tested: - kagiso, smirom
* [svn-r15475] More cleanup.Albert Cheng2008-08-151-16/+11
| | | | Renamed the reopen mode (-r) to write mode (-w) which is more intutive.
* [svn-r15474] Removed all the code that changed the caching or data sieving ↵Albert Cheng2008-08-151-49/+14
| | | | | | parameters. They does not affect the results and are not needed.
* [svn-r15452] Reworked journaling control code to remove journaling configurationJohn Mainzer2008-08-081-4/+4
| | | | | | | | | | | | | | | from the H5AC2_cache_config_t structure and the associated H5P/H5Fget/set_mdc_config() API calls, and into the newly created H5AC2_jnl_config_t structure and H5P/H5Fget/set_jnl_config() calls. Updated test code accordingly. Updated the trace file test code for journaling. Also folded in a fix to an assertion bug in H5C2pkh.h Tested serial on Phoenix and Linew, and parallel (with and without the trace file enabled) on kagiso.
* [svn-r15422] Added H5Pset_alignment to force data stored on known aligned ↵Albert Cheng2008-07-291-9/+18
| | | | | | | | | | addresses for easier octo dump of data file. Moved latest lib version to apply all the time. Tested: kagiso.
* [svn-r15406] Removed the patch mode and its code since it is not needed anymore.Albert Cheng2008-07-251-56/+67
| | | | | | Added -z option to turn OFF all caching. Tested: kagiso.
* [svn-r15396] Purpose: Mike McGreevy2008-07-231-70/+83
| | | | | | | | | | | | | | | | - Bug fixing and cleanup Description: - Fixed the problem where the recovery wasn't "sticking" on the first pass of using the tool. Now should only need to run the tool once to recover a file. - Uncommented out some lines generating more verbose output, so now entry size and addresses are visible with -v (--verbose) option. - Fixed off-by-one memory allocation error. - Cleaned up comments to allow for easier reading. Tested: - kagiso, smirom
* [svn-r15388] Description:Quincey Koziol2008-07-202-10/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Convert object header cache client to use the new metadata journaling cache, which included adding a new client for handling continuation chunks. Added "real" protect calls around modifying chunks in object headers. Switched a few more metadata cache library API routines to drop the file pointer, when it is not needed (pinning/unpinning entries, etc.) Fixed bug in journaling cache handling of 'image_len' callbacks and also changed cache to retry deserializing entries when the entry's size is larger than the speculative size initially tried. Retrying for 'image_len' callbacks has problems with the 'multi' VFD, so the h5dump and FORTRAN 'multi' tests are commented out, until the changes to the 'multi' VFD from the file free space branch are brought back into the trunk. Currently, the 'h5recover' tool has a bug which requires it to be run twice before replaying the journal "sticks". However, this is from an earlier checkin, since the code in the branch already has this behavior... :-( 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 10.5.4 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r15300] Description:Quincey Koziol2008-06-30126-653/+222359
| | | | | | | | | | | | | | | | | Bring revisions 15210:15289 from the trunk into the metadata journaling branch. 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 Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r15295] Description:Quincey Koziol2008-06-3021-155/+1336
| | | | | | | | | | | | | | | | | Merge revisions 15130:15210 from trunk into metadata journaling branch 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 Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r15282] Revised the whole work to model after enable_journaling.c.Albert Cheng2008-06-263-60/+216
| | | | | | Added -p for patch mode that is needed temporary. Tested: kagiso
* [svn-r15281] Changed the dataset dimension sizes smaller so that it is easier toAlbert Cheng2008-06-261-2/+2
| | | | | | view the h5dump output. Tested: kagiso.
* [svn-r15262] Description:Quincey Koziol2008-06-236-24/+385
| | | | | | | | | | | | | | | | | | Merge revisions 15037:15130 from trunk into metadata journaling branch 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 10.5.2 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r15239] Instead of just one H5Dwrite(), it now does 3 H5Dwrite() so ↵Albert Cheng2008-06-191-4/+7
| | | | | | | | that there will be at least 3 completed transactions. Tested: kagiso.
* [svn-r15237] Description:Quincey Koziol2008-06-1826-294/+737
| | | | | | | | | | | | | | | | | | Merge revisions 14900:15037 from trunk into metadata journaling branch 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 10.5.2 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r15236] Cleaned out some compiler warnings.Albert Cheng2008-06-182-12/+14
| | | | Tested: kagiso.
* [svn-r15234] Description:Quincey Koziol2008-06-187-12/+83
| | | | | | | | | | | | | | | | | | Bring revisions 14800:14900 from trunk into metadata journaling branch 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 10.5.2 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r15232] Description:Quincey Koziol2008-06-1812-1039/+1031
| | | | | | | | | | | | | | | | | | Bring back revisions 14700:14800 from the trunk 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 10.5.2 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r15231] Description:Quincey Koziol2008-06-1852-374/+981
| | | | | | | | | | | | | | | | | | Merge revisions 14525:14700 from trunk into metadata journaling branch 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 10.5.2 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r15229] Added a helppage to show how to use this tool.Albert Cheng2008-06-181-17/+81
| | | | | | | | Added a -c option to do create explicitly. Turn off data sieving in -r mode. Fixed an error in writedata() to write data correctly now. tested: kagison.
* [svn-r15226] Entered known problems/issues as the initial version.Albert Cheng2008-06-171-0/+26
| | | | | | | Other file recovery or Journaling related documents can be kept in this file for now. Will get them more organized later. Tested: eyeballed.
* [svn-r15221] Description:Quincey Koziol2008-06-1682-5999/+5705
| | | | | | | | | | | | | | | | | | Bring changes from trunk from the time the branch was created (r14280) up to the 1.8.0 release (r14525) back into the metadata journaling branch. 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 Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r15207] Purpose: Adding a quick fix to put the end of address (EOA) ↵Mike McGreevy2008-06-121-8/+38
| | | | | | | | | | | | | | | | | value into journal entries to be used by the recovery tool. This value is only really neded once per transaction, and only when the EOA changes, so rather than putting it into each journal entry, this should be moved into its own transaction type. However, in order to speed testing along, this quick fix has been implemented for the time being. Modified h5recover tool to use eoa value as well as journaling tests accordingly. Tested: kagiso
* [svn-r15206] Revamp the whole code to added in default, reopen and patch modes.Albert Cheng2008-06-121-68/+159
| | | | | | | | | | | | * How to use this: * ./enable_journaling # create JournalEG.h5 file * ./enable_journaling -r # reopen JournalEG.h5 with Journaling on and * # add more rows, then crash. * ./h5recover -j JournalEG.h5.jnl JournalEG.h5 # to recover the file. * ./enable_journaling -p # patch it with metadata of the added rows. * Then JournalEG.h5 should have all the expected written rows and data. Tested: kagiso. (-r failed with a library assertion error.)
* [svn-r15198] testh5recover.sh.in:Albert Cheng2008-06-112-15/+7
| | | | | | | | | | Sun does not like variable and function having a common name of H5DIFF. Rename the function as MYH5DIFF. trecover_writer.c: Change dataset datatype to the machine independent type of H5T_STD_I32LE. This allows the h5dump output easier to match the expectd output. Tested: smirom, linew, kagiso (serial passed).
* [svn-r15182] Purpose: Bug FixMike McGreevy2008-06-091-1/+1
| | | | | | | | | | | | | Description: Changed H5C2_jb__journal_entry function to make a copy of the incoming journal entry before doing anything with it. I was seeing errors in the journals produced by using the pointer passed to me, so copying the data beforehand looks to solve the problem. Also made a quick change to h5recover.c to use generated fapl when opening the recovered HDF5 file. (was previously using H5P_DEFAULT). Tested: kagiso
* [svn-r15177] testh5recover.sh.in:Albert Cheng2008-06-094-13/+3259
| | | | | | | | | | | | | | | | | | | | | | | | Updated to start using the real h5recover tool. But tests are not passing and have to patch it not to exit 1 at all. Also, h5diff tool has errors, therefore I made my own diff by using h5dumps. trecover_main.c: Changed the default to generate chunked storage datasets only since that is the only one that Journal code can do. default.txt: async_crash.txt: updated them to use current output which is not right anyway. Doing all these so that other team members can work on their code. Tested: kagiso. This line, and those below, will be ignored-- M h5recover/testh5recover.sh.in M h5recover/testfiles/default.txt M h5recover/testfiles/async_crash.txt M h5recover/trecover_main.c
* [svn-r15175] An example program showing how to turn on the Journaling feature.Albert Cheng2008-06-092-8/+20
| | | | | | | | | | Has has a temporary patch option (-p) to add datasets back in till the object header codes work. Makefile.am: also added more cleaning of temporary generated files. tested: kagiso. ------------------------------------------------------------------------
* [svn-r15174] An example program showing how to turn on the Journaling feature.Albert Cheng2008-06-091-0/+137
| | | | | | | Has has a temporary patch option (-p) to add datasets back in till the object header codes work. tested: kagiso.
* [svn-r15142] Purpose: adding recovery toolMike McGreevy2008-06-041-16/+689
| | | | | | | | | | | | Description: Adding recovery tool to the metadata_journaling repository. The tool still needs to go through some tweaks, especially regarding syntax changes, grabbing the journal name from an hdf5 file, confirming successful uncorruption of file, et cetera, but this should be enough to give Albert a chance to start using it in the trecover tests so we can work through additional debugging issues together to get that to run. Tested: kagiso
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