| Commit message (Collapse) | Author | Age | Files | Lines |
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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.
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- 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
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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.
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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
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specifically:
1) Fix for failure to detect journaling in progress on HDF5 files which
were not closed correctly. Also associated test code.
Note that this required addition of code to test for journaling in
progress and enable journaling at the end of H5F_flush(). In passing,
I was able to get rid of the wacky code that queued journaling setup
at cache creation time.
2) Test code for startup and shutdown of journaling on an open file.
3) Updates to start checking journal output against architype files
instead of just generating architypes at test time.
Note that per Quincey's request, I have checked in gziped versions
of the architype files. At some point, we will have to add code
to automatically unzip these files, but for the time being you will
have to go to test/testfiles and "gunzip *.gz". The journal tests
will still pass if you don't, but you will get a warning about
missing test files.
4) Fixed bug in journal entry logging code that allowed a comment to
appear in the journal file before the journal file header. (Mike M,:
Please review my fix to verify that I haven't clobbered anything.)
5) Additional test code.
Note that more test code would be a good idea, but this set of bug
fixes should be enough to get us through the basic demo -- at least
as far as the metadata cache is concerned.
Tested serial on Phoenix, and parallel on Kagiso. Also, tested serial
on Linew just prior to some last minute minor edits.
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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
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Added a pointer to the cache that an entry is contained within to the
cache entry structure. This allows us to remove the file pointer from some of
the H5AC2 calls, easing the conversion of some of the cache clients (the free
space section info and fractal heap direct blocks, and probably others).
Removed file pointer from the H5AC2_unpin_entry() call.
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
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Convert the symbol table node metadata cache client to use the new
journaling cache callbacks.
Also added a 'H5F_t *' parameter to the 'serialize' callback for the
journaling cache, which makes the client's job much easier.
Various minor coding cleanups, etc. also.
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 10.5.3 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Description: Fixing a couple of bugs in the journal logging code. Primarily,
H5C2_jb__bin2hex was WAY inefficient. I've cleaned it up a bit.
cache2_journal now finishes in less than a minute on kagiso. Also,
__DATE__ preprocessor macros are no longer used to generate
journal file headers.
Tested: kagiso
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I now have substantial tests for this code -- enough (I hope) for
Mike M. to get started. However, the code is my no means fully tested.
I don't expect any obvious problems, but there are probably quite a few
relatively subtle bugs remaining. I'll be chasing these in the next
week.
For an example of setting up the cache to journal, see
setup_cache_for_journaling() in test/cache2_journal.c
Warnings:
1) For now, only enable journaling at file creation time -- code to
do this after the file is opened exists, but it hasn't been tested.
2) Right now the journal logging code is very inefficient, so expect
things to run slowly until Mike M. checks in his changes to address
this problem.
3) I have not checked in exemplar journal output files pending a fix
another minor bug in the journal logging code. Until then, the
journal tests create exemplars and then test against them -- a poor
way to find errors.
4) The USE_CORE_DRIVER has been moved to cache2_common.h.
5) When USE_CORE_DRIVER is FALSE, cache2_journal runs VERY slowly on
some system (i.e. 4 hours on Phoenix) -- but it runs fast on Kagiso
(~10 minutes). Don't know why, but would guess that the quantity
of RAM on the system has much to do with it.
Tested serial debug on Phonenix, and parallel debug on Kagiso
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While this code doesn't break any of the existing tests, it HAS NOT
been tested beyond that.
Also mods needed to integrate the journaling code with Quincey's latest
mods, and to adapt existing test code to slight changes caused by the
addition of journaling.
Finally, fixed an undefined variable bug in the HL code exposed by the
journaling mods.
Tested serial under Linux (Phoenix) and parallel under Linux (Kagiso).
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Misc. cleanups found while compiling in other environments.
Still failing on linux machines with a memory corruption error and
not finished building in parallel yet either...
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
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Switch v1 B-tree nodes from using previous cache to use the new journaling
cache code. This is a major switch for the cache callbacks.
Switched the metadata caching code from having a pointer to the file it's
in to receiving a pointer to the file, when needed. This was necessary in
order to avoid crashing when two files IDs were open on the same underlying
file and one of those files was closed with cache entries using the file
pointers. Also took out the check in the caching code for reading off the
end of the file, which didn't play nicely with the multi-file VFD.
Switching the cache from having a pointer internally to requiring one
externally meant tweaking almost all the test code. :-/
Added correct exit codes to cache2 tests that didn't have them already,
so the 'make check' will stop when they fail.
Use the path to the h5diff in this build in the tools/h5recover testing
script, since we can't guarantee a user has HDF5 already installed.
Assorted minor tweaks to get everything to compile more cleanly and pass
all the tests (on my Mac :-).
Tested on:
Mac OS X (10.5.2) w/C++
(more testing coming up shortly, I just didn't have my "rsync testbed" set
up for this branch when I started making changes to the code)
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1) Code to read and write the metadata journaling configuration block
and associated test code. (Quincey: Just recalled that I have not
converted the memory type of the metadata journaling configuration
block to H5FD_MEM_SUPER per our email conversation. It will be in
the next checkin.)
2) Dummy begin/end transaction calls on the off chance that Quincey
gets to working on this before I check in the real ones.
3) Updates to cache2 in test to reduce the size of the test according
to the value of the HDF5TestExpress environment variable. Run times
on Phoenix using the core file driver are as follows:
HDF5TestExpress = 0 20:20
HDF5TestExpress = 1 4:56
HDF5TestExpress = 2 3:18
HDF5TestExpress = 3 0:25
With HDF5TestExpress = 3, I skip the smoke checks entirely. With
HDF5TestExpress = 2, I set the number of itterations as low as it
can go without a major re-write. (Albert: I hope running with
HDF5TestExpress = 2 will work for you. If it doesn't, we will just
have to run with HDF5TestExpress = 3 on RedStorm, and skip the
smoke checks for now.
Tested serial on Phonenix and parallel on kagiso.
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tests.
Description: Journal entry logging code has been upgraded. The code
now accurately tracks transactions that have made it
to disk, and converts data from binary to hex for
entry into the journal file. Various other minor
code modifications have been made based on suggestions
by John Mainzer.
More tests have been added to verify the functionality
of the logging code. Specifically, tests have been
written to verify functionality of the ring buffer, to
check validity of journal messages produced, and to
verify that transaction tracking is functioning
appropriately.
Tested: kagiso, smirom, linew, duty
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the journaling branch. Added several new errors, and made many edits
to Mike's code (don't worry Mike -- changes I made were on items I
neglected to discuss with you).
Serial test on Phoenix only.
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note that both the H5C and H5C2 code have been updated.
Also checked in code to track journaling status in the super block.
Note that this code has not been tested -- but as best I can tell,
it does not break the existing regression tests.
Tested serial (debug and production) on Phoenix. Also tested parallel
on kagiso.
Note that regression test fails on kagiso (but not on phoenix) if
the cache2 serial tests are configured to use the core file driver.
Thus this code is check in with the core file driver optimization
of the cache2 tests disabled. To turn it on, set the USE_CORE_DRIVER
#define to TRUE.
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branch -- this commit needed at I forgot to svn add the new files
created in support of metadata journaling.
Again, this version may not compile.
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