Well, after flailing for a while because I could simply not find any
information on what to do when svnadmin recover reports 'svn: bdb:
PANIC: DB_RUNRECOVERY: Fatal error, run database recovery', I took
matters into my own hands.
Because the errors stated that the berkeley db logfile
Projects/db/log.0000000047 was invalid, I examined it and found it to
be 541726 bytes of zeroes, followed by a few tens of bytes that looked
like Berkeley db logfiles. I moved this file and svnadmin recover
worked properly; however the repository was reverted to a slightly
earlier revision. (?? Is the repository corrupt now? Is it valid? I'm a
bit fearful of putting it back into production!)
This is still not good. There seem to be two issues here:
1) How did my commit somehow cause this totally invalid logfile?
2) 'svnadmin recover' reported
'svn: bdb: Ignoring log file: Projects/db/log.0000000047: magic number
0, not 40988'
however, it clearly did *not* ignore the logfile, because it was
subsequently tripped up by it. Only when I moved that logfile so it had
to ignore it did 'svnadmin recover' work. Given this, does the recover
procedure seems to be a bit more brittle than perhaps it could be?
Again, my repository was not stored on a network share, and the
permissions were set properly. Does anyone have any idea what the
problem was? I would prefer not to repeat it.
Zach Pincus
Department of Biochemistry and Program in Biomedical Informatics
Stanford University School of Medicine
On Feb 24, 2005, at 11:50 PM, Zachary Pincus wrote:
> Well, now I've gotten some sort of divine retribution for my
> bellyaching about file roll-back on the list earlier. Oh dear, I never
> set out to be a troublemaker!
>
> SUMMARY:
> After/during a failed svn commit over svn+ssh, my subversion
> repository became wedged. Subsequent recovery attempts with 'svnadmin
> recover' result in the error:
> 'svn: bdb: PANIC: DB_RUNRECOVERY: Fatal error, run database recovery'
> Moreover, this is *not* a permissions problem, as documented below.
>
> DETAILS:
> The transcript of the fatal commit is included below as #1. The
> transcript shows a successful commit of a property change to one
> directory, then an attempted commit of the rest of the trunk. The
> commit failed with a generic looking error, so I tried the same
> command again. This commit failed again, but with a new, scary looking
> error.
>
> I then got a variety of error messages when I tried to run various svn
> commands remotely or from the server machine itself. See transcripts
> #2 and #3 below.
>
> So I logged into the server again and tried to run svnadmin recover.
> The output was as follows:
> [b473-puff:~] zpincus% svnadmin recover Projects/
> Repository lock acquired.
> Please wait; recovering the repository may take some time...
> svn: DB_RUNRECOVERY: Fatal error, run database recovery
> svn: bdb: Ignoring log file: Projects/db/log.0000000047: magic number
> 0, not 40988
> svn: bdb: Invalid log file: log.0000000047: Invalid argument
> svn: bdb: PANIC: Invalid argument
> svn: bdb: PANIC: DB_RUNRECOVERY: Fatal error, run database recovery
>
> Output from svn --version and svnadmin --version information for the
> client and server machines is in transcript #4 below. Both client and
> server are running OS X 10.3.8, and subversion 1.1.3 (r12730).
>
> From the email archives, it appears that something like this is often
> a permission problem. I checked all the permissions in the repository
> and they are all:
> -rw-r--r-- zpincus zpincus # for files
> drwxr-xr-x zpincus zpincus # for directories
> I am running svnadmin recover as the zpincus user. I created the
> repository as this user, and I only ever accessed it locally or over
> svn+ssh as that user. Even if I copy the repository file and
> recursively change all permissions on it to a+rwx, recovery still
> doesn't work. It really doesn't seem like a permission problem.
>
> So, what do I do now? I can't find any suggestions in the email list
> archive for the right way out of this state when there is no
> permission problem.
>
> Thanks,
>
> Zach Pincus
> Department of Biochemistry and Program in Biomedical Informatics
> Stanford University School of Medicine
>
>
>
> ################ Transcript #1: the commit that broke things
> #################
> [axlotl:Projects/ShapeModelLevelSets/trunk] zpincus% svn status
> ? Output/Bestfit.png
> M src/ImageShapeModelFitter/Constants.cxx
> M src/Common/myPCAShapeSignedDistanceFunction.txx
> M src/Common/itkShapePriorImageCostFunction.txx
> M src/Common/myPCAShapeSignedDistanceFunction.h
> M src/ImageShapeModelScanner/ImageShapeModelScanner.cxx
> M src/ImageShapeModelScanner/Constants.cxx
> M bin
> [axlotl:Projects/ShapeModelLevelSets/trunk] zpincus% svn commit bin
> -m"Modified ignore properties"
> Sending bin
>
> Committed revision 3.
> [axlotl:Projects/ShapeModelLevelSets/trunk] zpincus% svn commit
> -m"Changes for faster interpolation of
> myPCAShapeSignedDistanceFunction, better optimizer constants, and
> better iteration region management for ImageShapeModelScanner."
> Sending trunk/src/Common/itkShapePriorImageCostFunction.txx
> Sending trunk/src/Common/myPCAShapeSignedDistanceFunction.h
> Sending trunk/src/Common/myPCAShapeSignedDistanceFunction.txx
> Sending trunk/src/ImageShapeModelFitter/Constants.cxx
> Sending trunk/src/ImageShapeModelScanner/Constants.cxx
> Sending
> trunk/src/ImageShapeModelScanner/ImageShapeModelScanner.cxx
> Transmitting file data ......subversion/libsvn_client/commit.c:765:
> (apr_err=210004)
> svn: Commit failed (details follow):
> subversion/libsvn_ra_svn/marshal.c:722: (apr_err=210004)
> svn: Malformed network data
> [axlotl:Projects/ShapeModelLevelSets/trunk] zpincus% svn commit
> -m"Changes for faster interpolation of
> myPCAShapeSignedDistanceFunction, better optimizer constants, and
> better iteration region management for ImageShapeModelScanner."
> Sending trunk/src/Common/itkShapePriorImageCostFunction.txx
> Sending trunk/src/Common/myPCAShapeSignedDistanceFunction.h
> Sending trunk/src/Common/myPCAShapeSignedDistanceFunction.txx
> Sending trunk/src/ImageShapeModelFitter/Constants.cxx
> Sending trunk/src/ImageShapeModelScanner/Constants.cxx
> Sending
> trunk/src/ImageShapeModelScanner/ImageShapeModelScanner.cxx
> Transmitting file data ......subversion/libsvn_client/commit.c:765:
> (apr_err=160029)
> svn: Commit failed (details follow):
> subversion/libsvn_fs_base/bdb/bdb-err.c:74: (apr_err=160029)
> svn: Berkeley DB error while committing Berkeley DB transaction for
> filesystem /Users/zpincus/Projects/db:
> Invalid argument
> subversion/libsvn_fs_base/fs.c:312: (apr_err=0)
> svn: bdb: Ignoring log file:
> /Users/zpincus/Projects/db/log.0000000047: magic number 0, not 40988
> subversion/libsvn_fs_base/fs.c:312: (apr_err=0)
> svn: bdb: DB_ENV->log_put: 47: Invalid argument
> subversion/libsvn_fs_base/fs.c:312: (apr_err=0)
> svn: bdb: Ignoring log file:
> /Users/zpincus/Projects/db/log.0000000047: magic number 0, not 40988
> subversion/libsvn_fs_base/fs.c:312: (apr_err=0)
> svn: bdb: DB_ENV->log_put: 47: Invalid argument
>
>
> ################ Transcript #2: error messages when logged into the
> server #################
> [b473-puff:~/Developer/Checkout] zpincus% svn up
> svn: Working copy '.' locked
> svn: run 'svn cleanup' to remove locks (type 'svn help cleanup' for
> details)
> [b473-puff:~/Developer/Checkout] zpincus% svn cleanup
> [b473-puff:~/Developer/Checkout] zpincus% svn up
> svn: Berkeley DB error while checkpointing after Berkeley DB
> transaction for filesystem /Users/zpincus/Projects/db:
> Invalid argument
> svn: bdb: Ignoring log file:
> /Users/zpincus/Projects/db/log.0000000047: magic number 0, not 40988
> svn: bdb: DB_ENV->log_put: 47: Invalid argument
> svn: bdb: txn_checkpoint: failed to flush the buffer cache Invalid
> argument
> Abort
>
> ################ Transcript #3: subsequent error messages when
> connecting as a client #################
> [axlotl:Development/Projects/ShapeModelLevelSets] svn commit -m
> "trying commit again"
> subversion/libsvn_client/commit.c:765: (apr_err=210004)
> svn: Commit failed (details follow):
> subversion/libsvn_ra_svn/marshal.c:722: (apr_err=210004)
> svn: Malformed network data
> subversion/clients/cmdline/util.c:381: (apr_err=210004)
> [axlotl:Development/Projects/ShapeModelLevelSets] zpincus% svn commit
> trunk/src/ImageShapeModelFitter/Constants.cxx -m"Better constants for
> optimizer"
> subversion/libsvn_client/commit.c:765: (apr_err=210004)
> svn: Commit failed (details follow):
> subversion/libsvn_ra_svn/marshal.c:722: (apr_err=210004)
> svn: Malformed network data
> [axlotl:Development/Projects/ShapeModelLevelSets] zpincus% svn up
> subversion/libsvn_ra_svn/marshal.c:722: (apr_err=210004)
> svn: Malformed network data
> [axlotl:Development/Projects/ShapeModelLevelSets] zpincus% svn ls
> subversion/libsvn_ra_svn/marshal.c:722: (apr_err=210004)
> svn: Malformed network data
>
> ################ Transcript #4: svn version information for client and
> server #################
> ### on the client ###
> [axlotl:Development/Projects/ShapeModelLevelSets] zpincus% svn
> --version
> svn, version 1.1.3 (r12730)
> compiled Jan 16 2005, 23:38:26
>
> Copyright (C) 2000-2004 CollabNet.
> Subversion is open source software, see http://subversion.tigris.org/
> This product includes software developed by CollabNet
> (http://www.Collab.Net/).
>
> The following repository access (RA) modules are available:
>
> * ra_dav : Module for accessing a repository via WebDAV (DeltaV)
> protocol.
> - handles 'http' schema
> - handles 'https' schema
> * ra_local : Module for accessing a repository on local disk.
> - handles 'file' schema
> * ra_svn : Module for accessing a repository using the svn network
> protocol.
> - handles 'svn' schema
>
> [axlotl:Development/Projects/ShapeModelLevelSets] zpincus% svnadmin
> --version
> svnadmin, version 1.1.3 (r12730)
> compiled Jan 16 2005, 23:38:26
>
> Copyright (C) 2000-2004 CollabNet.
> Subversion is open source software, see http://subversion.tigris.org/
> This product includes software developed by CollabNet
> (http://www.Collab.Net/).
>
> ### and on the server ###
> [b473-puff:~/Developer/Checkout] zpincus% svn --version
> svn, version 1.1.3 (r12730)
> compiled Feb 22 2005, 17:54:37
>
> Copyright (C) 2000-2004 CollabNet.
> Subversion is open source software, see http://subversion.tigris.org/
> This product includes software developed by CollabNet
> (http://www.Collab.Net/).
>
> The following repository access (RA) modules are available:
>
> * ra_dav : Module for accessing a repository via WebDAV (DeltaV)
> protocol.
> - handles 'http' schema
> * ra_local : Module for accessing a repository on local disk.
> - handles 'file' schema
> * ra_svn : Module for accessing a repository using the svn network
> protocol.
> - handles 'svn' schema
>
> [b473-puff:~/Developer/Checkout] zpincus% svnadmin --version
> svnadmin, version 1.1.3 (r12730)
> compiled Feb 22 2005, 17:54:37
>
> Copyright (C) 2000-2004 CollabNet.
> Subversion is open source software, see http://subversion.tigris.org/
> This product includes software developed by CollabNet
> (http://www.Collab.Net/).
>
>
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Received on Fri Feb 25 19:52:52 2005