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Repository broken; svnadmin recover says "PANIC: DB_RUNRECOVERY: Fatal error, run database recovery" (v. 1.1.3)

From: Zachary Pincus <zpincus_at_stanford.edu>
Date: 2005-02-25 08:50:58 CET

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 08:53:17 2005

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