Recover corrupted family tree
This troubleshooting documentation is oriented around a superseded dependency in Gramps. Reliance on the BSDDB database engine was removed in the 5.1 release.
Explanation of family tree and GRDB corruption, how to recover from it, and how to avoid it in the future.
- 1 Family Tree corruption
- 2 Version 2.2.x: GRDB corruption
- 3 See also
Family Tree corruption
What causes this corruption?
Not really known.
However, Gramps version 2.2.x made family tree Database corruption far less likely than with the previous format of storing.
- See 8875 Database corruption bugs
How do you know about it?
Gramps might give you on startup that recovery is needed via a dialog box:
Gramps has detected a problem in the underlying Berkeley database. This can be repaired by from the Family Tree Manager. Select the database and click on the Repair button
But it might happen no Repair button is present, or you obtain the error (visible in terminal)
(-30975, 'DB_RUNRECOVERY: Fatal error, run database recovery -- PANIC: Invalid argument').
What to do now?
It is advisable not to click the repair button right away. It should work, but Gramps might believe an error is present while this is in reality not true. Repairing your tree then will lead to loss of the last typed changes.
Instead, take a backup of the family tree that is given problems. In a terminal do:
This will give you a list with all family trees and the directory where they are stored, normally somewhere in the directory ~/.gramps/grampsdb. Look at your user directory. Copy the directory of the tree with problems so as to have a backup:
cp -a <target directory> <backup directory>
If the recover button was present on the Gramps family tree, click it. All should work again. If you notice you lost information, or the repair button does not work, then do the following.
If recovery worked, but you do not like the result, backup this data and place your backup taken above back in its original position. You now have again the bad family tree to work on. Next, obtain the BSDDB recovery tools, see your distributions package search page. The program is called db4.8_recover, where 4.8 might be an older or newer version number. See your BSDDB version into Help -> About dialog or with
gramps -v command.
Run this tool as follows:
cd /home/<user>/.gramps/grampsdb/<target directory> db4.8_recover -c
That should do the trick, and allow Gramps to load the family tree. If not, then start a ticket on the Gramps bug tracker.
- download Oracle tools on: http://www.oracle.com/technetwork/products/berkeleydb/downloads/index-082944.html
I have backup gbkp files
If you have a backup, you can try to recover the backup
.gbkp files. Do the following steps:
The procedure to recover your data from
.gbkp files is:
- Make note of the "Family Tree" name you are trying to recover, from the "Family Tree Manager".
- Close the Gramps program.
- Locate your User Directory dependent on your operating systems.
- Locate the
grampsdbfolder under your User Directory (Also known as folders on some operating systems.)
- Under the
grampsdbfolder are stored all your "Family Tree" databases each in separate directories (eg:If you have 10 Family Trees you will have 10 folders each with an automatically created system generated folder name), locate the database you are trying to recover by opening
name.txtfile in a text editor and seeing if the name matches the Family Tree you are trying to recover. If it does match, make note of the directory name.
- If that folder contains
.gbkpfiles, you can continue your attempt to recover the Family Tree.
- Copy all the
.gbkpfiles to a new directory that you must create in your database
grampsdbdirectory, eg. give the directory a unique name
- From the original Family tree directory copy the
name.txtfile to the new directory you created.
- In the new directory open
name.txtin a text editor and change the content to a unique name. eg: Family Tree 1 to Family Tree 1 recovery attempt
- In the new directory create a file with name
need_recover. Mind the underscore and the lack of an extension. The content of that file is unimportant. (Are you using Microsoft Windows and having difficulty creating this file then see 8665#c44245 for a possible work around)
- Start the Gramps program.
- Select the family tree with the name you adjusted in step 9 eg. Family Tree 1 recovery attempt (Do not double click on the family tree name). There should be a red stop sign next to that family tree name.
- Select the Repair button and the Repair Family Tree? dialog will show, at this point select the Proceed, I have taken a backup button or you can select Stop to exit the repair attempt.
- The Gramps program will attempt to repair and recover the family tree and if successful the red stop sign should disappear.
- From the Family Tree manager select the repaired family tree and you should be able to Load Database the family tree.
- From the menu select Family Trees > Make Backup.. and create a backup as insurance.
Implement more security
Your genealogy data contains a lot of work and man hours. So work out a backup scheme
If you work on Gramps regularly: backup the directory holding the family tree databases. These are very large files however.
If you know you work on Gramps sporadically only, or have no space to backup your trees regularly, then do backup in XML format (the .gramps format). Do not forget to disable privacy filters... The XML format will open up just fine over many years on another computer with another OS. This will probably not be the case for the databases a family tree is stored in. XML is machine- and human-readable. It is completely self-sufficient. It is also small. The following are good practices of backups :
1. Export to XML from time to time, especially after large edits. 2. Export to XML before making big changes, such as importing new data into an existing database from e.g. GEDCOM, merging records, running tools that may heavily modify the data, etc. 3. Export to XML before upgrading Gramps to a newer version. Apparently, export to XML with old version before you install the new one! 4. Export to XML before upgrading your OS.
Also, use XML format for any data migration. Moving to another machine, sending data to grandma, copying to another user on the same machine -- all of these cases should use XML, as there is no binary specific data.
Note that XML does not contain your media files. The gpkg output format contains XML and your media files, with the disadvantage of this being very large. If you already have a backup scheme for your media files, there is no need to also backup gpkg files.
ACI not ACID, upgrade, downgrade
Gramps protects your data using an ACI database. This means the last commit can be lost on an error, but not more than that. You should before an upgrade make sure Gramps closed your family tree correctly however.
There should be no error in opening a family tree with a newer version. See the long research in 3975, which does indicate version 4.7.25 of Bsddb contains a bug that can give a strange error message.
Trying to open a family tree after a downgrade is not supported. You will obtain an error that the database is created with a newer version.
Oracle Berkeley DB Command Line Utilities
db_recover -cv" for more verbose output.
dbdump dumps database in text format and dbload use that:
db_dump database.db > dump.txt
db_load database.db < dump.txt
Your log sequence number is out of sync so you need to reset them:
db_load -r lsn database.db < dump.txt
Version 2.2.x: GRDB corruption
This section refers to Gramps Version 2.2.x
What causes this corruption?
The leading cause of grdb corruption is moving the grdb file from its original location. Whether you move the file to another directory, rename it, copy into another file, transfer to another machine, or another user account -- all of those will "corrupt" the file.
What happens is that the grdb file needs its database environment -- a directory with log files, lock files, temp files, etc. The 2.2.x Gramps releases uses grdb files and stores the environment for each file, under a tree in a
~/.gramps/env directory. If your grdb file is
/home/user/genealogy/MyData.grdb then its environment is in the
So moving, copying, or renaming the file will copy the file's bytes, but not its environment. This is why the moved file appears corrupted.
Another cause can be an upgrade or downgrade of your operating system to a BSDDB database backend that does not support fully the previous form of the database (eg, changed hash versions). This will also seem like a corruption in Gramps, but actually means the BSDDB tools must be used to convert to data to a new version.
Not being able to open a /tmp/... file in Gramps 3.0.x on opening grdb files indicates database corruption. This is because the grdb file you want to open is copied to the /tmp dir, and then opened. All failure results in the '/tmp/tmpxxxxx could not be opened'
What do I do now?
The answer depends on whether or not you have the environment for that database. If you just copied one file into another then the environment may still work. If you modified the original database since then, the original environment has changed and there's no good environment for the new file. If you removed your
.gramps directory (why oh why?) then all environments are lost. So act depending on the situation, as explained below.
The environment still exists
If you have environment directory for that file, copy it under the above guidelines.
- You copied
/home/user/genealogy/backup/BackupData.grdband the new file is not working.
/home/user/.gramps/env/home/user/genealogy/backup/BackupData.grdband this should fix the problem.
The environment is lost
If you don't have the original environment for that file, you may try dumping and loading your data using Berkeley DB tools. Depending on your system, they may be called
db4.4_load, ... In Ubuntu you find them in the package
db4.8-util. You might need more recent versions depending on the version your distribution uses in its python package. So for eg Ubuntu Hardy created files, you will need
db4.8-util. Whatever they are called, there should be a dump tool and a load tool, and they should be version 4 or later. For Fedora 17 this is 'db4-utils-4.8.30-10.fc17'. For Fedora 18 this is 'libdb4-utils-4.8.30-5.fc18' (note the new package name).
Basically, you just dump the grdb into a text file, then create a new grdb from that text file:
$ db4.8_dump BackupData.grdb > somefile.txt $ db4.8_load newfile.grdb < somefile.txt
and then cross your heart and hope that
newfile.grdb will open in Gramps.
If you obtain the error:
db4.4_dump: eidtrans: unsupported hash version: 9
this is an indication you need a more recent version. So use db4.8 tools:
$ db4.8_dump BackupData.grdb > somefile.txt $ db4.8_load newfile.grdb < somefile.txt
Note: If you downgrade your distribution, it might be needed to do dump with 4.6 tools, and load with 4.4 or 4.5 tools.
How to prevent corruption?
While moving the file is the leading cause of corruption, apparently there are other less frequent causes that we don't fully know. So preventing corruption is not always possible.
What is possible though is to backup the data regularly. The backups should be in XML format (the
.gramps format). XML is machine- and human-readable. It is completely self-sufficient. It is also small. The following are good practices of backups:
- Export to XML from time to time, especially after large edits.
- Export to XML before making big changes, such as importing new data into an existing database from e.g. GEDCOM, merging records, running tools that may heavily modify the data, etc.
- Export to XML before upgrading Gramps to a newer version. Apparently, export to XML with old version before you install the new one!
- Export to XML before upgrading your OS.
Also, use XML format for any data migration. Moving to another machine, sending data to grandma, copying to another user on the same machine -- all of these cases should use XML.