SQLite Error 11: database disk image is malformed

Thomas Lohrum
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SQLite Error 11: database disk image is malformed

Postby Thomas Lohrum » Thu Feb 28, 2013 2:46 pm

Last night i had another crash with SQLite. This is the third time within three months. It is the second within one week. :( I had reported about that last crash here: viewtopic.php?f=6&t=1543

Again i wanted to cut a note from the inbox, when the crash occured. It appears that some errors occur only, when i use CintaNotes heavily. Some tasks i did along my daily work:
- read notes
- update notes
- change tags
- rename tags
- cut and paste notes

I use CintaNotes heavily all day long and have become dependent from the program. The second heavy crash within a couple of days really makes me worry. First time i had luck and got the system working again. Still it took me 1-2 hours to complete the task. This time it was even worse. At last i was able to fix the database. What a relieve.....! :) Again this took 2 hours and another two to document the issue and write a post here. After fixing the issue i was able to cut and paste that specific note without any problems. Thus i think it is the summary of tasks, that will cause the crash.

After last night's crash, i changed my sqlite-settings to what i think should be the most secure now:
sqlite.pragma.journal_mode = WAL
sqlite.pragma.synchronous = FULL

Let me share my experiences, when trying to fix the issue:

  • i could not export to xml, because when i opened cintanotes, i immediately got error 11
  • i could not import from db, because i got error 11 on import
  • i could not use ".read dump.sql", because i got an error "table 'NotesData_content' already exists"
  • i could not use ".read dump.sql" on an empty database, because CintaNotes complains the database was created by an old CintaNotes version.
    "Diese Notizbuchdatei "cintanotes.db" wurde von einer älteren Version von CintaNotes erstellt und kann nicht aktualisiert werden. Fehlermeldung: SQLite Error 1: there is already another table or index with this name: NoteCache"
    Alex, i think the latter is actually a bug! I checked sqlite's user version, which is 2001.

This is how i solved the issue:

Note: I took the steps mentioned here from an earlier report of Alex and changed it to my specific problem.

  • I installed the sqlite command line shell. You can get it here: http://www.sqlite.org/sqlite.html
  • for simplicity i copied the exe to the folder containing my database
  • i opened my database running "sqlite3 cintanotes.db" from the command line.
  • I ran the following command "pragma integrity_check;". You must write the semicolon!
  • The output "rowid 7706 missing from index ix_ParaFormat" showed the source of the problem. The index "ix_ParaFormat" had become corrupted.
  • I dropped the index with "DROP INDEX ix_ParaFormat;"
  • Recreated it with "CREATE INDEX ix_ParaFormat ON ParaFormat (noteid);"
  • Note: The task on how to get the specific statement to create the index is something i won't describe here.


Alex, the whole matter gets me to the following questions:

  • Does CN use SQLites's Backup API to create a backup or does it simply copy the database file?
  • When using sqlite.pragma.journal_mode=WAL, it seems that the WAL-files will not be part of the backup. When using sqlite.pragma.journal_mode=WAL together with sqlite.pragma.synchronous=FULL, i noticed that after a save/commit it takes a couple of seconds until a checkpoint gets executed and the WAL-file disappears. As i take it from sqlite's docs this is by intention. I think this is important, because from my observation i take it, that the WAL-file will not be part of the backup. Thus it appears to be best, to use the two settings together.
  • I also tried using Firefox's Addon "SQLite Manager", which gave me the following error, when exporting the database: "Likely SQL syntax error: SELECT * FROM "main","NotesData" {unknown tokenizer:my_unicode]"
  • SQLite is embedded/compiled into CintaNotes.exe, right? Do you actually use the latest SQLite-Version 3.7.15.2?
  • When i created a sql-dump i observed, that all notes are written without any formatting. Is this correct? This makes sqlite's sql dump meaningless for use with CintaNotes.
  • When i did a restore of the file "hourly.cintanotes.db" with a timestamp 23:02 i noticed that the most recent note had a timestamp of 21:57. Something is wrong here, since i am 100% sure, i had saved several notes between 22:00 and 23:00. It appears, that the backup goes wrong/incomplete.

After all, i find it strange, that no other users report such problems concerning sqlite stability. Still i suggest to provide more secure settings when installing CintaNotes. Tweaking sqlite to run faster should be a task for people, who understand what they're doing.

Thomas



Here are some Links to people interested on the issue:

SQLiteException "database disk image is malformed"
http://techblog.dorogin.com/2011/05/sql ... ge-is.html

Recovering a Corrupted Banshee Database
http://thelinuxexperiment.com/guinea-pi ... -database/

Creating and Dropping Indexes in SQLite
http://www.dbtalks.com/uploadfile/ca5be ... in-sqlite/

Write-Ahead logging concept in SQLite
http://www.dbtalks.com/uploadfile/ca5be ... in-sqlite/

-shm and -wal files in SQLite DB
http://stackoverflow.com/questions/1292 ... -sqlite-db
Thomas Lohrum
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Re: SQLite Error 11: database disk image is malformed

Postby Thomas Lohrum » Mon Mar 04, 2013 10:50 pm

I am impressed. It took me only one more day of extensive work with CintaNotes/SQLite to crash the database again. :( Should i consider myself lucky, because of my last experiences i was able to fix the database within two minutes this time?

What happened? Again i had created a new note just a couple of minutes before. The creation date was there, but no modification date. I am not sure, but maybe i had changed some text thereafter. Anyway, when i tried to delete the note again, i got "SQLite Error 19 - foreign key constraint failed". After closing and restarting CintaNotes, i got "SQLite Error 11: database disk image is malformed".

I checked the database integrity. Again the index ix_ParaFormat was corrupted: "rowid 5146 missing from index ix_ParaFormat". Recreating it fixed the issue. I was able to delete the note then, but when i tried to scroll to through the notes list, CN suddenly crashed, without any error message. After a restart i was able to work with CN again.

This is getting serious now. :( Three crashes within one week!!! This time i had set sqlite.pragma.synchronous = FULL and sqlite.pragma.journal_mode = WAL, which should have given me the best sqlite stability. Well, it is meaningless. The desaster is just the same as with the default settings. I had even rebuilded my database after the last crash, so database integrity should have been ok, prio to this crash.

This is a pain!!! How long before i will experience data loss???

I have activated debug-log now.

Alex, what else to do???? There seems to be some bug, that is causing these issues. Are you actually performing a rollback, when an exception was thrown?

Thomas
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Re: SQLite Error 11: database disk image is malformed

Postby CintaNotes Developer » Tue Mar 05, 2013 3:50 am

Thomas,
thanks for the information!

Yes, sure there is a rollback after an exception.

The problem is that we couldn't reproduce this error so far, so we can only guess what is happening.
But we are working on it.
Sorry for this problem anyway. The good news is that since only index gets corrupted, there is a very good chance there won't be data loss.

Am I correct that:
1) You don't use SN sync;
2) You have version 2.1 Beta?
3) Are you sure it is the same error as the one month ago?
Alex
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Re: SQLite Error 11: database disk image is malformed

Postby Thomas Lohrum » Tue Mar 05, 2013 8:06 am

CintaNotes Developer wrote:Yes, sure there is a rollback after an exception.

How come the sqlite database gets corrupted this way? Is stability really that bad? How can an application bug cause such problems?

CintaNotes Developer wrote:1) You don't use SN sync;

No, i don't use SimpleNote sync.

CintaNotes Developer wrote:2) You have version 2.1 Beta?

Yes.

CintaNotes Developer wrote:3) Are you sure it is the same error as the one month ago?

The result is always the same, in that i get "SQLiter Error 11: database disk image is malformed". The last two times i ran into these problems, when i wanted to leave off work. Just before that i did some clean up. I checked every section for the latest changes, made some modifications to the note's text or moved notes between sections. Either by using Ctrl+X/Ctrl+V or using the section selector. Moving notes between sections is the one thing, that makes me think this causes the problems. I also deleted notes. Please be aware that i usually delete from inside the notes editor using Ctrl+Del.

Thomas

PS: Did you read my questions from this post http://www.cintanotes.com/forum/viewtopic.php?f=3&t=1574#p6935?
Thomas Lohrum
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Re: SQLite Error 11: database disk image is malformed

Postby Thomas Lohrum » Tue Mar 05, 2013 10:27 am

I did a test with some pretty wild editing, deleting, cutting, pasting, inserting and updating notes. Though i was not able to repdroduce a crash, i became aware that i use bullet lists a lot in my day to day work. Since it is the ix_ParaFormat that was affected twice, this could be a good hint to where the problem might be located.

Thomas
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Re: SQLite Error 11: database disk image is malformed

Postby CintaNotes Developer » Tue Mar 05, 2013 12:06 pm

i could not use ".read dump.sql" on an empty database, because CintaNotes complains the database was created by an old CintaNotes version.
"Diese Notizbuchdatei "cintanotes.db" wurde von einer älteren Version von CintaNotes erstellt und kann nicht aktualisiert werden. Fehlermeldung: SQLite Error 1: there is already another table or index with this name: NoteCache"
Alex, i think the latter is actually a bug! I checked sqlite's user version, which is 2001.


Seems that your sql included some DDL statements which were not needed since the schema was already created.
To tell any further, I'd need to examine the dump.sql file.
I had no problems with:

Code: Select all

sqlite3.exe my.db .dump > dump.sql
sqlite3.exe
  .read dump.sql
  .backup my2.db
  .exit


Thomas Lohrum wrote:Does CN use SQLites's Backup API to create a backup or does it simply copy the database file?

CN uses the Backup API.

Thomas Lohrum wrote:When using sqlite.pragma.journal_mode=WAL, it seems that the WAL-files will not be part of the backup. When using sqlite.pragma.journal_mode=WAL together with sqlite.pragma.synchronous=FULL, i noticed that after a save/commit it takes a couple of seconds until a checkpoint gets executed and the WAL-file disappears. As i take it from sqlite's docs this is by intention. I think this is important, because from my observation i take it, that the WAL-file will not be part of the backup. Thus it appears to be best, to use the two settings together.

Thanks for the info. But I generally don't think that the problem has anything to do with sync mode or journal mode, so switching to WAL is not really justified. Both WAL and an ordinary transaction journal have approximately same resilience when it comes to DB corruption issues.
Please make sure you read this: http://www.sqlite.org/wal.html, especially the 'disadvantages' part.

Thomas Lohrum wrote: also tried using Firefox's Addon "SQLite Manager", which gave me the following error, when exporting the database: "Likely SQL syntax error: SELECT * FROM "main","NotesData" {unknown tokenizer:my_unicode]"

Yes, CN uses its own tokenizer. You need to export the NotesData_content table only, not NotesData itself (it is a virtual table created by FTS3 Full-Text Search engine).

Thomas Lohrum wrote:SQLite is embedded/compiled into CintaNotes.exe, right? Do you actually use the latest SQLite-Version 3.7.15.2?

Yes, SQlite is statically linked into cintanotes.exe. The version 3.7.13 is currently used. We plan to upgrade to 3.7.15.2 in 2.1 final.

Thomas Lohrum wrote:When i created a sql-dump i observed, that all notes are written without any formatting. Is this correct? This makes sqlite's sql dump meaningless for use with CintaNotes.

Formatting is stored separately in tables TextFormat and ParaFormat.

Thomas Lohrum wrote:When i did a restore of the file "hourly.cintanotes.db" with a timestamp 23:02 i noticed that the most recent note had a timestamp of 21:57. Something is wrong here, since i am 100% sure, i had saved several notes between 22:00 and 23:00. It appears, that the backup goes wrong/incomplete.

Did you just load the file, or you imported it?
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Re: SQLite Error 11: database disk image is malformed

Postby CintaNotes Developer » Tue Mar 05, 2013 12:12 pm

How come the sqlite database gets corrupted this way? Is stability really that bad? How can an application bug cause such problems?


As you can see here, there are a lot of possible reasons. Our task is to determine, which one it is in your case.

Thomas Lohrum wrote:The result is always the same, in that i get "SQLiter Error 11: database disk image is malformed". The last two times i ran into these problems, when i wanted to leave off work. Just before that i did some clean up. I checked every section for the latest changes, made some modifications to the note's text or moved notes between sections. Either by using Ctrl+X/Ctrl+V or using the section selector. Moving notes between sections is the one thing, that makes me think this causes the problems. I also deleted notes. Please be aware that i usually delete from inside the notes editor using Ctrl+Del.

Thanks for these details, it'll surely help.

Again i had created a new note just a couple of minutes before. The creation date was there, but no modification date. I am not sure, but maybe i had changed some text thereafter. Anyway, when i tried to delete the note again, i got "SQLite Error 19 - foreign key constraint failed". After closing and restarting CintaNotes, i got "SQLite Error 11: database disk image is malformed".

Hm, now we are getting somewhere! If only we could repeat this "foreign key constraint failed" error! Seems to be the reason for all that happens afterwards.

Thomas Lohrum wrote:This time i had set sqlite.pragma.synchronous = FULL and sqlite.pragma.journal_mode = WAL, which should have given me the best sqlite stability. Well, it is meaningless.

You're right, sync mode and journal mode seem to have nothing to do with this.
This is most probably a program logic error, tied to some specific sequence of actions that you do.

What will 100% help:
1) A sample of a corrupted db
2) A log file with the error taped on it
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Re: SQLite Error 11: database disk image is malformed

Postby CintaNotes Developer » Tue Mar 05, 2013 12:15 pm

Thomas Lohrum wrote:I did a test with some pretty wild editing, deleting, cutting, pasting, inserting and updating notes. Though i was not able to repdroduce a crash, i became aware that i use bullet lists a lot in my day to day work. Since it is the ix_ParaFormat that was affected twice, this could be a good hint to where the problem might be located.

Thomas

Thanks for this info as well.
Now we have two prime suspects:
1) Bullet lists
2) Ctrl+Del in note editor
Alex
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Re: SQLite Error 11: database disk image is malformed

Postby Thomas Lohrum » Tue Mar 05, 2013 2:28 pm

Alex,

thank you very much for your complete answers and the insight added to CN's usage of SQLite! :D

CintaNotes Developer wrote:Hm, now we are getting somewhere! If only we could repeat this "foreign key constraint failed" error! Seems to be the reason for all that happens afterwards.

Be aware that the first crash was caused by "id not unique". Both share the error code 19, which in the end marks an abort due to a constraint violation.

More infos and questions:

  • In the task manager i observed, that CN does read a huge amount of data over time. Yesterday i had a value of 700 MB E/A Bytes (read). My database is actually 4 MB in size.
  • Does CN use the ON CONFLICT statement? From the docs i read the default for this is "Abort", whereas "Rollback" should be used in my opinion. Please note "The ON CONFLICT algorithm does not apply to FOREIGN KEY constraints." check here http://sqlite.org/lang_conflict.html.
  • Does CN use explicit transactions using the "BEGIN TRANSACTION" statement?
  • Does CN use SAVEPOINTs?

Thomas
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Re: SQLite Error 11: database disk image is malformed

Postby Thomas Lohrum » Wed Mar 06, 2013 9:28 am

I did an analysis of the two relevant crashes regarding the note that was causing the missing row in ix_ParaFormat.

Note number one:
  • uses hierarchical tags with a dot, for example Contacts/Alex.Jenter
  • uses bullet lists a lot
  • uses sub-paragraphs, that is Shift+Enter, every line starts with "- "
  • uses underline as text formatting for headers

Note number one:
  • had no title and was created 45 minutes before the crash

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Re: SQLite Error 11: database disk image is malformed

Postby CintaNotes Developer » Wed Mar 06, 2013 9:51 am

Thomas,

Thomas Lohrum wrote:In the task manager i observed, that CN does read a huge amount of data over time. Yesterday i had a value of 700 MB E/A Bytes (read). My database is actually 4 MB in size.

It's probably hourly backup contributing to this. Also every time you search and scroll the list you're reading the DB. CN doesn't keep everything in RAM to keep memory footprint low.

Thomas Lohrum wrote:Does CN use the ON CONFLICT statement? From the docs i read the default for this is "Abort", whereas "Rollback" should be used in my opinion. Please note "The ON CONFLICT algorithm does not apply to FOREIGN KEY constraints." check here http://sqlite.org/lang_conflict.html.

No, CN doesn't use the ON CONFLICT statement. During nomal operation, there should be no constraint violations. In case there are, it's better to know about it at once and not sweep it under the rug.
But you're right, this can possibly be the reason of the db corruption. But it can't be the reason of a corrupted index, I think.
I'll investigate it further, thanks!

Thomas Lohrum wrote:Does CN use explicit transactions using the "BEGIN TRANSACTION" statement?

Yes.

Thomas Lohrum wrote:Does CN use SAVEPOINTs?[/list]

No.
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Re: SQLite Error 11: database disk image is malformed

Postby CintaNotes Developer » Wed Mar 06, 2013 10:08 am

Thomas Lohrum wrote:Note number one:
  • uses hierarchical tags with a dot, for example Contacts/Alex.Jenter
  • uses bullet lists a lot
  • uses sub-paragraphs, that is Shift+Enter, every line starts with "- "
  • uses underline as text formatting for headers

Note number one:
  • had no title and was created 45 minutes before the crash

Thomas


Thanks for the extra info. Still, no success in reproducing this :(
But since you're writing debug log, sooner or later we'll have it.
Just hope you have enough hard disk space)
Alex
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Re: SQLite Error 11: database disk image is malformed

Postby Thomas Lohrum » Wed Mar 06, 2013 10:34 am

CintaNotes Developer wrote:But since you're writing debug log, sooner or later we'll have it.
Just hope you have enough hard disk space)

I observed the debug-log growth can become as big as several hundred megabytes, even though it can be compressed tremendously. My hope is actually, that the debug-log will have enough information to catch the bug. Another concern is, that writing the debug log might have effects on the issue itself.
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Re: SQLite Error 11: database disk image is malformed

Postby Thomas Lohrum » Wed Mar 06, 2013 11:11 am

I can not download. I get an error "The attachment does not exist anymore".

UPDATE 12:19: ok, i got it now. Will run some tests....
Last edited by Thomas Lohrum on Wed Mar 06, 2013 11:19 am, edited 1 time in total.
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Re: SQLite Error 11: database disk image is malformed

Postby CintaNotes Developer » Wed Mar 06, 2013 11:16 am

Thomas, I think I have found something which may be the reason of the bug.
The database upgrade process from version 1800 to version 1901 contained a small bug.
This means that if you haven't re-created your db since then, it is very likely you have
this problem too.

Here are some simple tests to run:
1) Please load your .db into SQlite Manager and execute the following query:
SELECT COUNT(1) FROM TextFormat WHERE id IS NULL OR id = 0
It should return zero, if it returns anything else - your db has this problem.

2) Try the executable below (it should fix your db).
Make sure you have debug=1 in settings file before running it, so that in case
something happens, we have a log of it!

Of course, this may not be the end of it.. but there's hope)
Huge thanks!
Attachments
CintaNotes_MAR06.rar
(2.17 MiB) Downloaded 600 times
Alex
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Re: SQLite Error 11: database disk image is malformed

Postby Thomas Lohrum » Wed Mar 06, 2013 11:37 am

CintaNotes Developer wrote:Thomas, I think I have found something which may be the reason of the bug. The database upgrade process from version 1800 to version 1901 contained a small bug.
This means that if you haven't re-created your db since then, it is very likely you have
this problem too.

I did a rebuild of my database each time the database was malformed.

CintaNotes Developer wrote:1) Please load your .db into SQlite Manager and execute the following query:
SELECT COUNT(1) FROM TextFormat WHERE id IS NULL OR id = 0
It should return zero, if it returns anything else - your db has this problem.

I used sqlite3.exe. It does return zero, which i expected, because i did a rebuild of my database previously.

CintaNotes Developer wrote:2) Try the executable below (it should fix your db). Make sure you have debug=1 in settings file before running it, so that in case something happens, we have a log of it!

I did install that version anyway. Anything i should consider about doing not so? Any news with that version?

CintaNotes Developer wrote:Of course, this may not be the end of it.. but there's hope)
Huge thanks!

You're welcome. In german we have a saying "Die Hoffnung stirbt zuletzt". (engl. Hope dies at last). Lets see how this thing comes out.

Thomas
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Re: SQLite Error 11: database disk image is malformed

Postby CintaNotes Developer » Wed Mar 06, 2013 12:23 pm

Thanks, Thomas.
I've found another small issue, so please use the version below.

New things in it:
- "Create Link To File" context menu item in editor.
- Fixed: Recycle bin: unsaved note can't be moved to trash via editor
- Fixed: CN crashes if .db file is deleted while it is unlocked for synchronization
Attachments
CintaNotes_MAR06_2.rar
(2.17 MiB) Downloaded 530 times
Alex
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Re: SQLite Error 11: database disk image is malformed

Postby Thomas Lohrum » Wed Mar 06, 2013 1:24 pm

CintaNotes Developer wrote:I've found another small issue, so please use the version below.

Can you tell some details, please?! How would that help me? How can i verify it actually affects me?

CintaNotes Developer wrote:"Create Link To File" context menu item in editor.

When selecting a file which contains spaces, CN creates an invalid link. Spaces must be converted to %20, but they don't. Wasn't that, what the whole point was about?! I also noticed CN creates "file://" only. It runs, but i expected it to be a link like this "file:///".

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Re: SQLite Error 11: database disk image is malformed

Postby Thomas Lohrum » Wed Mar 06, 2013 2:56 pm

CintaNotes Developer wrote:Thanks, Thomas. I've found another small issue, so please use the version below.

Warning! After installing the file "CintaNotes_MAR06_2.rar" i was no longer able to open my database file due to a version mismatch. I recommend other users not to install this version.
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Re: SQLite Error 11: database disk image is malformed

Postby CintaNotes Developer » Thu Mar 07, 2013 5:42 am

Thomas Lohrum wrote:Can you tell some details, please?! How would that help me? How can i verify it actually affects me?

In versions before MAR06-2:
1) Create a note
2) Add a link to some other note
3) Save the note
4) Delete this note
5) Create another note
6) Add a link to some other note
7) Save the note -> PRIMARY KEY CONSTRAINT violation error.

In version MAR06-2 this has been fixed.

Thomas Lohrum wrote:When selecting a file which contains spaces, CN creates an invalid link. Spaces must be converted to %20, but they don't. Wasn't that, what the whole point was about?! I also noticed CN creates "file://" only. It runs, but i expected it to be a link like this "file:///".

Yes, we'll fix this, thanks!

Thomas Lohrum wrote:Warning! After installing the file "CintaNotes_MAR06_2.rar" i was no longer able to open my database file due to a version mismatch. I recommend other users not to install this version.

Sorry, my fault! Will release 2.1 Beta 2 that will fix this.

UPD: Please try 2.1 Beta 2
Alex

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