Re: [sqlite] SQL error: disk I/O error and symlink

[Simon Slavin]

On 18 Nov 2009, at 8:38pm, priimak wrote:

> I understand that. However, that would not present a problem if I access 
> database by its symlink for reading only and database directly if I am 
> updating isn't?

According to the documentation that could be a problem.  The update application 
creates a journal file in the directory where the database file actually is.  
The application which reads the database file looks for a journal in the 
directory where the alias is, and doesn't find it.

Please note that I haven't read the source code for sqlite3, and I don't know 
if that's really how it works.

> By the way the reason for that usage ( though there are work arounds ) 
> is that I keep two instances of db file a.db.1 and a.db.2 with symlink 
> a.db pointing to one or there db file. If a.db -> a.db.1 I apply update 
> to a.db.2, swap symlink and then update a.db.2. Symlink a.db used by 
> webapp, which performs *only* select queries.

Rather than use a symbolic link, store something in the database files 
themselves which says which one is being updated.  Or use two different tables 
in the same database file.

I understand your use of symbolic links and it makes sense with atomic files -- 
files where you open the file, read the whole thing, then close it.  But it 
would seem to be a problem with SQLite files.

Simon.
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Re: [sqlite] SQL error: disk I/O error and symlink

[priimak]

Pavel Ivanov wrote:
>> That should not be a problem if I use symlink to access database for
>> reads only and
>> actual db file name for updating, isn't?
>> 
>
> I believe there can be a problem with such scenario. I don't know
> exactly but I doubt that file system can operate with locks on file
> handle open via symlink and via actual name interchangeably. And if it
> doesn't your reader can read corrupted data if it reads in the middle
> of writer's transaction...
>   

I see and can certainly change that, but you can see that my
problem is sort of opposite. I can also make any other symlink to a.db.1
then access db through it, but not directly. For example I can do

% ln -s a.db.1 foobar.db
and then access it through foobar.db, but not directly.
What could cause such problem?

--
Dmitri Priimak

> Pavel
>
> On Wed, Nov 18, 2009 at 2:15 PM, priimak  wrote:
>   
>> D. Richard Hipp wrote:
>> 
>>> On Nov 18, 2009, at 1:53 PM, priimak wrote:
>>>
>>>
>>>   
 Hi.

 I have a strange problem. I have a database a.db.1 and symlink a.db
 which points to a.db.1
 When I use command line sqlite3 command I get following.

 % echo "select max(id) from t;" | sqlite3 a.db.1
 SQL error near line 1: disk I/O error

 but

 % echo "select max(id) from t;" | sqlite3 a.db
 4461066

 Could that be explained? I use sqlite3 version 3.6.7


 
>>> Having multiple names for the same database file (either symbolic
>>> links or hard links) can lead to database corruption following an
>>> application crash if a different application reopens the same database
>>> via a different name.  See paragraph 9.5 in 
>>> http://www.sqlite.org/atomiccommit
>>>   to understand why.  Please do not create aliases of any kind for
>>> your database files.
>>>
>>>   
>> I see. However, the problem is related to journal been named after the
>> database name.
>> That should not be a problem if I use symlink to access database for
>> reads only and
>> actual db file name for updating, isn't?
>>
>> --
>> Dmitri Priimak
>>
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>>
>> 
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Re: [sqlite] SQL error: disk I/O error and symlink

[priimak]

Simon Slavin wrote:
> On 18 Nov 2009, at 7:15pm, priimak wrote:
>
>   
>> I see. However, the problem is related to journal been named after the 
>> database name.
>> That should not be a problem if I use symlink to access database for 
>> reads only and
>> actual db file name for updating, isn't?
>> 
>
> If you use a symbolic link for a database file, there's some doubt about 
> where the journal file belongs.  The documentation says
>
> "The rollback journal is always located in the same directory as the database 
> file and has the same name as the database file except with the 8 characters 
> "-journal" appended."
>
> The problem is that there's no way for sqlite to tell that your symbolic link 
> is not the real database file.  So it could create the journal file in the 
> directory containing the link rather than the directory containing the actual 
> database.  And if another application opens the database directly rather than 
> using the link, it will not find the journal file, so it will not deal with 
> anything needing the journal file correctly.  This is mentioned in section 6 
> of
>
> 
>
> If that documentation is right, then for symbolic links, that might be 
> considered a bug in sqlite.  It should be possible to do a 'resolve links' on 
> the file specification before deciding where to create the journal.  On the 
> other hand, for hard links this is not possible: the hard linking system does 
> not have a 'real' location for the file and other pointers to it, instead 
> each link to the file is equally valid.  But either way it is documented that 
> you shouldn't use links.
I understand that. However, that would not present a problem if I access 
database by its symlink for reading only and database directly if I am 
updating isn't?
By the way the reason for that usage ( though there are work arounds ) 
is that I keep two instances of db file a.db.1 and a.db.2 with symlink 
a.db pointing to one or there db file. If a.db -> a.db.1 I apply update 
to a.db.2, swap symlink and then update a.db.2. Symlink a.db used by 
webapp, which performs *only* select queries.
And yes, I do have a.db.1-journal and a.db.2-journal files, but not 
a.db-journal

That seems safe, isn't?

--
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Re: [sqlite] SQL error: disk I/O error and symlink

[Pavel Ivanov]

> That should not be a problem if I use symlink to access database for
> reads only and
> actual db file name for updating, isn't?

I believe there can be a problem with such scenario. I don't know
exactly but I doubt that file system can operate with locks on file
handle open via symlink and via actual name interchangeably. And if it
doesn't your reader can read corrupted data if it reads in the middle
of writer's transaction...

Pavel

On Wed, Nov 18, 2009 at 2:15 PM, priimak  wrote:
> D. Richard Hipp wrote:
>> On Nov 18, 2009, at 1:53 PM, priimak wrote:
>>
>>
>>> Hi.
>>>
>>> I have a strange problem. I have a database a.db.1 and symlink a.db
>>> which points to a.db.1
>>> When I use command line sqlite3 command I get following.
>>>
>>> % echo "select max(id) from t;" | sqlite3 a.db.1
>>> SQL error near line 1: disk I/O error
>>>
>>> but
>>>
>>> % echo "select max(id) from t;" | sqlite3 a.db
>>> 4461066
>>>
>>> Could that be explained? I use sqlite3 version 3.6.7
>>>
>>>
>>
>>
>> Having multiple names for the same database file (either symbolic
>> links or hard links) can lead to database corruption following an
>> application crash if a different application reopens the same database
>> via a different name.  See paragraph 9.5 in 
>> http://www.sqlite.org/atomiccommit
>>   to understand why.  Please do not create aliases of any kind for
>> your database files.
>>
> I see. However, the problem is related to journal been named after the
> database name.
> That should not be a problem if I use symlink to access database for
> reads only and
> actual db file name for updating, isn't?
>
> --
> Dmitri Priimak
>
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Re: [sqlite] SQL error: disk I/O error and symlink

[Simon Slavin]

On 18 Nov 2009, at 7:15pm, priimak wrote:

> I see. However, the problem is related to journal been named after the 
> database name.
> That should not be a problem if I use symlink to access database for 
> reads only and
> actual db file name for updating, isn't?

If you use a symbolic link for a database file, there's some doubt about where 
the journal file belongs.  The documentation says

"The rollback journal is always located in the same directory as the database 
file and has the same name as the database file except with the 8 characters 
"-journal" appended."

The problem is that there's no way for sqlite to tell that your symbolic link 
is not the real database file.  So it could create the journal file in the 
directory containing the link rather than the directory containing the actual 
database.  And if another application opens the database directly rather than 
using the link, it will not find the journal file, so it will not deal with 
anything needing the journal file correctly.  This is mentioned in section 6 of



If that documentation is right, then for symbolic links, that might be 
considered a bug in sqlite.  It should be possible to do a 'resolve links' on 
the file specification before deciding where to create the journal.  On the 
other hand, for hard links this is not possible: the hard linking system does 
not have a 'real' location for the file and other pointers to it, instead each 
link to the file is equally valid.  But either way it is documented that you 
shouldn't use links.

Simon.
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Re: [sqlite] SQL error: disk I/O error and symlink

[priimak]

D. Richard Hipp wrote:
> On Nov 18, 2009, at 1:53 PM, priimak wrote:
>
>   
>> Hi.
>>
>> I have a strange problem. I have a database a.db.1 and symlink a.db
>> which points to a.db.1
>> When I use command line sqlite3 command I get following.
>>
>> % echo "select max(id) from t;" | sqlite3 a.db.1
>> SQL error near line 1: disk I/O error
>>
>> but
>>
>> % echo "select max(id) from t;" | sqlite3 a.db
>> 4461066
>>
>> Could that be explained? I use sqlite3 version 3.6.7
>>
>> 
>
>
> Having multiple names for the same database file (either symbolic  
> links or hard links) can lead to database corruption following an  
> application crash if a different application reopens the same database  
> via a different name.  See paragraph 9.5 in 
> http://www.sqlite.org/atomiccommit 
>   to understand why.  Please do not create aliases of any kind for  
> your database files.
>   
I see. However, the problem is related to journal been named after the 
database name.
That should not be a problem if I use symlink to access database for 
reads only and
actual db file name for updating, isn't?

--
Dmitri Priimak

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Re: [sqlite] SQL error: disk I/O error and symlink

[D. Richard Hipp]

On Nov 18, 2009, at 1:53 PM, priimak wrote:

> Hi.
>
> I have a strange problem. I have a database a.db.1 and symlink a.db
> which points to a.db.1
> When I use command line sqlite3 command I get following.
>
> % echo "select max(id) from t;" | sqlite3 a.db.1
> SQL error near line 1: disk I/O error
>
> but
>
> % echo "select max(id) from t;" | sqlite3 a.db
> 4461066
>
> Could that be explained? I use sqlite3 version 3.6.7
>


Having multiple names for the same database file (either symbolic  
links or hard links) can lead to database corruption following an  
application crash if a different application reopens the same database  
via a different name.  See paragraph 9.5 in http://www.sqlite.org/atomiccommit 
  to understand why.  Please do not create aliases of any kind for  
your database files.

SQLite uses O_NOFOLLOW, not for this reason, but to prevent an attack  
using symbolic links that could allow an unprivileged user to trick  
SQLite into deleting a file that the unprivileged user does not have  
access rights for.

D. Richard Hipp
d...@hwaci.com



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[sqlite] SQL error: disk I/O error and symlink

[priimak]

Hi.

I have a strange problem. I have a database a.db.1 and symlink a.db 
which points to a.db.1
When I use command line sqlite3 command I get following.

% echo "select max(id) from t;" | sqlite3 a.db.1
SQL error near line 1: disk I/O error

but

% echo "select max(id) from t;" | sqlite3 a.db
4461066

Could that be explained? I use sqlite3 version 3.6.7

--
Dmitri Priimak


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Re: [sqlite] SQL error: disk I/O error

[pierr]

Nuno Lucas-2 wrote:
> 
> On 5/23/07, Shilpa Sheoran  wrote:
>> Linux 2.6.9
>> and the media is Nand Flash memory.
>> /dir1/dir2/dir3
>>
>> /dir1/dir2 is readonly (cramfs)
>> dir3 is read write (Flash mem). and I'm creating the database in dir3.
> 
> There is your problem. The file system on that directory (I would
> guess JFS2 or similar), doesn't support the fsync() call.
> 
> 
This might not be true. See below:
http://www.linux-mtd.infradead.org/faq/jffs2.html
"
On NOR FLASH each write goes directly into the FLASH.

On NAND FLASHM and NOR ECC FLASH we have a write-buffer for writing only
full pages to the chips. There could be a loss of data, when the
write-buffer is not flushed before power down. There are some mechanisms to
ensure, that the write-buffer is flushed. You can force the flush of the
write-buffer by using fsync() or sync() in your application. JFFS2 has a
timed flush of the write buffer, which forces the flush of the buffer to
flash, if there are no writes to the filesystem for more than about 5
seconds. The time depends on the cycle-time of kupdated, which can be
adjusted via /proc/sys/vm/dirty_expire_centisecs."

-- 
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Sent from the SQLite mailing list archive at Nabble.com.

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Re: [sqlite] SQL error: disk I/O error, for attached DBs on power PC

[France Hsu]

Hi! All,

After using strace, we found the root cause.
SQLite will use some temporary files to keep the select (with union all) 
result.
See: http://www.sqlite.org/tempfiles.html

In our system, we allocated 32M for /, and there are only 19M after 
booting up the system.
SQLite can not get enough space for the temporary files (strace shows 
"write error: space is not enough")
After adding a compiling configuration -DSQLITE_TEMP_STORE=3 to SQLIte's 
Makefile, we can finish this job.
http://www.sqlite.org/compile.html#temp_store

Also, we can change the location of the temporary files to solve this 
issue.

France Hsu wrote:
> Hi! All,
>
> We recently got an error "Disk I/O error" while using the select 
> command on attached DBs.
> These DBs have same table format
> We only execute select, insert, and attach commands
>
> The environment is as follows:
> SQLite: V3.5.6
> OS: Linux 2.6.24.2
> Platform Power PC (MPC8543)
> Memory: 256M
> DB Location: SATA hard drive, within a 512-maga-byte partition
>
> The error is happened when the size of one DB file is larger than 10M,
> Ex:
> -rw-r--r--1 root root 10600448 Aug  1 14:38 system_log-07.db
> -rw-r--r--1 root root27648 Aug  7 22:18 system_log-08.db
>
> ./sqlite3 system_log-08.db
> sqlite> attach ''system_log-07.db' as db1;
> sqlite> select * from main.disk_log union all select * from 
> db1.disk_log order by timestamp desc;
> SQL error: disk I/O error
>
> Available partition size: 467.2M
> Sometimes I executed the command "select count(*) ..." successfully, 
> but sometimes failed.
> The total number of the result is about 15.
> Sometimes I executed the command "select * ... limit 0, 3" 
> successfully, but sometimes failed.
> As observing top when executing sqlite, the available memory is enough 
> (about 120-140M).
>
> Would you provide some comments or some solutions?
> Thank you all very much.
>

-- 

Best Regards,
France Hsu 


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[sqlite] SQL error: disk I/O error, for attached DBs on power PC

[France Hsu]

Hi! All,

We recently got an error "Disk I/O error" while using the select command 
on attached DBs.
These DBs have same table format
We only execute select, insert, and attach commands

The environment is as follows:
SQLite: V3.5.6
OS: Linux 2.6.24.2
Platform Power PC (MPC8543)
Memory: 256M
DB Location: SATA hard drive, within a 512-maga-byte partition

The error is happened when the size of one DB file is larger than 10M,
Ex:
-rw-r--r--1 root root 10600448 Aug  1 14:38 system_log-07.db
-rw-r--r--1 root root27648 Aug  7 22:18 system_log-08.db

./sqlite3 system_log-08.db
sqlite> attach ''system_log-07.db' as db1;
sqlite> select * from main.disk_log union all select * from db1.disk_log 
order by timestamp desc;
SQL error: disk I/O error

Available partition size: 467.2M
Sometimes I executed the command "select count(*) ..." successfully, but 
sometimes failed.
The total number of the result is about 15.
Sometimes I executed the command "select * ... limit 0, 3" 
successfully, but sometimes failed.
As observing top when executing sqlite, the available memory is enough 
(about 120-140M).

Would you provide some comments or some solutions?
Thank you all very much.

-- 
Best Regards,
France Hsu

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[sqlite] SQL error: disk I/O error

[Robert Citek]

Hello all,

I recently got an error while running a long query with sqlite3 on
Ubuntu Gutsy 7.10:

SQL error: disk I/O error

I googled for a solution but didn't find anything relevant.  After a
bit of sleuthing on my machine, I discovered that I was running out of
disk space.  I freed up some disk space, reran the query, and it
finished this time without giving an error.

Figured I'd post just in case someone else might run into something similar.

Regards,
- Robert
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Re: [sqlite] SQL error: disk I/O error

[Nuno Lucas]

On 5/23/07, Shilpa Sheoran <[EMAIL PROTECTED]> wrote:

Linux 2.6.9
and the media is Nand Flash memory.
/dir1/dir2/dir3

/dir1/dir2 is readonly (cramfs)
dir3 is read write (Flash mem). and I'm creating the database in dir3.


There is your problem. The file system on that directory (I would
guess JFS2 or similar), doesn't support the fsync() call.

The reason has probably to do with the fact the system driver reserves
the right to choose when to do the real write (else a bugged program
or even a malicious user could wear off the device).

That is probably done every 5 seconds or so (is usually configurable
by a kernel parameter), but has the drawback of messing with the ACID
nature of SQLite.


Regards,
~Nuno Lucas


Somehow I don't have a problem in a tmpfs.
The strace showed no diff between tmpfs and this directory where it is
giving I/O error.

Thanks

On 5/22/07, Joe Wilson <[EMAIL PROTECTED]> wrote:
> What is the OS you're using and what kind of media is it?
> Hard drive or USB key or ???
>
> --- Shilpa Sheoran <[EMAIL PROTECTED]> wrote:
> > It seems that  rc = fsync(fd); is failing in function
> >  static int full_fsync(int fd, int fullSync, int dataOnly) in file os_unix.c
> > {
> > #else /* if !defined(F_FULLSYNC) */
> >   if( dataOnly ){
> > rc = fdatasync(fd);
> >   }else{
> >
> > //*this call is failing
> >rc = fsync(fd);
> >   }
> >
> > }
> >
> > using -DSQLITE_NO_SYNC in the Makefile works
> > What is the way out for this problem?
> > What happens if we use this option -DSQLITE_NO_SYNC ?


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Re: [sqlite] SQL error: disk I/O error

[Shilpa Sheoran]

Linux 2.6.9
and the media is Nand Flash memory.
/dir1/dir2/dir3

/dir1/dir2 is readonly (cramfs)
dir3 is read write (Flash mem). and I'm creating the database in dir3.

Somehow I don't have a problem in a tmpfs.
The strace showed no diff between tmpfs and this directory where it is
giving I/O error.

Thanks

On 5/22/07, Joe Wilson <[EMAIL PROTECTED]> wrote:

What is the OS you're using and what kind of media is it?
Hard drive or USB key or ???

--- Shilpa Sheoran <[EMAIL PROTECTED]> wrote:
> It seems that  rc = fsync(fd); is failing in function
>  static int full_fsync(int fd, int fullSync, int dataOnly) in file os_unix.c
> {
> #else /* if !defined(F_FULLSYNC) */
>   if( dataOnly ){
> rc = fdatasync(fd);
>   }else{
>
> //*this call is failing
>rc = fsync(fd);
>   }
>
> }
>
> using -DSQLITE_NO_SYNC in the Makefile works
> What is the way out for this problem?
> What happens if we use this option -DSQLITE_NO_SYNC ?




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Re: [sqlite] SQL error: disk I/O error

[Joe Wilson]

What is the OS you're using and what kind of media is it?
Hard drive or USB key or ???

--- Shilpa Sheoran <[EMAIL PROTECTED]> wrote:
> It seems that  rc = fsync(fd); is failing in function
>  static int full_fsync(int fd, int fullSync, int dataOnly) in file os_unix.c
> {
> #else /* if !defined(F_FULLSYNC) */
>   if( dataOnly ){
> rc = fdatasync(fd);
>   }else{
> 
> //*this call is failing
>rc = fsync(fd);
>   }
> 
> }
> 
> using -DSQLITE_NO_SYNC in the Makefile works
> What is the way out for this problem?
> What happens if we use this option -DSQLITE_NO_SYNC ?



   
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Re: [sqlite] SQL error: disk I/O error

[Shilpa Sheoran]

It seems that  rc = fsync(fd); is failing in function
static int full_fsync(int fd, int fullSync, int dataOnly) in file os_unix.c
{
#else /* if !defined(F_FULLSYNC) */
 if( dataOnly ){
   rc = fdatasync(fd);
 }else{

//*this call is failing
  rc = fsync(fd);
 }

}

using -DSQLITE_NO_SYNC in the Makefile works
What is the way out for this problem?
What happens if we use this option -DSQLITE_NO_SYNC ?

Thanks
Shilpa


On 5/21/07, Joe Wilson <[EMAIL PROTECTED]> wrote:

If you're using Linux, try:

echo "create table t1(a);" |strace ./sqlite3 my.db 2>&1 |less

and examine the output. See where it differs from the successful
tmpfs run.

Newer versions of sqlite3 may have better IO error messages.

> I'm running the command line tool to create sqlite3 db.
> My directory permissions are  drwxrwxrwt.
> I'm getting the following error.
>
> > ./sqlite3 newdb
> SQLite version 3.3.12
> Enter ".help" for instructions
> sqlite> create table tbl1(one varchar(10), two smallint);
> SQL error: disk I/O error
>
> If I try the same thing in  a tmpfs, it works.




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Re: [sqlite] SQL error: disk I/O error

[Joe Wilson]

If you're using Linux, try:

echo "create table t1(a);" |strace ./sqlite3 my.db 2>&1 |less

and examine the output. See where it differs from the successful
tmpfs run.

Newer versions of sqlite3 may have better IO error messages.

> I'm running the command line tool to create sqlite3 db.
> My directory permissions are  drwxrwxrwt.
> I'm getting the following error.
> 
> > ./sqlite3 newdb
> SQLite version 3.3.12
> Enter ".help" for instructions
> sqlite> create table tbl1(one varchar(10), two smallint);
> SQL error: disk I/O error
> 
> If I try the same thing in  a tmpfs, it works.



   
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[sqlite] SQL error: disk I/O error

[Shilpa Sheoran]

I'm running the command line tool to create sqlite3 db.
My directory permissions are  drwxrwxrwt.
I'm getting the following error.


./sqlite3 newdb

SQLite version 3.3.12
Enter ".help" for instructions
sqlite> create table tbl1(one varchar(10), two smallint);
SQL error: disk I/O error

If I try the same thing in  a tmpfs, it works.

What could be the reason for this?

Thanks,
Shilpa

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