Re: [scipion-users] Scipion and sqlite database or disk full error

[Jose M. de la R. T. <del...@gm...>]

Ok, thanks a lot for the feedback! Please don't hesitate to let us know.

On Sat, Nov 2, 2019 at 11:42 AM Juha Huiskonen <juh...@he...>
wrote:

> It's possible that my database file was corrupted.  When I copied run.db
> (from the most recent successful run) over project.sqlite things started to
> work.  However at the same time I added SQLITE_TMPDIR environmental
> variable pointing to a large scratch partition. So either of these could
> have been the solution... Our other users who have seen the same error will
> keep testing and I will report back.
>
> On Sat, Nov 2, 2019 at 12:32 PM Jose Miguel de la Rosa Trevin <
> del...@gm...> wrote:
>
>> Hum...probably Sqlite library generates some of these temporary files
>> under the hood
>> while operating with databases if necessary. As far as I know, these
>> temporary files
>> are in the same places of the main sqlite file. We don't use some of the
>> operations
>> described there, so I guess not all are used in our case. Anyway, non of
>> these are
>> handled by our code...I'm curious what is causing your troubles.
>>
>> On Fri, Nov 1, 2019 at 1:12 PM Juha Huiskonen <juh...@he...>
>> wrote:
>>
>>> So no temporary files whatsoever? Nothing like the ones explained here?
>>> --> https://www.sqlite.org/tempfiles.html
>>>
>>> On Fri, Nov 1, 2019 at 1:50 PM Jose Miguel de la Rosa Trevin <
>>> del...@gm...> wrote:
>>>
>>>> Hi,
>>>>
>>>> All sqlite databases are written inside the project folder. Some are
>>>> run.db inside each run folder.
>>>> Others are the .sqlite files for output sets.
>>>>
>>>> Best,
>>>> Jose Miguel
>>>>
>>>>
>>>>
>>>> On Fri, Nov 1, 2019 at 12:33 PM Juha Huiskonen <
>>>> juh...@he...> wrote:
>>>>
>>>>> Hi Jose Miquel,
>>>>>
>>>>> We need to investigate and it would be good to know where the file is
>>>>> written? Is it only the one written in the project directory (we do have
>>>>> plenty of space there)?  Or are there temporary files written somewhere
>>>>> else? (If yes where? /tmp? ~/?)
>>>>>
>>>>> Best wishes,
>>>>> Juha
>>>>>
>>>>>
>>>>> On Fri, Nov 1, 2019 at 1:12 PM Jose Miguel de la Rosa Trevin <
>>>>> del...@gm...> wrote:
>>>>>
>>>>>> Hi Juha,
>>>>>>
>>>>>> Many temporary SQL database are kept in memory and final output
>>>>>> written to disk.
>>>>>> Have you check quota errors or if there is space left on disk?
>>>>>>
>>>>>> Best,
>>>>>> Jose Miguel
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Nov 1, 2019 at 11:47 AM Juha Huiskonen <
>>>>>> juh...@he...> wrote:
>>>>>>
>>>>>>> Dear All,
>>>>>>>
>>>>>>> We are seeing this error with large datasets (over 1M particles).
>>>>>>> Where is Scipion writing temporary sql files? I suspect there might be a
>>>>>>> limit in the file system, causing this error.   Or can it be because of
>>>>>>> something else? Have others experienced this error and solved it?
>>>>>>>
>>>>>>> Best wishes,
>>>>>>> Juha
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>>>>>>>
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