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

[Juha H. <juh...@he...>]

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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