Re: [scipion-users] xmipp movie extract 'ProgrammingError' recursive use of commas not allowed

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

Dear Teige,

>From your error log it seems that there is a bug in this Xmipp protocol in
line:

00095:     File "/beebylab/software/scipion/1.2/scipion/pyworkflow/em/
packages/xmipp3/protocol_extract_particles_movies.py", line 434, in
_filterMovie
00096:       micrograph = micSet[movieId]

Where the micSet (internally a .sqlite database) is accessed from multiple
threads. I think this should be fixed by removing this query in the way it
is now.
In the meantime, as David suggested, you could try to run with only 1
processor, but not sure how long it will take.

I'm sorry for this issue.
Best,
Jose Miguel


On Tue, Aug 7, 2018 at 4:03 PM David Maluenda <dma...@cn...> wrote:

> This sounds like it's trying to read/write to .sqlite in threads and
> sqlite doesn't support threating.
>
> Therefore, try to run the protocol with *1 thread* and *1 MPI*.
>
>
> Thanks for your comment!
>
> <http://ucm.es/>
>
> *_____Dr. David Maluenda Niubó*
> dma...@cn... - (+34) 619 029 310
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> On Tue, Aug 7, 2018 at 2:49 PM Matthews-Palmer, Teige Rowan Seal <
> t.m...@im...> wrote:
>
>> Dear Scipion users,
>>
>> I am getting the following error in Caligula v1.2, from the protocol
>> xmipp3 extract movie particles:
>>
>> Any ideas or help greatly appreciated.
>> All the best,
>>
>> Teige
>>
>>
>> 00086:   Traceback (most recent call last):
>> 00087:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/executor.py",
>> line 137, in run
>> 00088:       self.step._run()  # not self.step.run() , to avoid race
>> conditions
>> 00089:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/protocol.py",
>> line 233, in _run
>> 00090:       resultFiles = self._runFunc()
>> 00091:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/protocol.py",
>> line 229, in _runFunc
>> 00092:       return self._func(*self._args)
>> 00093:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/em/protocol/protocol_movies.py",
>> line 234, in processMovieStep
>> 00094:       if self._filterMovie(movie):
>> 00095:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/em/packages/xmipp3/protocol_extract_particles_movies.py",
>> line 434, in _filterMovie
>> 00096:       micrograph = micSet[movieId]
>> 00097:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1040,
>> in __getitem__
>> 00098:       return self._getMapper().selectById(itemId)
>> 00099:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1025,
>> in _getMapper
>> 00100:       self.load()
>> 00101:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1117,
>> in load
>> 00102:       self._idCount = self._mapper.maxId()
>> 00103:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/mapper/sqlite.py", line
>> 900, in maxId
>> 00104:       return 0 if self.doCreateTables else self.db.maxId()
>>
>>
>> *00105:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/mapper/sqlite.py", line
>> 1201, in maxId 00106:
>> self.executeCommand(self.selectCmd('1').replace('*', 'MAX(id)')) 00107:
>> ProgrammingError: Recursive use of cursors not allowed.*
>>
>>
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