Re: [scipion-users] relion classification of xmipp binned particles

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

Hi Juha,

What is the protocol that make a single stack? The binning one or the
normalization? Apart from this specific issue later in Relion protocol,
maybe would be good idea to keep an stack per micrograph name.

Bests,
Jose Miguel


On Tue, Jun 27, 2017 at 3:35 PM, Juha Huiskonen <ju...@st...>
wrote:

> Hi Laura,
>
> Is your test with multiple nodes or GPUs? I wonder what happens in Relion
> if there is just one stack, when it's splitting it. Also I guess memory can
> be an issue when opening a large single stack on GPUs? I have 160,000
> particles that were originally 300 pix and now they are 100 pix. I was
> running 3D classification and it indeed crashed in the Estimating Initial
> Noise step
>
> Best wishes,
> Juha
>
> On Tue, Jun 27, 2017 at 2:28 PM, ldelcano <lde...@cn...> wrote:
>
>> Hi Jose Miguel,
>>
>> I have tested with a project that I have. Particles 200 px resized to 66
>> px (factor 0.333) and normalized with Xmipp. Then I run Relion 2D
>> classification and it arrives to Iteration 1 without errors.  I guess the
>> error that Juha is reporting is on Estimating Initial Noise Expectra. I
>> will try tomorrow with another dataset.
>>
>> cheers
>>
>> Laura
>>
>> On 27/06/17 15:03, Jose Miguel de la Rosa Trevin wrote:
>>
>> Laura, have you checked if the same error happens (or not) with a
>> tutorial dataset, for example?
>>
>> On Tue, Jun 27, 2017 at 3:02 PM, Laura del Caño <
>> su...@bc...> wrote:
>>
>>> Hi Juha,
>>>
>>> could you send us protocol parameters for the binning and normalization,
>>> as well as particle size (and maybe logs) to try to reproduce the problem?
>>>
>>> thanks
>>> Laura
>>>
>>>
>>> Activo Mar, 27 Junio at 1:21 PM , Juha Huiskonen <ju...@st...>
>>> Escrito:
>>> Dear all,
>>>
>>> I need to run a fairly large classification run. To speed it up, I have
>>> run xmipp-crop/resize particles to achieve binning by factor of 3 and then
>>> normalised the particles again with xmipp-preprocess particles.
>>>
>>> Without binning/renormalization the job runs fine (albeit slowly). With
>>> binning/renormalization I get a segmentation fault referring to libfftw3
>>> right when the 'Estimating initial noise spectra' starts. I am running on
>>> GPU.
>>>
>>> The only difference I can see between the two is that after
>>> binning/renormalization all the particles are in one large stack, whereas
>>> normally they are in several separate stacks. Has anyone else seen this
>>> behaviour? Any suggestions?
>>>
>>> Best wishes,
>>> Juha
>>>
>>> 168:553135
>>>
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