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

[Juha H. <ju...@st...>]

It seems binning results in one big stack called output_images.stk

On Tue, Jun 27, 2017 at 3:04 PM, Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> 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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>>>
>>>
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