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

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

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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