Re: [scipion-users] installation running issues

[Pablo C. <pc...@cn...>]

Dear Dmitry....this happens when none of the movies worked. Usually is 
related to the configuration which is a combination of matching:

1.- The binary file used (specified in the config.file),

2.- The cuda version used

3.- In some cases the GPU architecture also affects the success


This apply to all software that is distributed as binaries.

Check the plugin page, https://github.com/scipion-em/scipion-em-motioncorr


You need to play with MOTIONCOR2_CUDA_LIB, and MOTIONCOR2 variables.


Example: (I've got motioncor2 1.2.1)


1.- ls -l <scipion__home>/software/em/motioncor2-1.2.1/bin/

MotionCor2_1.2.1-Cuda80
MotionCor2_1.2.1-Cuda91
MotionCor2_1.2.1-Cuda92


Set MOTIONCOR2 to the one matching your CUDA version installed

2.- If CUDA_LIB at scipion.conf does not match you'll need to set 
MOTIONCOR2_CUDA_LIB to match the chosen binary.


In this case, the GPU architecture does not affect.


scipion printenv | grep MOTIONCOR2


will help you to check those values.


On 27/5/20 16:12, Dmitry A. Semchonok wrote:
> Dear colleagues,
>
> During the test of SCIPION on the new server we got the error on 
> during motion correction step (original files are in the attachment)
>
> How to fix this issue?
>
> Thank you!
>
> Sincerely,
> Dmitry
>
>
>
>
>
>
> =========================================
> run
>
> 2020-05-27 15:47:19,297 INFO:  STARTED: waitForThreadStep, 
> step 12
> 2020-05-27 15:47:19,297 INFO:    2020-05-27 15:47:19.297160
> 2020-05-27 15:47:19,301 INFO:  FINISHED: waitForThreadStep, 
> step 12
> 2020-05-27 15:47:19,301 INFO:    2020-05-27 15:47:19.299252
> 2020-05-27 15:47:19,302 INFO:  STARTED: createOutputStep, step 13
> 2020-05-27 15:47:19,302 INFO:    2020-05-27 15:47:19.302209
> 2020-05-27 15:47:19,305 ERROR:  Protocol failed: All movies 
> failed, didn't create outputMicrographs.Please review movie processing 
> steps above.
> 2020-05-27 15:47:19,308 INFO:  FAILED: createOutputStep, step 13
> 2020-05-27 15:47:19,308 INFO:    2020-05-27 15:47:19.304107
> 2020-05-27 15:47:19,311 INFO:  ------------------- PROTOCOL 
> FAILED (DONE 13/13)
> 2020-05-27 15:47:19,321 INFO:  ------------------- PROTOCOL 
> FAILED (DONE 13/13)
>
>
>
> ==========================================
> run.stdout
>
>
> ...... Frame ( 25) shift: 0.000 0.000
> ...... Frame ( 26) shift: 0.000 0.000
> ...... Frame ( 27) shift: 0.000 0.000
> ...... Frame ( 28) shift: 0.000 0.000
> ...... Frame ( 29) shift: 0.000 0.000
> ...... Frame ( 30) shift: 0.000 0.000
>
> ERROR: Movie failed
>
> FINISHED: processMovieStep, step 11
> 2020-05-27 15:47:19.274026
> WARNING: Movie 
> Runs/000002_ProtImportMovies/extra/FoilHole_22185017_Data_22186404_22186405_20190522_2012_Fractions.mrc 
> has empty alignment data, can't add it to output set.
> WARNING: Micrograph 
> Runs/000085_ProtMotionCorr/extra/FoilHole_22185017_Data_22186404_22186405_20190522_2012_Fractions_aligned_mic.mrc 
> was not generated, can't add it to output set.
> WARNING: Micrograph 
> Runs/000085_ProtMotionCorr/extra/FoilHole_22185017_Data_22186404_22186405_20190522_2012_Fractions_aligned_mic_DW.mrc 
> was not generated, can't add it to output set.
> STARTED: waitForThreadStep, step 12
> 2020-05-27 15:47:19.297160
> FINISHED: waitForThreadStep, step 12
> 2020-05-27 15:47:19.299252
> STARTED: createOutputStep, step 13
> 2020-05-27 15:47:19.302209
> Traceback (most recent call last):
> File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 186, 
> in run
> self._run()
> File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 237, 
> in _run
> resultFiles = self._runFunc()
> File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 233, 
> in _runFunc
> return self._func(*self._args)
> File 
> "/usr/local/scipion/pyworkflow/em/protocol/protocol_align_movies.py", 
> line 117, in createOutputStep
> raise Exception(redStr("All movies failed, didn't create 
> outputMicrographs."
> Exception: All movies failed, didn't create 
> outputMicrographs.Please review movie processing steps above.
> Protocol failed: All movies failed, didn't create 
> outputMicrographs.Please review movie processing steps above.
> FAILED: createOutputStep, step 13
> 2020-05-27 15:47:19.304107
> ------------------- PROTOCOL FAILED (DONE 13/13)
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*