Re: [scipion-users] Error running relion

[Dmitry S. <Sem...@gm...>]

Yes, it exists.

I installed relion 3.1.2 via the plugin and currently it runs fine.


But there is still a riddle - how to run the relion 4.0b2?

Sincerely,
Dmitry


> On 27. Sep 2021, at 13:53, Grigory Sharov <sha...@gm...> wrote:
> 
> Thank you. You don't have to update as the new plugin should work with relion 3.
> 
> Does /home/user/Data/Software/scipion3/software/em/relion-3.1.2 exist?
> 
> Best regards,
> Grigory
> 
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
> 
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228>
> e-mail: gs...@mr... <mailto:gs...@mr...>
> 
> 
> On Mon, Sep 27, 2021 at 12:51 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote:
> Dear Grigory,
> 
> [user@dataanalysisserver1 ~]$ scipion3 config -p relion
> Scipion v3.0.9 - Eugenius
> Variables defined by plugin 'relion':
> 
> RELION_HOME = /home/user/Data/Software/scipion3/software/em/relion-3.1.2
> RELION_CUDA_LIB = /usr/local/cuda/lib64
> RELION_PYTHON = None
> 
> These variables can be added/edited in '/home/user/Data/Software/scipion3/config/scipion.conf’
> 
> 
> 
> 
> So it seems to be 3.1.2. 
> 
> Shall I update for the 4.0 via the plugin command?
> 
> Sincerely,
> Dmitry
> 
> 
> 
> 
> 
>> On 27. Sep 2021, at 13:47, Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote:
>> 
>> You can see the version via scipion config -p relion
>> 
>> Best regards,
>> Grigory
>> 
>> --------------------------------------------------------------------------------
>> Grigory Sharov, Ph.D.
>> 
>> MRC Laboratory of Molecular Biology,
>> Francis Crick Avenue,
>> Cambridge Biomedical Campus,
>> Cambridge CB2 0QH, UK.
>> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228>
>> e-mail: gs...@mr... <mailto:gs...@mr...>
>> 
>> 
>> On Mon, Sep 27, 2021 at 12:44 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote:
>> Dear Grigory,
>> 
>> Sorry, but how to verify the version? 
>> 
>> I the plugin I see scipion-em-relion
>> Relion-3.1.3
>> 
>> 
>> Shall I also update for relion-4.0?
>> 
>> Sincerely,
>> 
>> Dmitry
>> 
>> 
>> 
>>> On 27. Sep 2021, at 13:40, Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote:
>>> 
>>> Hi Dmitry,
>>> 
>>> you are looking at a wrong tab, check run.stderr. Also, are you running relion 3.1?
>>> 
>>> Best regards,
>>> Grigory
>>> 
>>> --------------------------------------------------------------------------------
>>> Grigory Sharov, Ph.D.
>>> 
>>> MRC Laboratory of Molecular Biology,
>>> Francis Crick Avenue,
>>> Cambridge Biomedical Campus,
>>> Cambridge CB2 0QH, UK.
>>> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228>
>>> e-mail: gs...@mr... <mailto:gs...@mr...>
>>> 
>>> 
>>> On Mon, Sep 27, 2021 at 12:18 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote:
>>> Dear Grigory & colleagues,
>>> 
>>> Error running updated relion plugin. 
>>> 
>>> 
>>> Any ideas?
>>> 
>>> Thank you
>>> 
>>> Sincerely,
>>> Dmitry
>>> 
>>> 
>>> 
>>> 
>>> File 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't existFile 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't exist00001:   Logging configured. STDOUT --> Runs/004970_ProtRelionClassify2D/logs/run.stdout , STDERR --> Runs/004970_ProtRelionClassify2D/logs/run.stderr
>>> 00002:   RUNNING PROTOCOL -----------------
>>> 00003:   Protocol starts
>>> 00004:   Hostname: localhost4.localdomain4
>>> 00005:   PID: 99422
>>> 00006:   pyworkflow: 3.0.17
>>> 00007:   plugin: relion
>>> 00008:   plugin v: 4.0b2
>>> 00009:   currentDir: /home/user/Data/ScipionUserData/projects/Quentin__august__PSI
>>> 00010:   workingDir: Runs/004970_ProtRelionClassify2D
>>> 00011:   runMode: Continue
>>> 00012:             MPI: 6
>>> 00013:         threads: 4
>>> 00014:    Starting at step: 1
>>> 00015:    Running steps 
>>> 00016:   STARTED: convertInputStep, step 1, time 2021-09-27 13:14:18.891805
>>> 00017:   Converting set from 'Runs/001948_ProtUserSubSet/particles.sqlite' into 'Runs/004970_ProtRelionClassify2D/input_particles.star'
>>> 00018:   convertBinaryFiles: creating soft links.
>>> 00019:      Root: Runs/004970_ProtRelionClassify2D/extra/input -> Runs/001072_ProtRelionExtractParticles/extra
>>> 00020:   FINISHED: convertInputStep, step 1, time 2021-09-27 13:14:20.274397
>>> 00021:   STARTED: runRelionStep, step 2, time 2021-09-27 13:14:20.279078
>>> 00022:    mpirun -np 6  `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf  --zero_mask  --K 24 --norm  --scale  --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc  --pool 3 --gpu   --j 4
>>> 00023:   Protocol failed: Command ' mpirun -np 6  `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf  --zero_mask  --K 24 --norm  --scale  --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc  --pool 3 --gpu   --j 4' returned non-zero exit status 213.
>>> 00024:   FAILED: runRelionStep, step 2, time 2021-09-27 13:14:20.303854
>>> 00025:   *** Last status is failed 
>>> 00026:   ------------------- PROTOCOL FAILED (DONE 2/3)
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