Re: [scipion-users] Error running relion

[Grigory S. <sha...@gm...>]

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 <+44%201223%20267228>
e-mail: gs...@mr...


On Mon, Sep 27, 2021 at 12:51 PM Dmitry Semchonok <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...>
> 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 <+44%201223%20267228>
> e-mail: gs...@mr...
>
>
> On Mon, Sep 27, 2021 at 12:44 PM Dmitry Semchonok <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...>
>> 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 <+44%201223%20267228>
>> e-mail: gs...@mr...
>>
>>
>> On Mon, Sep 27, 2021 at 12:18 PM Dmitry Semchonok <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)
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>