Menu
▾
▴
Re: [scipion-users] Error running relion
|
From: Dmitry S. <Sem...@gm...> - 2021-09-27 12:04:07
|
Ah, ok, undestand. Thank you! Sincerely, Dmitry > On 27. Sep 2021, at 14:02, Grigory Sharov <sha...@gm...> wrote: > > I don't understand what you are trying to do :) > > The plugin v4.0b2 can work with both 3.1.2 and 4.0 Relion binaries. The 4.0 binaries are not provided by Scipion, you have to install them yourself. > > 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 12:58 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > 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... <mailto: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) >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... <mailto:sci...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
