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Re: [scipion-users] relion - 2D classification failed (done 2/3)
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From: Joseph Ho <sbd...@gm...> - 2018-05-03 14:28:56
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Hi, Jose: I ran relion particle extraction.. still not working. I also don't do downscaling in the Xmipp but still not working. Only I use --dont_check_norm. Then the relion 2D classification process. Not sure why all the normalise doesn't work in my Ximpp/relion particle extraction? Thanks for your help. Joseph On Thu, May 3, 2018 at 7:22 PM, Jose Miguel de la Rosa Trevin <del...@gm...> wrote: > Hi Joseph, > > Have you extracted the particles with xmipp protocol? > Can you try extracting with relion and check if the error remains? > I think the relion - extract particles protocol is not in the menu (we need > to fix that > for the upcoming bugfix release) but you can find it with Ctrl + F in the > searching dialog. > > If the relion 2D jobs still complains about the normalization when using the > particles > extracted with relion (I have observed this when downscaling). You can try > to use > the advanced option '--dont_check_norm' > > Hope this helps, > Jose Miguel > > > On Thu, May 3, 2018 at 12:49 PM, Joseph Ho <sbd...@gm...> wrote: >> >> Hi, Grigory: >> >> Thanks for your reply and help. I notice that normalised error. I also >> puzzle about this. Because I do click the normalise function during >> the particle extraction of scipion. I followed the scipion youtube >> (beta-gal) setup. Normalise type:Ramp; Background radius -1, >> >> Thanks for your help >> >> Joseph >> >> On Thu, May 3, 2018 at 6:19 PM, Gregory Sharov <sha...@gm...> >> wrote: >> > Hello Joseph, >> > >> > the error message states precisely what is wrong with your job: >> > >> > 00341: ERROR: It appears that these images have not been normalised to >> > an >> > average background value of 0 and a stddev value of 1. >> > 00342: Note that the average and stddev >> > values for the background are calculated: >> > 00343: (1) for single particles: outside >> > a >> > circle with the particle diameter >> > 00344: (2) for helical segments: outside >> > a >> > cylinder (tube) with the helical tube diameter >> > 00345: You can use the relion_preprocess >> > program to normalise your images >> > 00346: If you are sure you have >> > normalised >> > the images correctly (also see the RELION Wiki), you can switch off this >> > error message using the --dont_check_norm command line option >> > >> > >> > 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 267542 >> > e-mail: gs...@mr... >> > >> > On Thu, May 3, 2018 at 4:02 AM, Joseph Ho <jo...@ga...> >> > wrote: >> >> >> >> Dear Sir: >> >> >> >> >> >> >> >> Relion 2D was running but I stopped it. After I tried to restart, I got >> >> this error msg. I could not get Relion 2D running anymore. I also tried >> >> MPI >> >> is 1 but it still failed. I use scipion v.1.2 and I installed it from >> >> source. >> >> >> >> >> >> >> >> The msg from run.stdout >> >> >> >> >> >> >> >> 00309: The deprecated forms *will* disappear in a future version of >> >> Open >> >> MPI. >> >> 00310: Please update to the new syntax. >> >> 00311: >> >> >> >> -------------------------------------------------------------------------- >> >> 00312: >> >> >> >> -------------------------------------------------------------------------- >> >> 00313: [[50020,1],0]: A high-performance Open MPI point-to-point >> >> messaging module >> >> 00314: was unable to find any relevant network interfaces: >> >> 00315: >> >> 00316: Module: OpenFabrics (openib) >> >> 00317: Host: spgpu3 >> >> 00318: >> >> 00319: Another transport will be used instead, although this may >> >> result >> >> in >> >> 00320: lower performance. >> >> 00321: >> >> >> >> -------------------------------------------------------------------------- >> >> 00322: === RELION MPI setup === >> >> 00323: + Number of MPI processes = 3 >> >> 00324: + Master (0) runs on host = spgpu3 >> >> 00325: + Slave 1 runs on host = spgpu3 >> >> 00326: + Slave 2 runs on host = spgpu3 >> >> 00327: ================= >> >> 00328: uniqueHost spgpu3 has 2 ranks. >> >> 00329: Slave 1 will distribute threads over devices 1 2 3 >> >> 00330: Thread 0 on slave 1 mapped to device 1 >> >> 00331: Slave 2 will distribute threads over devices 1 2 3 >> >> 00332: Thread 0 on slave 2 mapped to device 1 >> >> 00333: Device 1 on spgpu3 is split between 2 slaves >> >> 00334: Running CPU instructions in double precision. >> >> 00335: [spgpu3:17287] 2 more processes have sent help message >> >> help-mpi-btl-base.txt / btl:no-nics >> >> 00336: [spgpu3:17287] Set MCA parameter "orte_base_help_aggregate" to >> >> 0 >> >> to see all help / error messages >> >> 00337: + WARNING: Changing psi sampling rate (before oversampling) >> >> to >> >> 5.625 degrees, for more efficient GPU calculations >> >> 00338: Estimating initial noise spectra >> >> 00339: 1/ 20 sec ..~~(,_,"> fn_img= >> >> 067786@Runs/000695_XmippProtCropResizeParticles/extra/output_images.stk >> >> bg_avg= 0.429345 bg_stddev= 0.852297 bg_radius= 14.0174 >> >> 00340: ERROR: >> >> 00341: ERROR: It appears that these images have not been normalised >> >> to >> >> an average background value of 0 and a stddev value of 1. >> >> 00342: Note that the average and stddev >> >> values for the background are calculated: >> >> 00343: (1) for single particles: outside >> >> a >> >> circle with the particle diameter >> >> 00344: (2) for helical segments: outside >> >> a >> >> cylinder (tube) with the helical tube diameter >> >> 00345: You can use the relion_preprocess >> >> program to normalise your images >> >> 00346: If you are sure you have >> >> normalised >> >> the images correctly (also see the RELION Wiki), you can switch off >> >> this >> >> error message using the --dont_check_norm command line option >> >> 00347: File: >> >> /usr/local/scipion/software/em/relion-2.1/src/ml_optimiser.cpp line: >> >> 1879 >> >> 00348: >> >> >> >> -------------------------------------------------------------------------- >> >> 00349: MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD >> >> 00350: with errorcode 1. >> >> 00351: >> >> 00352: NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >> >> processes. >> >> 00353: You may or may not see output from other processes, depending >> >> on >> >> 00354: exactly when Open MPI kills them. >> >> 00355: >> >> >> >> -------------------------------------------------------------------------- >> >> 00356: Traceback (most recent call last): >> >> 00357: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", >> >> line >> >> 186, in run >> >> 00358: self._run() >> >> 00359: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", >> >> line >> >> 233, in _run >> >> 00360: resultFiles = self._runFunc() >> >> 00361: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", >> >> line >> >> 229, in _runFunc >> >> 00362: return self._func(*self._args) >> >> 00363: File >> >> "/usr/local/scipion/pyworkflow/em/packages/relion/protocol_base.py", >> >> line >> >> 880, in runRelionStep >> >> 00364: self.runJob(self._getProgram(), params) >> >> 00365: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", >> >> line >> >> 1138, in runJob >> >> 00366: self._stepsExecutor.runJob(self._log, program, arguments, >> >> **kwargs) >> >> 00367: File "/usr/local/scipion/pyworkflow/protocol/executor.py", >> >> line >> >> 56, in runJob >> >> 00368: env=env, cwd=cwd) >> >> 00369: File "/usr/local/scipion/pyworkflow/utils/process.py", line >> >> 51, >> >> in runJob >> >> 00370: return runCommand(command, env, cwd) >> >> 00371: File "/usr/local/scipion/pyworkflow/utils/process.py", line >> >> 65, >> >> in runCommand >> >> 00372: check_call(command, shell=True, stdout=sys.stdout, >> >> stderr=sys.stderr, env=env, cwd=cwd) >> >> 00373: File >> >> "/usr/local/scipion/software/lib/python2.7/subprocess.py", >> >> line 186, in check_call >> >> 00374: raise CalledProcessError(retcode, cmd) >> >> 00375: CalledProcessError: Command 'mpirun -np 3 -bynode `which >> >> relion_refine_mpi` --gpu 1,2,3 --tau2_fudge 2 --scale >> >> --dont_combine_weights_via_disc --iter 25 --norm --psi_step 10.0 >> >> --ctf >> >> --offset_range 5.0 --oversampling 1 --pool 3 --o >> >> Runs/000827_ProtRelionClassify2D/extra/relion --i >> >> Runs/000827_ProtRelionClassify2D/input_particles.star >> >> --particle_diameter >> >> 200 --K 200 --flatten_solvent --zero_mask --offset_step 2.0 --angpix >> >> 7.134 >> >> --j 1' returned non-zero exit status 1 >> >> 00376: Protocol failed: Command 'mpirun -np 3 -bynode `which >> >> relion_refine_mpi` --gpu 1,2,3 --tau2_fudge 2 --scale >> >> --dont_combine_weights_via_disc --iter 25 --norm --psi_step 10.0 >> >> --ctf >> >> --offset_range 5.0 --oversampling 1 --pool 3 --o >> >> Runs/000827_ProtRelionClassify2D/extra/relion --i >> >> Runs/000827_ProtRelionClassify2D/input_particles.star >> >> --particle_diameter >> >> 200 --K 200 --flatten_solvent --zero_mask --offset_step 2.0 --angpix >> >> 7.134 >> >> --j 1' returned non-zero exit status 1 >> >> 00377: FAILED: runRelionStep, step 2 >> >> 00378: 2018-05-03 10:35:36.970022 >> >> >> >> >> >> >> >> >> >> >> >> Thanks for your help >> >> >> >> >> >> >> >> Meng-Chiao (Joseph) Ho >> >> >> >> Assistant Research Fellow >> >> >> >> Institute of Biological Chemistry, Academia Sinica >> >> >> >> No. 128, Sec 2, Academia Road, Nankang, Taipei 115, Taiwan >> >> >> >> Tel: 886-2-27855696 ext 3080/3162 >> >> >> >> Email: jo...@ga... >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> Check out the vibrant tech community on one of the world's most >> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >> _______________________________________________ >> >> scipion-users mailing list >> >> sci...@li... >> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > Check out the vibrant tech community on one of the world's most >> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> > _______________________________________________ >> > scipion-users mailing list >> > sci...@li... >> > https://lists.sourceforge.net/lists/listinfo/scipion-users >> > >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
