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Re: [scipion-users] relion - 2D classification failed (done 2/3)
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From: Gregory S. <sha...@gm...> - 2018-05-03 10:19:34
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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 <+44%201223%20267542> 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 > > |
