Re: [scipion-users] relion - 2D classification failed (done 2/3)

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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...
> >>
> >>
> >>
> >>
> >>
> >> ------------------------------------------------------------
> ------------------
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> >> https://lists.sourceforge.net/lists/listinfo/scipion-users
> >>
> >
> >
> > ------------------------------------------------------------
> ------------------
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> >
>
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Re: [scipion-users] relion - 2D classification failed (done 2/3)

Image processing framework to integrate EM software packages.

Re: [scipion-users] relion - 2D classification failed (done 2/3)