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

[Joseph Ho <sbd...@gm...>]

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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>
>
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