Hi Dieters,
These types of errors are usually related to weird particles, for which
the norm or scale correction goes wrong. If you can identify the particles
the program complaints about (mic_id = the group - 1) and remove them from
the data, then typically things will improve.
Hope that helps,
Sjors
> Hi Sjors and all,
> I am having the following issue (relion-1.2-b8):
>
> dataset of roughly 150 images: preprocessing runs fine. However, when I
> run ml2d or 3dr I get messages similar to (see below).Presumably mic_id
> 57 has problems but how to find which one it is. When running
> xmipp_alingn2d on these images I do not see any problems, so I suppose
> that the images are fine. But what is wrong then?
>
> .68/2.68 min
> ............................................................~~(,_,">
> 24/ 24 sec
> ............................................................~~(,_,">
> 0.90/2.77 min ...................~~(,_,"> exp_thisparticle_sumweight=
> nan [oo]
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> exp_part_id= 197exp_iimage=1
> mic_id= 57 mymodel.scale_correction[mic_id]= 0
> exp_ipass= 0
> sampling.NrDirections(0, true)= 2 sampling.NrDirections(0, false)= 2
> sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0,
> false)= 24
> mymodel.sigma2_noise[exp_ipart]=
> -nan
> -nan
>
> repeated many times
>
> wsum_model.sigma2_noise[exp_ipart]=
> 0
> 0
> 0
> repeated many times
>
> wsum_model.pdf_direction[exp_ipart]=
> 12.808049
> 11.167964
>
> mymodel.avg_norm_correction= 0.996711
> wsum_model.avg_norm_correction= 23.9302
> written out Mweight.spi
> exp_thisparticle_sumweight= nan
> exp_min_diff2[exp_ipart]= 9.9e+100
> slave 1 encountered error: ERROR!!! zero sum of weights....
> File: src/ml_optimiser.cpp line: 3937
> +++ RELION: command line arguments (with defaults for optional ones
> between parantheses) +++
> ====== General options =====
> --i : Input images (in a star-file or a
> stack)
> --o : Output rootname
> --angpix : Pixel size (in Angstroms)
> --iter (50) : Maximum number of iterations to
> perform
> --tau2_fudge (1) : Regularisation parameter (values
> higher than 1 give more weight to the data)
> --K (1) : Number of references to be
> refined
> --particle_diameter (-1) : Diameter of the circular mask
> that will be applied to the experimental images (in Angstroms)
> --zero_mask (false) : Mask surrounding background in
> particles to zero (by default the solvent area is filled with random
> noise)
> --flatten_solvent (false) : Perform masking on the references
> as well?
> --solvent_mask (None) : User-provided mask for the
> references (default is to use spherical mask with particle_diameter)
> --solvent_mask2 (None) : User-provided secondary mask
> (with its own average density)
> --tau (None) : STAR file with input
> tau2-spectrum (to be kept constant)
> --split_random_halves (false) : Refine two random halves of the
> data completely separately
> --low_resol_join_halves (-1) : Resolution (in Angstrom) up to
> which the two random half-reconstructions will not be independent to
> prevent diverging orientations
> ====== Initialisation =====
> --ref (None) : Image, stack or star-file with
> the reference(s). (Compulsory for 3D refinement!)
> --offset (3) : Initial estimated stddev for the
> origin offsets
> --firstiter_cc (false) : Perform CC-calculation in the
> first iteration (use this if references are not on the absolute
> intensity scale)
> --ini_high (-1) : Resolution (in Angstroms) to
> which to limit refinement in the first iteration
> ====== Orientations =====
> --oversampling (1) : Adaptive oversampling order to
> speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
> --healpix_order (2) : Healpix order for the angular
> sampling (before oversampling) on the (3D) sphere: hp2=15deg,
> hp3=7.5deg, etc
>
>
> I have no clue of what is wrong......
> Many thanks for hints, best, Dieter
>
> --
> Dr. Dieter Blaas
> Max F. Perutz Laboratories,
> Inst. Med. Biochem.,
> Med. Univ. Vienna
> Dr. Bohr Gasse 9/3
> A-1030 Vienna, Austria
> Tel. 0043 1 4277 61630
> Fax 0043 1 4277 9616
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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