crash while running parallel particle extraction and sorting

[bforsbe]

Originally reported by: Wolfgang Lugmayr (Bitbucket: wlugmayr, GitHub: Unknown)

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i did the normal particle extraction on the local machine (64 cores) with GUI MPI=1 no cluster.
in parallel i tried to sort an imported particle file with also GUI MPI=1 no cluster and relion died with the following message:

$ relion
PipeLine::addNode ERROR: Adding an empty nodename. Did you fill in all Node names correctly?
File: /sw/relion/2.0beta-mpi/src/pipeliner.cpp line: 30

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• Bitbucket: https://bitbucket.org/tcblab/relion2-beta/issue/124

[bforsbe]

Original comment by Wolfgang Lugmayr (Bitbucket: wlugmayr, GitHub: Unknown):

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running the particle sorting after the particle extraction on the generated file gives the same error.

$ head -30 Extract/autopick_local/particles.star

data_

loop_
_rlnMicrographName #1
_rlnCoordinateX #2
_rlnCoordinateY #3
_rlnVoltage #4
_rlnDefocusU #5
_rlnDefocusV #6
_rlnDefocusAngle #7
_rlnSphericalAberration #8
_rlnDetectorPixelSize #9
_rlnCtfFigureOfMerit #10
_rlnMagnification #11
_rlnAmplitudeContrast #12
_rlnAutopickFigureOfMerit #13
_rlnImageName #14
Micrographs/20151224_hole3only_1_00008k2gr_00067k2sq_v02_00006k2hl_00002k2ed-a_movie_DW.mrc 1728.000000 296.000000 300.000000 29788.162109 27641.228516 3.307724 2.000000 0.970000 0.004586 10000.000000 0.100000 0.549423 000001@Extract/job004/Micrographs/20151224_hole3only_1_00008k2gr_00067k2sq_v02_00006k2hl_00002k2ed-a_movie_DW.mrcs
:

[bforsbe]

Original comment by Sjors Scheres (Bitbucket: scheres, GitHub: scheres):

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Hi Wolfgang,
Did you provide the references for the autopicking that you used for this extraction? Remember, sorting always needs references, so you can only sort autopicked ones, not manually picked ones. The GUI wasn't checking for an empty 'autopick references' field, so I'll fix that.

[bforsbe]

Original comment by Wolfgang Lugmayr (Bitbucket: wlugmayr, GitHub: Unknown):

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no, you are right.
i did not give a reference.
i used an imported file, with also imported coordinates from relion 1.4
& gautomatch.

sorry for the inconvenience, i'm still learning how to use relion2 ;-)

cheers,
wolfgang

[bforsbe]

Original comment by Sjors Scheres (Bitbucket: scheres, GitHub: scheres):

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Not a problem, Wolfgang! Your post has still improved the code, as I now intercept the empty field for the autopicking references on the GUI. So, thanks for that!