Hello all, 

I'm going through the relion tutorial and trying to complete the Extracting and normalising particles step. 

In the previous Manual particle picking procedure, I used e2boxer.py to pick and generate coordinate (.box) files. Out of 571 micrographs, I picked from 19 to get ~3000 to use as my class 2d average template. 

In my current efforts to extract and normalise particles, I'm following the tutorial closely except deviating from the Coordinate-file suffix and Particle box size parameters. Otherwise everything else is identical. But when I try to run the extraction process via the gui or script, I get 

File: src/image.cpp line: 80

--------------------------------------------------------------------------

MPI_ABORT was invoked on rank 14 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.

--------------------------------------------------------------------------

When the run completes, I get a new Particles directory  (not /Particles/Micrographs) with directories for each of the 19 coordinate files (all of which are empty). Additionally, I don't get a particles_manual.star output file despite naming it in the Extract rootname (which backs up the idea that nothing is getting extracted). 

Perhaps the MPI error is a server-related issue but I wanted to ask. And as the other hiccups are concerned (e.g., missing particles_manual.star, etc) are these a consequence of using e2boxer.py and missing an intermediate step before attempting an extraction? 

Thank you very, very much for you help!

(P.S., perhaps it would behoove me to note that I also get warning messages for "missing coordinate files" of the micrographs I haven't picked Though I would fully expect that, perhaps this is a sources of error that I've overlooked). 

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