Manpage of prmParser
Section: User Commands (1)
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prmParser - parse parameter file and create command files for parallel processing
prmParser parses file.prm and outputs a complete set of .com command files for
parallel processing. The first file, -start.com, runs prepareEM and
prepareRef. Subsequent results vary, depending on the number of
volumes and particles to be processed. When multiple volumes are to
be processed (indicated by multiple lines in the eTomo Volume Table, or,
equivalently, by multiple entries in the parameter file fnVolume array),
when the total number of particles present is more than 100, and when
at least one volume contains more than 10 particles,
parallel averaging is used; if not, serial averaging is used.
Multiple references to the same volume are treated as multiple volumes.
This provides a way to force parallel averaging when a single volume
containing many particles is to be processed. Conversely, parallel
averaging may be disabled by setting flgAllowParallelAveraging = 0
in the parameter file.
For serial averaging, numbered files run alignSubset on a specified
subset of the particles. A numbered -sync.com file is used at the end
of each iteration, or an unnumbered -finish.com file after the final
iteration, to run checkAlignmentLogs, mergeEM , optionally removeDuplicates,
For parallel averaging, two groups of numbered files, each followed by a
-sync.com or a -finish.com, are written for each iteration. A first groups of
numbered files runs alignSubset, as in serial averaging. This is
followed by a -sync.com which runs checkAlignmentLogs, mergeEM,
and, optionally, removeDuplicates. Next a second series of numbered
files, one per volume, runs averageAll in parallel mode. Finally, a
numbered -sync.com, or unnumbered finish.com for the final iteration,
invokes averageAll again to collect results from the parallel
computations and to write the resulting volume(s).
The parameter file is a MATLAB readable text file that specifies the parameter
values in MATLAB syntax. See PEET(1) man page for a description of the
parameter file options and syntax.
The file name of the parameter file.
Sample parameter files are available in $PARTICLE_DIR/templates.
PEET(1), prepareEM(1), prepareRef(1), alignSubset(1), averageAll(1),
mergeEM(1), removeDuplicates(1), calcFSC(1), and calcSSNR(1)
- SEE ALSO
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Time: 18:16:05 GMT, January 11, 2021