splittilt(1) General Commands Manual splittilt(1)
NAME
splittilt - Produce multiple command files for running Tilt in parallel
SYNOPSIS
splittilt [options] Tilt_command_file
DESCRIPTION
splittilt will take a command file for running the Tilt program for
tomogram generation and produce multiple command files that can be run
in parallel by Processchunks. It takes into account the computa-
tional implications of some of the parameter settings when determining
how many chunks to divide the task into.
The only argument that the typical user needs to give is -n to specify
the expected number of processors to be used. Only an approximate num-
ber is needed. The default value is printed out by the program's usage
statement. Thus, a typical command might be
splittilt -n 6 tilta.com
After giving this command, there will be a series of command files
tilta-nnn.com to compute the chunks, and a file tilta-finish.com to
finish the task and clean up intermediate files. One can then enter
processchunks machine_list tilta
where "machine_list" is the comma-separated list of machines to use, or
just the number of processors to use on the local machine.
The problem in dividing up the Tilt task is that the smaller the chunks
are, the greater the total amount of resources needed because of the
overhead involved in doing each chunk; whereas the larger the chunks,
the greater the chance that a slow machine will hold up the entire
process. The overhead takes two forms: the file I/O and preprocessing
involved in accessing all of the projection data needed to reconstruct
a given number of slices; and the extra "vertical" slices that must be
computed when there is X-axis tilting but no local alignments. The
former overhead is minimized simply by having a minimum number of
slices in each chunk. The latter overhead is explicitly minimized by
taking into account the penalty for doing old-style X-axis tilting
(direct backprojection of each output slice) versus interpolation
between vertical slices.
Initially, the program aims for a target number of chunks that is a
fixed multiple of the expected number of processors (or that is entered
with the -t option). If the command file uses fixed X-axis tilting but
no local alignments or Z factors, then the program drops back to a
smaller number, referred to as the minimum number of chunks. If the
extra computational burden from computing vertical slices is greater
than the defined penalty for doing old-style tilting, the program then
switches to old-style tilting unless the -v option is given. In that
case, vertical slices are still computed but the number of chunks is
further reduced until the penalty for doing vertical slices matches the
penalty for switching to old-style tilting, and the number of chunks is
allowed to go as low as the expected number of machines. In all cases,
the number of chunks is constrained by the minimum number of slices in
each chunk.
The program will also operate on a command file for reprojecting from a
tomogram; here, it just maintains a minimum number of slices per chunk.
OPTIONS
Splitblend uses the PIP package for input (see the manual page for
pip). Options can be specified either as command line arguments
(with the -) or one per line in a command file (without the -).
Options can be abbreviated to unique letters; the currently valid
abbreviations for short names are shown in parentheses.
-CommandFile File name
Tilt command file. It can be entered with or without extension,
i.e., as "tilt", "tilt.", or "tilt.com".
-outroot (-ou) OR -RootNameOfOutput Text string
Root name for output command files (default is root of input
file)
-naming (-na) OR -NamingStyle Integer
0 if image files have descriptive extensions like ".preali", or
1 or 2 if descriptive text is before the extension ".mrc" or
".hdf". This entry is needed only if the style cannot be deter-
mined from files in the dataset.
-n OR -ProcessorNumber Integer
The number of machines that you expect to run the command files
on. The default is 8
-s OR -SliceMinimum Integer
Minimum number of slices per chunk (default 50)
-t OR -TargetChunks Integer
Target number of chunks (default 5 times expected # of machines)
-m OR -ChunkMinimum Integer
Minimum number of chunks, except when vertical slices are speci-
fied with the -v option. The default is 2 times the expected
number of machines, but with vertical slices, the minimum
becomes one chunk per machine.
-p OR -OldStyleXtiltPenalty Floating point
Computational penalty for old-style X-axis tilting (default
1.33)
-v OR -VerticalSlices
Do vertical slices instead of old-style X-axis tilting, regard-
less of the penalty.
-c OR -SeparateChunks
Write chunks to separate files named setname-nnn.rec and assem-
ble the output file from these at the end. The default is to
write directly to the output file.
-b OR -BoundaryPixels Integer
Number of pixels at each boundary between chunks to save in sep-
arate boundary files (named setname-nnn.rbound) and rewrite to
the output file in the -finish.com file, when directly writing
to the output file. The default is 2048. This capability to
rewrite lines at the boundary should make it unnecessary to
write chunks to separate files.
-i OR -InitialComNumber Integer
Start with given command file number instead of 1. When this
option is entered, the program will not delete any existing com-
mand files. If data are being written directly to output file,
the first file is named -nnn-sync.com instead of -start.com.
-o OR -OpenForMoreComs
Leave the command file set open by naming the command file for
reassembly -nnn-sync.com instead of -finish.com, and by not
cleaning up command and log files in the reassembly file.
-unique (-un) OR -UniqueInfoFile
Attach the first command file number to a boundary info file
-d OR -DimensionsOfStack Two integers
Use the given values as the dimensions of the aligned stack.
This option is needed when calling from Sirtsetup if the log
of the stack is being used or if a subarea is being done.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input
FILES
The finishing command file deletes all the command and log files for
the chunks after collecting minimun, maximum, and mean density informa-
tion from the log files. If the -c option is given, the temporary
reconstruction files are deleted too.
AUTHOR
David Mastronarde <mast at colorado dot edu>
SEE ALSO
processchunks, tilt
IMOD 5.2.0 splittilt(1)