mcx(1) USER COMMANDS mcx(1)
NAME
mcx - perform various computations on graphs and matrices
SYNOPSIS
mcx <mode> [mode-options] [mode-files]
DESCRIPTION
mcx implements a variety of computations on graphs and matrices. The first argument to mcx should be a mode, which is a string establishing
the type of computation to invoke. Each mode mode is described in the mcxmode manual page. The currently available modes are convert, diame-
ter, clcf, q and ctty. The convert mode is thus described in the mcxconvert manual page.
Invoking mcx without arguments causes it to print out a list of available modes with a short description of the type of command line
expected by that mode.
Invoking mcx with just a mode will print out a longer listing of options available for that particular mode. Modes that are able to func-
tion normally without arguments can be invoked by adding the --nop argument.
Several options are shared between all mcx modes. Note that these options are specified after the mode. See OPTIONS.
The --version causes mcx to print out version and license information.
Issuing mcx help mode will cause mcx to look for a manual page describing mode and display it if found. This requires that the MANPATH envi-
ronment variable contains the directory in which the MCL-edge manual pages were installed. This will usually be PREFIX/share, where PREFIX
is the path with which the software was configured.
OPTIONS
These are options that pertain to all modes. They should be specified after the mode argument.
-h (synopsis)
--help (synopsis)
List available options.
--nop (no-op)
Not an option. This option has no effect then to increment the argument count. This can be useful for mcx modes which are able to function
without any options. Such a mode typically reads from STDIN, writes to STDOUT, and uses default settings. However, simply specifying a
mode without options leads mcx to output a list of available options for that mode. This can be prevented by using the --nop option.
-set (key=val)
Sets the key key to value val in the environment. Some modes allow adjustment of settings in this manner.
-progress <num> (progress interval size)
Defines the interval that defines the progress frequency.
--debug (turn on debugging)
Turn debugging on.
--version (show version)
Show version.
AUTHOR
Stijn van Dongen.
SEE ALSO
mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.
mcx 12-068 8 Mar 2012 mcx(1)
Check Out this Related Man Page
mcx ctty(1) USER COMMANDS mcx ctty(1)
NAME
mcx ctty - compute betweenness centrality for network nodes
SYNOPSIS
mcx ctty [options] [matrix-file]
mcxctty is not in actual fact a program. This manual page documents the behaviour and options of the mcx program when invoked in mode ctty.
The options -h, --apropos, --version, -set, --nop, -progress <num> are accessible in all mcx modes. They are described in the mcx manual
page.
mcx ctty [-abc <fname> (specify label input)] [-imx <fname> (specify matrix input)] [-extent <int> (only consider paths of length at most
<int>)] [-o <fname> (output file name)] [-tab <fname> (use tab file)] [-t <int> (use <int> threads)] [-J <intJ> (a total of <intJ> jobs are
used)] [-j <intj> (this job has index <intj>)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version,
exit)]
DESCRIPTION
mcx ctty computes betweenness centrality for all nodes in a graph, using the between centrality update algorithm from [1].
The input graph/matrix, if specified with the -imx option, has to be in mcl matrix/graph format. You can use label input instead by using
the -abc option. Refer to mcxio(5) for a description of these two input formats. By default mcx diameter reads from STDIN and expects
matrix format. To specify label input from STDIN use -abc -.
OPTIONS
-abc <fname> (label input)
The file name for input that is in label format.
-imx <fname> (input matrix)
The file name for input. STDIN is assumed if not specified.
-o <fname> (output file name)
The name of the file to write output to.
-extent <int> (only consider paths of length at most <int>)
This option will lead to different results. Results will still be informative however, being representative for the local context in which
nodes reside. It does probably not make sense to use values smaller than four or five.
-tab <fname> (use tab file)
This option causes the output to be printed with the labels found in the tab file. With -abc this option will, additionally, construct a
graph only on the labels found in the tab file. If this option is used in conjunction with -imx the tab domain and the matrix domain are
required to be identical.
-t <int> (use <int> threads)
-J <intJ> (a total of <intJ> jobs are used)
-j <intj> (this job has index <intj>)
Computing centrality scores in a graph is time-intensive. If you have multiple CPUs available consider using as many threads. Addition-
ally it is possible to spread the computation over multiple jobs/machines. Conceptually, each job takes a number of threads from the
total thread pool. If job control is used (the -J option is used) then the number of jobs should not exceed the number of threads. The
total number of threads divided by the total number of jobs defines the number of threads that will be used by the current job. Addition-
ally, the number of threads specified signifies the total added amount of all threads across all machines and must be the same for all
jobs. This number is used by each job to infer its own set of tasks. The following set of options, if given to as many commands, defines
three jobs, each running four threads.
-t 12 -G 3 -g 0
-t 12 -G 3 -g 1
-t 12 -G 3 -g 2
REFERENCES
[1] Ulrik Brandes, A Faster Algorithm for Betweenness Centrality. Journal of Mathematical Sociology 25(2): 163-177, (2001). http://cite-
seerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.11.2024
SEE ALSO
mcxio(5), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.
mcx ctty 12-068 8 Mar 2012 mcx ctty(1)