The clm manual
Keywords: manual

16 May 2014 clm 14-137

1.
NAME
2.
SYNOPSIS
3.
DESCRIPTION
4.
OPTIONS
5.
AUTHOR
6.
SEE ALSO

## NAME

clm — perform various computations on graphs and clusterings

## SYNOPSIS

clm <mode> [mode-options] [mode-files]

## DESCRIPTION

clm implements a variety of computations on graphs and clusterings. The first argument to clm should be a mode, which is a string establishing the type of computation to invoke. Each mode mode is described in the clmmode manual page. The currently available modes are clm dist, clm info, clm meet, clm mate, clm close, clm order, clm imac, clm vol, and clm residue. The dist mode is thus described in the clmdist manual page.

Invoking clm 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 clm with just a mode will print out a longer listing of options available for that particular mode. Modes that are able to function normally without arguments can be invoked by adding the --nop argument.

Several options are shared between all clm modes. Note that these options are specified after the mode. See OPTIONS.

The --version option causes clm to print out version and license information.

Issuing clm help mode will cause clm to look for a manual page describing mode and display it if found. This requires that the MANPATH environment 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 clm 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 clm to output a list of available options for that mode. This can be averted by using the --nop option.

-set key=val (set key-value pair)

Sets the key key to value val in the environment. Some modes allow adjustment of settings in this manner.

-debug <int> (set debug level/flags)
--debug (turn default debugging on)
--test (turn default testing on)

The first two turn on debugging, the last is for testing. The effect of these options is otherwise undocumented.

--progress (enable progress reporting)

This will enable some kind of progress reporting, by writing to STDERR.

## AUTHOR

Stijn van Dongen.

## SEE ALSO

mclfamily for an overview of all the documentation and the utilities in the mcl family.