mcx diameter(1) 						  USER COMMANDS 						   mcx diameter(1)

  NAME
      mcx diameter - compute the diameter of a graph

  SYNOPSIS
      mcx diameter [options]

      mcxdiameter  is  not  in actual fact a program. This manual page documents the behaviour and options of the mcx program when invoked in mode
      diameter. The options -h, --apropos, --version, -set, --nop, -progress <num> are accessible in all mcx modes. They are described in the  mcx
      manual page.

      mcx  diameter  [-abc <fname> (specify label input)] [-imx <fname> (specify matrix input)] [-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>)]	[--summary
      (output diameter and average shortest path length)] [--list (list eccentricity for all nodes)] [-h (print synopsis, exit)] [--apropos (print
      synopsis, exit)] [--version (print version, exit)]

  DESCRIPTION
      mcx diameter computes the diameter of a graph. The input graph should be symmetric. Results will be unpredictable for directed graphs.   For
      label input this is irrelevant as mcx diameter will create a symmetric graph from the input.

      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 that is in mcl native matrix format.

      -o <fname> (output file name)
	The name of the file to write output to.

      -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  the diameter of a graph is time-intensive.  If you have multiple CPUs available consider using as many threads. Additionally 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.  Additionally, 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 run-
	ning four threads.

	-t 12 -G 3 -g 0
	-t 12 -G 3 -g 1
	-t 12 -G 3 -g 2

      --list (list eccentricity for all nodes)
      --summary (output diameter and average eccentricity)
	The  default  mode  is --list, which results in output of the eccentricity of all nodes. The eccentricity of a node is the distance to any
	node that is the furthest away from it. The diameter of a graph is the maximum of the eccentricity taken over all nodes in  a  graph.	In
	this mode mcx diameter will not output the diameter itself. Use --summary to output just the diameter and the average eccentricity.

  SEE ALSO
      mcxio(5), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.

  mcx diameter 12-068						      8 Mar 2012						     mcx diameter(1)