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 for large graphs.
        If you have multiple CPUs available consider using as many threads.
        Additionally it is possible to spread the computation over multiple
        jobs/machines.  These three options are described in the clmprotocols
        manual page.  The following set of options, if given to as many
        commands, defines three jobs, each running four threads.

        -t 4 -J 3 -j 0 -o out.0
        -t 4 -J 3 -j 1 -o out.1
        -t 4 -J 3 -j 2 -o out.2

        The output can then be collected with

        mcx collect --add-column -o out.all out.[0-2]


      --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 14-137               16 May 2014                  mcx diameter(1)
