16 May 2014 mcx diameter 14-137
mcx diameter — compute the diameter of a graph
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)]
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 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 -.
The file name for input that is in label format.
The file name for input that is in mcl native matrix format.
The name of the file to write output to.
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.
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.
The output can then be collected with
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.
mcxio, and mclfamily for an overview of all the documentation and the utilities in the mcl family.