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otfprofile-mpi(1) [debian man page]

OTFPROFILE-MPI(1)						   User Commands						 OTFPROFILE-MPI(1)

NAME
otfprofile-mpi - otfprofile-mpi DESCRIPTION
otfprofile-mpi - generate a profile of a trace in LaTeX format. Syntax: otfprofile-mpi [options] <input file name> options: -h, --help show this help message -V show OTF version -v increase output verbosity (can be used more than once) -p show progress -f <n> max. number of filehandles available per rank (default: 50) -b <size> set buffersize of the reader (default: 1048576) -o <prefix> specify the prefix of output file(s) (default: result) -g <n> max. number of process groups in LaTeX output (range: 1-16, default: 16) -c, --cluster[ <alg>] do additional clustering of processes/threads using comparison algorithm <alg> (KMEANS or CLINKAGE) (default comparison algorithm: KMEANS) -m <mapfile> write cluster mapping to <mapfile> (implies -c, default: result.map) -s <prefix> call otfshrink to apply the cluster mapping to input trace and produce a new trace named <prefix> with symbolic links to the origi- nal (implies -c) -H use hard groups for CLINKAGE clustering (implies --cluster CLINKAGE) -q <0-1> quality threshold for CLINKAGE clustering (implies --cluster CLINKAGE, default: 0.1) --stat read only summarized information, no events --[no]csv enable/disable producing CSV output (default: disabled) --[no]tex enable/disable producing LaTeX output (default: enabled) PDF creation requires the PGFPLOTS package version >1.4 http://sourceforge.net/projects/pgfplots/ otfprofile-mpi - generate a profile of a trace in LaTeX format. Syntax: otfprofile-mpi [options] <input file name> options: -h, --help show this help message -V show OTF version -v increase output verbosity (can be used more than once) -p show progress -f <n> max. number of filehandles available per rank (default: 50) -b <size> set buffersize of the reader (default: 1048576) -o <prefix> specify the prefix of output file(s) (default: result) -g <n> max. number of process groups in LaTeX output (range: 1-16, default: 16) -c, --cluster[ <alg>] do additional clustering of processes/threads using comparison algorithm <alg> (KMEANS or CLINKAGE) (default comparison algorithm: KMEANS) -m <mapfile> write cluster mapping to <mapfile> (implies -c, default: result.map) -s <prefix> call otfshrink to apply the cluster mapping to input trace and produce a new trace named <prefix> with symbolic links to the origi- nal (implies -c) -H use hard groups for CLINKAGE clustering (implies --cluster CLINKAGE) -q <0-1> quality threshold for CLINKAGE clustering (implies --cluster CLINKAGE, default: 0.1) --stat read only summarized information, no events --[no]csv enable/disable producing CSV output (default: disabled) --[no]tex enable/disable producing LaTeX output (default: enabled) PDF creation requires the PGFPLOTS package version >1.4 http://sourceforge.net/projects/pgfplots/ otfprofile-mpi 1.10.2 May 2012 OTFPROFILE-MPI(1)

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mclcm(1)							  USER COMMANDS 							  mclcm(1)

  NAME
      mclcm - hierarchical clustering of graphs with mcl

  SYNOPSIS
      mclcm <-|fname> [mclcm-options] [-- "mcl options"*]

      mclcm <-|fname> -a "-I 4 --shadow=vl"
      mclcm <-|fname> -a "-I 3" -- "-I 5"
      mclcm <-|fname> -a "-I 3" -b1 "" -- "-ph 3 --shadow=vl -I 5"

      mclcm  <-fname> [--contract (contraction mode)] [--dispatch (dispatch mode)] [--integrate (integrate mode)] [--subcluster (subcluster mode)]
      [-a <opts> (shared mcl options)] [-b1 <opts> (dedicated base 1 mcl options)] [-b2 <opts> (dedicated base 2 mcl options)]	[-tf  spec  (apply
      tf-spec  to  input  matrix)]  [-c <fname> (input clustering)] [-n <num> (iteration limit)] [--root (ensure universe root clustering)] [-cone
      <fname> (nested cluster stack file)] [-stack <fname> (expanded cluster stack  file)]  [-coarse  <fname>  (coarsened  graphs  file)]  [-write
      (stack,cone,coarse,steps)]  [-write-base <fname> (write base matrix)] [-stem <str> (prefix for all outputs)] [--mplex=y/n (write clusterings
      separately)] [-annot str (dummy annotation option)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)]  [--version  (print  ver-
      sion, exit)] [-q spec (log levels)] [-z (show default shared options)] [-- "mcl options"*]

  DESCRIPTION
      The  mclcm  options may be followed by a number of trailing arguments.  The trailing arguments should be separated from the mclcm options by
      the separator --.  Normally each trailing argument should consist of a set of zero, one, or more mcl arguments enclosed in quotes or  double
      quotes  to  group them together.	These arguments are passed to the successive stages of hierarchical clustering. They are combined with the
      default options. If an option is specified both in the default options list and in a trailing options list the  latter  specification  over-
      rides  the  former.   When the --integrate option is specified the trailing arguments must be names of files containing mcl clusterings; see
      further below.  mclcm has four major modes of operation, namely contraction (default), integration, dispatch, and subcluster. Each  mode	is
      described  a  little  below.  Note though that dispatch mode is not the best mode to use for hierarchical clustering. It is mostly useful to
      generate multiple mcl clusterings in a single run.

      In all modes mclcm will generate a file, by default called mcl.cone.  This is a representation of a hierarchical clustering that is particu-
      lar to mcl. It can be converted to newick format like this:

	       mcxdump -imx-tree mcl.cone --newick -o NEWICKFILE
	 OR    mcxdump -imx-tree mcl.cone --newick -o NEWICKFILE -tab TABFILE

      In  the last example, TABFILE should be a file containing a mapping from mcl labels to application labels. Refer to mcxio(5) for more infor-
      mation about tab files and mcl input/ouput formats.

  OPTIONS
      --contract (repeated contraction mode)
	This is the default mode of operation.	At each successive step of constructing the hierarchy on top of the first  level  mcl  clustering,
	mclcm uses a matrix derived from the input matrix and the last computed clustering to compute a contracted graph.  The contracted graph is
	a graph where the nodes represent the clusters of the last clustering. The matrix derived from the input graph that is used  to  construct
	the  contracted graph is called the base matrix. The base matrix can be either the start matrix or the expansion matrix.  The start matrix
	is the input matrix after transformations have been applied to it (if any).  The expansion matrix is the first expanded matrix of some mcl
	process applied to the input graph.

	By default the base matrix is constructed from either the start matrix or the expansion matrix obtained from the first mcl process.  It is
	possible to use a start matrix derived from special purpose mcl transformation parameters (such as -ph and -tf)  or  an  expansion  matrix
	derived from a special purpose mcl process.  The -b1 and -b2 parameters provide the interfaces to this functionality.

	You  are  advised  to start with a high inflation value for the input graph and to use shadowing, e.g. include --shadow=vl in the -a argu-
	ment.  This generally leads to hierarchies that are better balanced.  Shadowing is a transformation where nodes are added  to  the  graph,
	preventing  relatively	distant  nodes from unwanted chaining.	For more information refer to the mcl manual.  The invocations in SYNOPSIS
	are a good starting point.

      --dispatch (different mcl processes)
	In this mode each trailing argument is specified as a set of options to pass to an mcl process. For each trailing argument an mcl  process
	is thus computed. The set of resulting clusterings is integrated into a hierarchy.

      --integrate (existing clusterings)
	This  mode is similar to dispatch mode. The difference is that with this option mclcm simply integrates a set of already existing cluster-
	ings.  Each trailing argument must be the name of a file containing a clustering.  The set of clusterings  thus  specified  is	integrated
	into a hierarchy.

      --subcluster (repeated sub-clustering)
	In  this mode each trailing argument specifies a set of options to pass to an mcl process. The second clustering process is applied to the
	graph of components induced by the first clustering, resulting in a further subdivision of the first clustering. This approach is repeated
	with each further trailing argument. With this approach, the first clustering will be the most coarse clustering. Hence, subsequent trail-
	ing arguments will typically specify increasingly higher inflation values, pre-inflation values, and optionally more stringent transforma-
	tion parameters in order to achieve further subdivsions.

      -a <opts> (shared mcl options)
	Use this to change and/or set the default mcl options for all iterations. Use quotes if necessary.  Example of usage: -a "-I 5".

      -b1 <opts> (dedicated base 1 mcl options)
	This  will  apply  the	mcl  options opts to the input matrix. The resulting start matrix is used as the base matrix for constructing con-
	tracted graphs.

      -b2 <opts> (dedicated base 2 mcl options)
	This will apply the mcl options opts to the input matrix and compute the first	iterand  of  the  corresponding  mcl  process.	The  first
	iterand, aka the expansion matrix, is used as the base matrix for constructing contracted graphs.

      -tf <tf-spec> (transform input matrix values)
	Transform the input matrix values according to the syntax described in mcxio(5).

      -c <fname> (input clustering)
	The hierarchical clustering process will be kicked off by the clustering found in <fname>.

      -n <num> (iteration limit)
	This puts an upper bound to the number of contractions that will be performed.

      --root (ensure universe root clustering)
	In case the graph consists of different connected components, the last clustering computed by the mclcm process will correspond with those
	connected components. This option simply adds an artificial clustering where all nodes have been joined into a single cluster.

      -cone <fname> (nested cluster stack file)
	File to write the nested cluster stack to.  The nested cluster stack contains a sequence of clusterings, each written as  an  MCL  matrix.
	The  first (bottom) clustering is a clustering of the nodes in the input graph. Each subsequent clustering is a clustering where the nodes
	are the clusters of the previous clustering.  mcxdump can dump this format if the file name is given as the -imx-stack option. The  expla-
	nation	for  the  cone/stack  discrepancy  is simple. To mcxdump the contents are simply a stack of matrices. It does not care whether the
	stack is cone shaped, cylindrical, or yet another shape.

      -stack <fname> (expanded cluster stack file)
	File to write the expanded cluster stack to. The expanded cluster stack is similar to the nested cluster stack except  that  each  cluster
	lists all the nodes in the input graph it contains.  mcxdump can dump this format if the file name is given as the -imx-stack option.

      -coarse <fname> (coarsened graphs file)
	File to write the sequence of coarsened graphs to. Each clustering induces a coarsened graph where the nodes represent the clusters and an
	edge between two nodes represents the connectivity between the corresponding two clusters. The computation of this connectivity takes into
	account all edges between the two clusters in in the original graph.

      -write <tag> (select output modes)
	Use  this  option to explicitly specify all of the output types you want written in a comma-separated string. <tag> may contain any of the
	strings stack, cone, coarse, steps.  The current default is to write all of these except coarse.  The latter dumps the intermediate coars-
	ened (aka contracted) graphs to a single file.

      -write-base <fname> (write base matrix)
	Write the base matrix to file. This can be useful for debugging expectations.

      -stem <str> (prefix for all outputs)
	All output files share the same prefix. The default is mcl and can be changed with this option.

      --mplex=y/n (write clusterings separately)
	If  turned  on	each clustering is written in a separate file. The first clustering is written to the file <stem>.3 where <stem> is deter-
	mined by the -stem option. For each subsequent clustering the index is incremented by two, so clusterings are written to files	for  which
	the name ends with an odd index.

      -annot str (dummy annotation option)
	mclcm writes the command line with which it was invoked to the output file (either of the cone or stack files). Use this option to include
	any additional information. mclcm does nothing with this option except copying it as just described.

      -q spec (log levels)
	Set the quiet level. Read tingea.log(7) for syntax and semantics.

      -z (show default shared options)
	Show the default mcl options. These are used for each mcl invocation as successively applied to the input graph and succeeding	contracted
	graphs.

  AUTHOR
      Stijn van Dongen.

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

  mclcm 12-068							      8 Mar 2012							    mclcm(1)
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