cdec cleanup, remove bayesian stuff, parsing stuff

1 files changed, 0 insertions, 583 deletions

diff --git a/jam-files/boost-build/tools/mpi.jam b/jam-files/boost-build/tools/mpi.jam
deleted file mode 100644
index 0fe490be..00000000
--- a/jam-files/boost-build/tools/mpi.jam
+++ /dev/null
@@ -1,583 +0,0 @@
-# Support for the Message Passing Interface (MPI)
-#
-# (C) Copyright 2005, 2006 Trustees of Indiana University
-# (C) Copyright 2005 Douglas Gregor
-#
-# Distributed under the Boost Software License, Version 1.0. (See accompanying 
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt.)
-#
-# Authors: Douglas Gregor
-#          Andrew Lumsdaine
-#
-# ==== MPI Configuration ====
-# 
-# For many users, MPI support can be enabled simply by adding the following 
-# line to your user-config.jam file:
-#
-#   using mpi ;
-#
-# This should auto-detect MPI settings based on the MPI wrapper compiler in 
-# your path, e.g., "mpic++". If the wrapper compiler is not in your path, or
-# has a different name, you can pass the name of the wrapper compiler as the
-# first argument to the mpi module:
-#
-#   using mpi : /opt/mpich2-1.0.4/bin/mpiCC ;
-#
-# If your MPI implementation does not have a wrapper compiler, or the MPI 
-# auto-detection code does not work with your MPI's wrapper compiler,
-# you can pass MPI-related options explicitly via the second parameter to the 
-# mpi module:
-#
-#    using mpi : : <find-shared-library>lammpio <find-shared-library>lammpi++
-#                  <find-shared-library>mpi <find-shared-library>lam 
-#                  <find-shared-library>dl ;
-#
-# To see the results of MPI auto-detection, pass "--debug-configuration" on
-# the bjam command line.
-#
-# The (optional) fourth argument configures Boost.MPI for running
-# regression tests. These parameters specify the executable used to
-# launch jobs (default: "mpirun") followed by any necessary arguments
-# to this to run tests and tell the program to expect the number of
-# processors to follow (default: "-np").  With the default parameters,
-# for instance, the test harness will execute, e.g.,
-#  
-#    mpirun -np 4 all_gather_test
-#
-# ==== Linking Against the MPI Libraries ===
-#
-# To link against the MPI libraries, import the "mpi" module and add the 
-# following requirement to your target:
-# 
-#   <library>/mpi//mpi 
-#
-# Since MPI support is not always available, you should check 
-# "mpi.configured" before trying to link against the MPI libraries.
-
-import "class" : new ;
-import common ;
-import feature : feature ;
-import generators ;
-import os ;
-import project ;
-import property ;
-import testing ;
-import toolset ;
-import type ;
-import path ;
-
-# Make this module a project
-project.initialize $(__name__) ;
-project mpi ;
-
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ]
-{
-  .debug-configuration = true ;
-}
-
-# Assuming the first part of the command line is the given prefix
-# followed by some non-empty value, remove the first argument. Returns
-# either nothing (if there was no prefix or no value) or a pair
-#
-#   <name>value rest-of-cmdline
-#
-# This is a subroutine of cmdline_to_features
-rule add_feature ( prefix name cmdline ) 
-{
-    local match = [ MATCH "^$(prefix)([^\" ]+|\"[^\"]+\") *(.*)$" : $(cmdline) ] ;
-
-    # If there was no value associated with the prefix, abort
-    if ! $(match) {
-      return ;
-    }
-
-    local value = $(match[1]) ;
-
-    if [ MATCH " +" : $(value) ] {
-      value = "\"$(value)\"" ;
-    }
-
-    return "<$(name)>$(value)" $(match[2]) ;
-}
-
-# Strip any end-of-line characters off the given string and return the
-# result.
-rule strip-eol ( string )
-{
-  local match = [ MATCH "^(([A-Za-z0-9~`\.!@#$%^&*()_+={};:'\",.<>/?\\| -]|[|])*).*$" : $(string) ] ;
-
-  if $(match)
-  {
-    return $(match[1]) ;
-  }
-  else
-  {
-    return $(string) ;
-  }
-}
-
-# Split a command-line into a set of features. Certain kinds of
-# compiler flags are recognized (e.g., -I, -D, -L, -l) and replaced
-# with their Boost.Build equivalents (e.g., <include>, <define>,
-# <library-path>, <find-library>). All other arguments are introduced
-# using the features in the unknown-features parameter, because we
-# don't know how to deal with them. For instance, if your compile and
-# correct. The incoming command line should be a string starting with
-# an executable (e.g., g++ -I/include/path") and may contain any
-# number of command-line arguments thereafter. The result is a list of
-# features corresponding to the given command line, ignoring the
-# executable.
-rule cmdline_to_features ( cmdline : unknown-features ? )
-{
-    local executable ;
-    local features ;
-    local otherflags ;
-    local result ;
-
-    unknown-features ?= <cxxflags> <linkflags> ;
-
-    # Pull the executable out of the command line. At this point, the
-    # executable is just thrown away.
-    local match = [ MATCH "^([^\" ]+|\"[^\"]+\") *(.*)$" : $(cmdline) ] ;
-    executable = $(match[1]) ;
-    cmdline = $(match[2]) ;
-
-    # List the prefix/feature pairs that we will be able to transform. 
-    # Every kind of parameter not mentioned here will be placed in both
-    # cxxflags and linkflags, because we don't know where they should go.
-    local feature_kinds-D = "define" ;
-    local feature_kinds-I = "include" ;
-    local feature_kinds-L = "library-path" ;
-    local feature_kinds-l = "find-shared-library" ;
-
-    while $(cmdline) {
-
-        # Check for one of the feature prefixes we know about. If we
-        # find one (and the associated value is nonempty), convert it
-        # into a feature.
-        local match = [ MATCH "^(-.)(.*)" : $(cmdline) ] ;
-        local matched ;
-        if $(match) && $(match[2]) {
-           local prefix = $(match[1]) ;
-           if $(feature_kinds$(prefix)) {
-               local name = $(feature_kinds$(prefix)) ;
-               local add = [ add_feature $(prefix) $(name) $(cmdline) ] ;
-
-               if $(add) {
-
-                  if $(add[1]) = <find-shared-library>pthread
-                  {
-                      # Uhm. It's not really nice that this MPI implementation
-                      # uses -lpthread as opposed to -pthread. We do want to
-                      # set <threading>multi, instead of -lpthread.
-                      result += "<threading>multi" ;
-                      MPI_EXTRA_REQUIREMENTS += "<threading>multi" ;                      
-                  }
-                  else
-                  {                      
-                      result += $(add[1]) ;                  
-                  }
-                                     
-                  cmdline = $(add[2]) ;
-                  matched = yes ;
-               }
-           }
-        }
-
-        # If we haven't matched a feature prefix, just grab the command-line
-        # argument itself. If we can map this argument to a feature
-        # (e.g., -pthread -> <threading>multi), then do so; otherwise,
-        # and add it to the list of "other" flags that we don't
-        # understand.
-        if ! $(matched) {
-           match = [ MATCH "^([^\" ]+|\"[^\"]+\") *(.*)$" : $(cmdline) ] ;
-           local value = $(match[1]) ;
-           cmdline = $(match[2]) ;
-
-           # Check for multithreading support
-           if $(value) = "-pthread" || $(value) = "-pthreads"
-           {
-             result += "<threading>multi" ;
-
-             # DPG: This is a hack intended to work around a BBv2 bug where
-             # requirements propagated from libraries are not checked for
-             # conflicts when BBv2 determines which "common" properties to
-             # apply to a target. In our case, the <threading>single property
-             # gets propagated from the common properties to Boost.MPI
-             # targets, even though <threading>multi is in the usage 
-             # requirements of <library>/mpi//mpi.
-             MPI_EXTRA_REQUIREMENTS += "<threading>multi" ;
-           }
-           else if [ MATCH "(.*[a-zA-Z0-9<>?-].*)" : $(value) ] {
-              otherflags += $(value) ;
-           }
-        }
-    }
-
-    # If there are other flags that we don't understand, add them to the
-    # result as both <cxxflags> and <linkflags>
-    if $(otherflags) {
-       for unknown in $(unknown-features)
-       {
-         result += "$(unknown)$(otherflags:J= )" ;
-       }
-    }
-
-    return $(result) ;
-}
-
-# Determine if it is safe to execute the given shell command by trying
-# to execute it and determining whether the exit code is zero or
-# not. Returns true for an exit code of zero, false otherwise.
-local rule safe-shell-command ( cmdline )
-{
-  local result = [ SHELL "$(cmdline) > /dev/null 2>/dev/null; if [ "$?" -eq "0" ]; then echo SSCOK; fi" ] ;
-  return [ MATCH ".*(SSCOK).*" : $(result) ] ;
-}
-
-# Initialize the MPI module.  
-rule init ( mpicxx ? : options * : mpirun-with-options * )
-{
-  if ! $(options) && $(.debug-configuration)
-  {
-    ECHO "===============MPI Auto-configuration===============" ;
-  }
-    
-  if ! $(mpicxx) && [ os.on-windows ]
-  {  
-    # Try to auto-configure to the Microsoft Compute Cluster Pack
-    local cluster_pack_path_native = "C:\\Program Files\\Microsoft Compute Cluster Pack" ;
-    local cluster_pack_path = [ path.make $(cluster_pack_path_native) ] ;
-    if [ GLOB $(cluster_pack_path_native)\\Include : mpi.h ]
-    {
-      if $(.debug-configuration)
-      {
-        ECHO "Found Microsoft Compute Cluster Pack: $(cluster_pack_path_native)" ;
-      }
-      
-      # Pick up either the 32-bit or 64-bit library, depending on which address
-      # model the user has selected. Default to 32-bit.
-      options = <include>$(cluster_pack_path)/Include 
-                <address-model>64:<library-path>$(cluster_pack_path)/Lib/amd64
-                <library-path>$(cluster_pack_path)/Lib/i386
-                <find-static-library>msmpi
-                <toolset>msvc:<define>_SECURE_SCL=0
-              ;
-              
-      # Setup the "mpirun" equivalent (mpiexec)
-      .mpirun = "\"$(cluster_pack_path_native)\\Bin\\mpiexec.exe"\" ;
-      .mpirun_flags = -n ;
-    }
-    else if $(.debug-configuration)
-    {
-      ECHO "Did not find Microsoft Compute Cluster Pack in $(cluster_pack_path_native)." ;
-    }
-  } 
-   
-  if ! $(options)
-  { 
-    # Try to auto-detect options based on the wrapper compiler
-    local command = [ common.get-invocation-command mpi : mpic++ : $(mpicxx) ] ;
-
-    if ! $(mpicxx) && ! $(command) 
-    {
-      # Try "mpiCC", which is used by MPICH 
-      command = [ common.get-invocation-command mpi : mpiCC ] ;
-    }
-
-    if ! $(mpicxx) && ! $(command) 
-    {
-      # Try "mpicxx", which is used by OpenMPI and MPICH2
-      command = [ common.get-invocation-command mpi : mpicxx ] ;
-    }
-
-    local result ;
-    local compile_flags ;
-    local link_flags ;
-
-    if ! $(command)
-    { 
-      # Do nothing: we'll complain later
-    }
-    # OpenMPI and newer versions of LAM-MPI have -showme:compile and 
-    # -showme:link.
-    else if [ safe-shell-command "$(command) -showme:compile" ] &&
-              [ safe-shell-command "$(command) -showme:link" ]
-    {
-      if $(.debug-configuration)
-      {
-        ECHO "Found recent LAM-MPI or Open MPI wrapper compiler: $(command)" ;
-      }
-
-      compile_flags = [ SHELL "$(command) -showme:compile" ] ;
-      link_flags = [ SHELL "$(command) -showme:link" ] ;
-   
-      # Prepend COMPILER as the executable name, to match the format of 
-      # other compilation commands.
-      compile_flags = "COMPILER $(compile_flags)" ;
-      link_flags = "COMPILER $(link_flags)" ;
-    }
-    # Look for LAM-MPI's -showme
-    else if [ safe-shell-command "$(command) -showme" ]
-    {
-      if $(.debug-configuration)
-      {
-        ECHO "Found older LAM-MPI wrapper compiler: $(command)" ;
-      }
-
-      result = [ SHELL "$(command) -showme" ] ;
-    }
-    # Look for MPICH
-    else if [ safe-shell-command "$(command) -show" ]
-    {
-      if $(.debug-configuration)
-      {
-        ECHO "Found MPICH wrapper compiler: $(command)" ;
-      }
-      compile_flags = [ SHELL "$(command) -compile_info" ] ;
-      link_flags = [ SHELL "$(command) -link_info" ] ;
-    }
-    # Sun HPC and Ibm POE
-    else if [ SHELL "$(command) -v 2>/dev/null" ]
-    {
-      compile_flags = [ SHELL "$(command) -c -v -xtarget=native64 2>/dev/null" ] ;
-
-      local back = [ MATCH "--------------------(.*)" : $(compile_flags) ] ;
-      if $(back)
-      {
-        # Sun HPC
-        if $(.debug-configuration)
-        {
-          ECHO "Found Sun MPI wrapper compiler: $(command)" ;
-        }
-
-        compile_flags = [ MATCH "(.*)--------------------" : $(back) ] ;
-        compile_flags = [ MATCH "(.*)-v" :  $(compile_flags) ] ;
-        link_flags = [ SHELL "$(command) -v -xtarget=native64 2>/dev/null" ] ;
-        link_flags = [ MATCH "--------------------(.*)" : $(link_flags) ] ;
-        link_flags = [ MATCH "(.*)--------------------" : $(link_flags) ] ;
-
-        # strip out -v from compile options
-        local front = [ MATCH "(.*)-v" :  $(link_flags) ] ;
-        local back = [ MATCH "-v(.*)" :  $(link_flags) ] ;
-        link_flags = "$(front) $(back)" ;
-        front = [ MATCH "(.*)-xtarget=native64" :  $(link_flags) ] ;
-        back = [ MATCH "-xtarget=native64(.*)" :  $(link_flags) ] ;
-        link_flags = "$(front) $(back)" ;
-      }
-      else
-      {
-        # Ibm POE
-        if $(.debug-configuration)
-        {
-          ECHO "Found IBM MPI wrapper compiler: $(command)" ;
-        }
-
-        # 
-        compile_flags = [ SHELL "$(command) -c -v 2>/dev/null" ] ;
-        compile_flags = [ MATCH "(.*)exec: export.*" : $(compile_flags) ] ;
-        local front = [ MATCH "(.*)-v" :  $(compile_flags) ] ;
-        local back = [ MATCH "-v(.*)" :  $(compile_flags) ] ;
-        compile_flags = "$(front) $(back)" ;
-        front = [ MATCH "(.*)-c" :  $(compile_flags) ] ;
-        back = [ MATCH "-c(.*)" :  $(compile_flags) ] ;
-        compile_flags = "$(front) $(back)" ;
-        link_flags = $(compile_flags) ;
-
-        # get location of mpif.h from mpxlf
-        local f_flags = [ SHELL "mpxlf -v 2>/dev/null" ] ;
-        f_flags = [ MATCH "(.*)exec: export.*" : $(f_flags) ] ;
-        front = [ MATCH "(.*)-v" :  $(f_flags) ] ;
-        back = [ MATCH "-v(.*)" :  $(f_flags) ] ;
-        f_flags = "$(front) $(back)" ;
-        f_flags = [ MATCH "xlf_r(.*)" : $(f_flags) ] ;
-        f_flags = [ MATCH "-F:mpxlf_r(.*)" : $(f_flags) ] ;
-        compile_flags = [ strip-eol $(compile_flags) ] ;
-        compile_flags = "$(compile_flags) $(f_flags)" ;
-      }
-    }
-
-    if $(result) || $(compile_flags) && $(link_flags)
-    {
-      if $(result)
-      {
-         result = [ strip-eol $(result) ] ;
-         options = [ cmdline_to_features $(result) ] ;
-      }
-      else 
-      { 
-         compile_flags = [ strip-eol $(compile_flags) ] ;
-         link_flags = [ strip-eol $(link_flags) ] ;
-
-         # Separately process compilation and link features, then combine
-         # them at the end.
-         local compile_features = [ cmdline_to_features $(compile_flags) 
-                                                        : "<cxxflags>" ] ; 
-         local link_features = [ cmdline_to_features $(link_flags) 
-                                                     : "<linkflags>" ] ; 
-         options = $(compile_features) $(link_features) ;
-      }
-
-      # If requested, display MPI configuration information.
-      if $(.debug-configuration)
-      {
-        if $(result)
-        {
-          ECHO "  Wrapper compiler command line: $(result)" ;
-        }
-        else
-        {
-	  local match = [ MATCH "^([^\" ]+|\"[^\"]+\") *(.*)$" 
-                                : $(compile_flags) ] ;
-          ECHO "MPI compilation flags: $(match[2])" ;
-	  local match = [ MATCH "^([^\" ]+|\"[^\"]+\") *(.*)$" 
-                                : $(link_flags) ] ;
-          ECHO "MPI link flags: $(match[2])" ;
-        }
-      }
-    } 
-    else 
-    {
-      if $(command)
-      {
-        ECHO "MPI auto-detection failed: unknown wrapper compiler $(command)" ;
-        ECHO "Please report this error to the Boost mailing list: http://www.boost.org" ;
-      }     
-      else if $(mpicxx)
-      {
-        ECHO "MPI auto-detection failed: unable to find wrapper compiler $(mpicxx)" ;
-      } 
-      else
-      {
-        ECHO "MPI auto-detection failed: unable to find wrapper compiler `mpic++' or `mpiCC'" ;
-      }
-      ECHO "You will need to manually configure MPI support." ;
-    }
- 
-  }
-
-  # Find mpirun (or its equivalent) and its flags
-  if ! $(.mpirun)
-  {
-    .mpirun = 
-        [ common.get-invocation-command mpi : mpirun : $(mpirun-with-options[1]) ] ;
-    .mpirun_flags = $(mpirun-with-options[2-]) ;
-    .mpirun_flags ?= -np ;
-  }
-  
-  if $(.debug-configuration)
-  {
-    if $(options)
-    {
-      echo "MPI build features: " ;
-      ECHO $(options) ;
-    }
-
-    if $(.mpirun)
-    {
-      echo "MPI launcher: $(.mpirun) $(.mpirun_flags)" ;
-    }
-        
-    ECHO "====================================================" ;
-  }
-
-  if $(options)  
-  {
-    .configured = true ;
-
-    # Set up the "mpi" alias 
-    alias mpi : : : : $(options) ;
-  }
-}
-
-# States whether MPI has bee configured
-rule configured ( )
-{
-  return $(.configured) ;
-}
-
-# Returs the "extra" requirements needed to build MPI. These requirements are
-# part of the /mpi//mpi library target, but they need to be added to anything
-# that uses MPI directly to work around bugs in BBv2's propagation of
-# requirements.
-rule extra-requirements ( )
-{
-  return $(MPI_EXTRA_REQUIREMENTS) ;
-}
-
-# Support for testing; borrowed from Python
-type.register RUN_MPI_OUTPUT ;
-type.register RUN_MPI : : TEST ;
-
-class mpi-test-generator : generator
-{
-    import property-set ;
-
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-        self.composing = true ;
-    }
-
-    rule run ( project name ? : property-set : sources * : multiple ? )
-    {  
-      # Generate an executable from the sources. This is the executable we will run.
-      local executable = 
-        [ generators.construct $(project) $(name) : EXE : $(property-set) : $(sources) ] ;
-
-      result = 
-        [ construct-result $(executable[2-]) : $(project) $(name)-run : $(property-set) ] ;
-    }
-}
-
-# Use mpi-test-generator to generate MPI tests from sources
-generators.register 
-  [ new mpi-test-generator mpi.capture-output : : RUN_MPI_OUTPUT ] ;
-
-generators.register-standard testing.expect-success 
-  : RUN_MPI_OUTPUT : RUN_MPI ;
-
-# The number of processes to spawn when executing an MPI test.
-feature mpi:processes : : free incidental ;
-
-# The flag settings on testing.capture-output do not
-# apply to mpi.capture output at the moment.
-# Redo this explicitly.
-toolset.flags mpi.capture-output ARGS <testing.arg> ;
-rule capture-output ( target : sources * : properties * )
-{
-    # Use the standard capture-output rule to run the tests
-    testing.capture-output $(target) : $(sources[1]) : $(properties) ;
-
-    # Determine the number of processes we should run on.
-    local num_processes = [ property.select <mpi:processes> : $(properties) ] ;
-    num_processes = $(num_processes:G=) ;
-
-    # serialize the MPI tests to avoid overloading systems
-    JAM_SEMAPHORE on $(target) = <s>mpi-run-semaphore ;
-
-    # We launch MPI processes using the "mpirun" equivalent specified by the user.
-    LAUNCHER on $(target) =  
-      [ on $(target) return $(.mpirun) $(.mpirun_flags) $(num_processes) ] ;
-}
-
-# Creates a set of test cases to be run through the MPI launcher. The name, sources, 
-# and requirements are the same as for any other test generator. However, schedule is 
-# a list of numbers, which indicates how many processes each test run will use. For 
-# example, passing 1 2 7 will run the test with 1 process, then 2 processes, then 7
-# 7 processes. The name provided is just the base name: the actual tests will be 
-# the name followed by a hypen, then the number of processes. 
-rule mpi-test ( name : sources * : requirements * : schedule * )
-{        
-    sources ?= $(name).cpp ;
-    schedule ?= 1 2 3 4 7 8 13 17 ;
-
-    local result ;
-    for processes in $(schedule)
-    {  
-      result += [ testing.make-test 
-        run-mpi : $(sources) /boost/mpi//boost_mpi
-          : $(requirements) <toolset>msvc:<link>static <mpi:processes>$(processes) : $(name)-$(processes) ] ;
-    }
-    return $(result) ;
-}