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‎.boost‎

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# You can set BOOST paths here.
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# BOOST_PATH=/usr/include
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# BOOST_HDRS=$BOOST_PATH/boost

‎.cuda‎

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# You can set CUDA compiler and options here.
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# NVCC=nvcc
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# NVCCFLAGS="-arch sm_13"
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# CUDAFLAGS="-L/usr/local/cuda/lib64"
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# CUDALIBS="-lcudart"

‎COPYING‎

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‎Jambase.Misc‎

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# $Id: Jambase.Misc 597 2010-06-23 01:06:56Z zola $
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# Author: Jaroslaw Zola <jaroslaw.zola@gmail.com>
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# Copyright (c) 2008-2010 Jaroslaw Zola
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# Distributed under the MIT License.
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# See accompanying LICENSE.
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# This file is part of x-build.
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# CUDA compiler
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rule Nvcc {
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Depends $(1) : $(2) ;
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Clean clean : $(1) ;
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}
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# Workaround for CXX and CUDA files
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rule UserObject {
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switch $(2) {
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case *.cu : Nvcc $(1) : $(2) ;
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case *.cxx : C++ $(1) : $(2) ;
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}
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}
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# Installs files in the given directory
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rule InstallFiles {
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local i ;
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for i in $(2) {
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InstallFile $(1) : $(i) ;
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}
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}
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# Creates directory during installation
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rule InstallDir {
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Depends install : $(1) ;
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MkDir1 $(1) ;
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}
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# Removes directory, works only for UNIX-like systems
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DELTREE ?= "rm -rf" ;
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rule CleanDir
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{
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Always $(1) ;
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NotFile $(1) ;
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NoCare $(2) ;
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}
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# *** Actions ***
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ECHO ?= "echo" ;
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actions piecemeal together existing CleanDir {
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$(DELTREE) $(2)
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}
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actions Nvcc {
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$(NVCC) -c -o $(1) $(NVCCFLAGS) $(2)
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}

‎Jamfile‎

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include Jambase.Misc ;
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TOP = . ;
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SubInclude TOP src ;
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SubInclude TOP tools ;
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SubInclude TOP obj ;
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CleanDir distclean : bin ;
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Depends distclean : clean ;

‎Jamrules‎

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TARGET = tinge-mi$(SUFFIX) ;
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TARGETS = ;
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if $(C++) = "" | $(C++) = "cc" {
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C++ = mpiCC ;
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}
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HDRS = "." ;
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if $(CXX_HDRS) != "" {
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HDRS += $(CXX_HDRS) ;
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}
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C++FLAGS = "$(CXX_EXTRA)" ;
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OPTIM = "$(CXX_OPTIM)" ;
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LINK = $(C++) ;
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ALL_LOCATE_TARGET = $(TOP)/obj ;

‎README‎

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TINGe - Tool Inferring Networks of GEnes (using Mutual Information)
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See doc directory for more information.

‎build/LICENSE‎

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Copyright (c) 2007-2009 Jaroslaw Zola <jaroslaw.zola@gmail.com>
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Permission is hereby granted, free of charge, to any person
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obtaining a copy of this software and associated documentation
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files (the "Software"), to deal in the Software without
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restriction, including without limitation the rights to use,
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copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the
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Software is furnished to do so, subject to the following
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conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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OTHER DEALINGS IN THE SOFTWARE.

‎build/bgl‎

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# Name suffix
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SUFFIX=".bg"
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# C++ compiler
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CXX=blrts_xlc++
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# C++ optimisation options (you may tune them for your environment)
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CXX_OPTIM="-O3 -qhot=level=1 -qipa=level=2 -qarch=440"
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# CXX_OPTIM="-qnoeh -O3 -qhot=level=1 -qipa=level=2 -qarch=440"
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# C++ extra headers
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CXX_HDRS="/bgl/BlueLight/ppcfloor/bglsys/include /usr/local/include"
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# C++ extra options (other than -Ox and -I)
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CXX_EXTRA="-g -DNDEBUG -DMPICH_IGNORE_CXX_SEEK"
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# Linker flags
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LINKFLAGS="$CXX_OPTIM -L/bgl/BlueLight/ppcfloor/bglsys/lib -L/usr/local/lib"
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# Linker libs
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LINKLIBS="-lmpich.rts -lcxxmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -lmass -lmassv"

‎build/bgp‎

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# Name suffix
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SUFFIX=".bgp"
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# C++ compiler
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CXX=mpixlcxx
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# C++ optimisation options (you may tune them for your environment)
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CXX_OPTIM="-O3 -qhot=level=1 -qipa=level=2 -qarch=450"

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