Difference between revisions of "Flow engines on ubuntu 12.04"

From Yade
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* type "sudo make install", to install the library (this step may give harmless error messages even if it actually compiled (it failed at post-built test stages), ignore them and just check that /src/taucs.h and /lib/linux/libtaucs.a are present).
  
* type "sudo make install", to install the library (this step may give harmless error messages even if it actually compiled (it failed at post-built test stages), ignore them and just check that /src/taucs.h and /lib/linux/libtaucs.a are present).
   
  +
== Cholmod ==
−
== 3. configure the compilation of yade/lib/triangulation ==
  
  +
[http://www.cise.ufl.edu/research/sparse/cholmod/ CHOLMOD] is a set of ANSI C routines for sparse Cholesky factorization and update/downdate. A MATLAB interface is provided. The simplest way to get CHOLMOD and its dependencies is to just download all of SuiteSparse. Do this.
   
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=== Prerequisities and Download ===
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It should be possible to do it all in the scons.profile, but for the moment I just modified /trunk/lib/sconscript like this:
 
  +
Install LaPack (Linear Algebra Package) and “suitesparse-metis” package in Ubuntu (collection of libraries for computations for sparse matrices)
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* sudo apt-get install liblapack-dev libsuitesparse-metis-dev
   
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Download the SuiteSparse sources from [http://www.cise.ufl.edu/research/sparse/SuiteSparse/ here] (ATTENTION, download version 3.7.1)
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# vim: set filetype=python :
  
   
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=== Compilation ===
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env.Install('$LIBDIR/lib',env.SharedLibrary('yade-support',[
  
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To compile, place you into the folder that contains the sources and type:
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env.Combine('yade-support.cpp',['base/Math.cpp']+
  
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*make
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['factory/ClassFactory.cpp','factory/DynLibManager.cpp','multimethods/Indexable.cpp','serialization/Serializable.cpp','pyutil/gil.cpp']
  
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*sudo make install
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# compile TesselationWrapper only if cgal is enabled in features
  
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+(Split('triangulation/KinematicLocalisationAnalyser.cpp triangulation/Timer.cpp triangulation/basicVTKwritter.cpp
  
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triangulation/FlowBoundingSphere.cpp triangulation/PeriodicFlow.cpp triangulation/Tenseur3.cpp triangulation/TriaxialState.cpp')
  
−
if 'cgal' in env['features'] else [])
  
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+(['opengl/GLUtils.cpp'] if 'opengl' in env['features'] else [])
  
−
),
  
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],LIBS=['dl','m']+([''''taucs','metis','openblas','gomp','gfortran''''] if 'cgal' in env['features'] else [])
  
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+[l for l in env['LIBS'] if l!='yade-support']+(['glut','GL','GLU'] if 'opengl' in env['features'] else []),
  
−
LINKFLAGS=env['LINKFLAGS']+[''''-L/path/to/taucs_full/lib/linux'''',''''-L/path/to/metis-4.0''' ''(if compiled)'' ',
  
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''''-L/path/to/lib/openblas/lib/'''','-pthread','-Wl','-Bsymbolic-function','-ansi'],CXXFLAGS=env['CXXFLAGS']+['-fPIC','-frounding-math','-ansi']
  
−
))
  
   
 
== 5. Compile Yade with linsolv enabled ==
  
== 5. Compile Yade with linsolv enabled ==

Revision as of 16:19, 28 September 2012

Download Yade

You can install either a release (numbered version, which is frozen) or the current developement version (updated by the developers frequently).

Release version

Releases can be downloaded from the download page[1], as compressed archive. Uncompressing the archive gives you a directory with the sources.

Once you downloaded the sources, you have to install dependencies following the instructions from here: https://yade-dem.org/doc/installation.html#prerequisities

Current development version

Developement version (trunk) can be obtained from the code repository at github. Follow instructions from here to download: https://www.yade-dem.org/wiki/Yade_on_github#Setup

Once you downloaded the sources, you have to install dependencies following the instructions from here: https://yade-dem.org/doc/installation.html#prerequisities

Flow Engine

To add the flow engine and perform coupled fluid-particle simulations, follow the instructions below. Basically there are just a number of dependencies that need to be satisfied.

Openblas

Openblas is a packaged version of Kazushige Goto's gotoblas, which is recommended by most matrix library developpers. It is available precompiled in 12.04 but it breaks python's matplotlib because it provides a different version of lapack, which is a dependency of matplotlib.

Download and compilation

You should download the sources at github: https://github.com/xianyi/OpenBLAS/zipball/master

Prerequisites:

  • gfortran - type on a terminal "sudo apt-get install gfortran"

Optional:

  • pthread - type on a terminal "sudo apt-get install libpthread-stubs0-dev"

Open a terminal and place you into the folder where the openblas sources have been downloaded. Unpack the compressed file. To compile, do this:

  • type "make FC=gfortran" so as to use the right compiler;
  • type "sudo make install", to install the library.

Make a symlink to /path/to/libopenblas.so.0 in the standard path so that yade will find it at startup:

  • sudo ln -s /path/to/libopenblas.so.0 /usr/lib/libopenblas.so.0

Note for ubuntu 10.04 users: it may be easier on 10.04 to compile the ancestor of openblas: gotoblas

Taucs

TAUCS is a C library of sparse linear solvers. You have two options:

  • Download taucs sources already configured for 12.04 + openblas here
  • Download taucs sources from the CGAL project. In this case you'll have to configure the build by editing /config/linux.mk (you need at least to set the path to openblas, or to other libs you may want to use).

Prerequisities and Compilation

As a prerequisite, you have to install ParMETIS (Parallel Graph Partitioning and Fill-reducing Matrix Ordering). To do this open a terminal and type:

  • sudo apt-get install libparmetis-dev

You can also download and compile your own metis-4.0.1 (it doesn't really matter both ways should work)

To compile, open a terminal and place you into the folder where the taucs sources have been downloaded. To compile, do this:

  • type "make"
  • type "sudo make install", to install the library (this step may give harmless error messages even if it actually compiled (it failed at post-built test stages), ignore them and just check that /src/taucs.h and /lib/linux/libtaucs.a are present).

Cholmod

CHOLMOD is a set of ANSI C routines for sparse Cholesky factorization and update/downdate. A MATLAB interface is provided. The simplest way to get CHOLMOD and its dependencies is to just download all of SuiteSparse. Do this.

Prerequisities and Download

Install LaPack (Linear Algebra Package) and “suitesparse-metis” package in Ubuntu (collection of libraries for computations for sparse matrices)

  • sudo apt-get install liblapack-dev libsuitesparse-metis-dev

Download the SuiteSparse sources from here (ATTENTION, download version 3.7.1)

Compilation

To compile, place you into the folder that contains the sources and type:

  • make
  • sudo make install

5. Compile Yade with linsolv enabled

As usual, get the "linsolv" version of flow engines and compile yade with cgal enabled, and -DFLOW_ENGINE, -DLINSOLV in Yade's compile flags.

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