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courses:yamsnotes [2014/03/07 04:10] (current)
rgladstone created
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 +Some notes on preparing your system for Fabien'​s mesh generation scripts. ​ This worked on Linux Mint running on VMWare on a Windows 7 laptop. ​ It should be pretty similar on any Mint or Ubuntu installation.
 +
 +  #!/bin/bash
 +  ​
 +  # script for getting software needed for Fabien'​s approach to mesh generation
 +  ​
 +  # This worked on my laptop running Linux Mint in VMWare with a Wondows 7 host.
 +  # Elmer was already installed, and I used the Elmer installof blas and lapack ​
 +  # (which Fabien'​s code uses). ​ I installed yams and medit using Fabien'​s makefiles ​
 +  # with some minor adjustments. ​ I installed GLUT, a pre-req for medit. ​ OpenGL ​
 +  # was already installed on my system.
 +  #
 +  # I compiled Fabien'​s mesh generation code and ran the examples provided in his 
 +  # zip files.
 +  #
 +  # This script gets the files needed and carries out the above installations and 
 +  # generates Fabien'​s example meshes.
 +  # But it comes with no error checking or safety mechanisms. ​ Maybe it will work for 
 +  # you.
 +  ​
 +  # Rupert Gladstone (rupertgladstone1972@gmail.com) March 2014.
 +  ​
 +  # download source files
 +  wget http://​www.ann.jussieu.fr/​frey/​ftp/​archives/​freeyams.2012.02.05.tgz
 +  wget http://​www.ann.jussieu.fr/​frey/​ftp/​archives/​medit.2012.02.05.tgz
 +  wget http://​elmerice.elmerfem.org/​wiki/​lib/​exe/​fetch.php?​media=courses:​gillet_meshadaptation.pdf -O gillet_meshadaptation.pdf
 +  wget http://​elmerice.elmerfem.org/​wiki/​lib/​exe/​fetch.php?​media=courses:​meshadaptation.tar.gz -O meshadaptation.tar.gz
 +  wget http://​elmerice.elmerfem.org/​wiki/​lib/​exe/​fetch.php?​media=courses:​yamsmakefiles_ubuntu64-bit.tar.gz -O yamsmakefiles_ubuntu64-bit.tar.gz
 +  ​
 +  # unpack
 +  mkdir yams
 +  mv freeyams.2012.02.05.tgz yams
 +  cd yams
 +  gunzip freeyams.2012.02.05.tgz ​
 +  tar -xf freeyams.2012.02.05.tar
 +  cd ..
 +  ​
 +  mkdir medit
 +  mv medit.2012.02.05.tgz medit
 +  cd medit
 +  gunzip medit.2012.02.05.tgz ​
 +  tar -xf medit.2012.02.05.tar
 +  cd ..
 +  ​
 +  tar -xf meshadaptation.tar.gz
 +  tar -xf yamsmakefiles_ubuntu64-bit.tar.gz
 +  ​
 +  # use Fabien'​s make files for yams and medit instead of the default ones
 +  cp medit.2012.02.05/​* medit
 +  rm -rf medit.2012.02.05
 +  cp freeyams.2012.02.05/​* yams
 +  rm -rf freeyams.2012.02.05
 +  ​
 +  # install yams
 +  cd yams
 +  # there is a function call that may cause a seg fault. ​ work around is to comment it out.
 +  cd sources
 +  sed -i '​s@outqua1_a(sm);​@/​* outqua1_a(sm);​ */@g' yams.c
 +  cd ..
 +  make
 +  cd ..
 +  ​
 +  # medit needs openGL plus GLUT. most systems will have openGL already, but 
 +  # you may need to install GLUT.
 +  ​
 +  #install GLUT in Linux Mint
 +  sudo apt-get install g++ cmake
 +  sudo apt-get install freeglut3 freeglut3-dev
 +  #check where these files were installed
 +  #dpkg --listfiles freeglut3
 +  #dpkg --listfiles freeglut3-dev
 +  #probably here: /​usr/​lib/​x86_64-linux-gnu/​libglut.a
 +  ​
 +  # need libxmu for medit as well...
 +  sudo apt-get install libxmu-dev
 +  ​
 +  # install medit
 +  cd medit
 +  make linux
 +  cd ..
 +  ​
 +  # we can now make and run Fabien'​s mesh generation code for the first example
 +  cd MeshAdaptation/​Case0_Gaussian
 +  make
 +  ​
 +  # for Greenland we need to download and process (in Matlab) the measures data
 +  cd ../Data
 +  wget ftp://​sidads.colorado.edu/​pub/​DATASETS/​nsidc0478_MEASURES_greenland_V01/​2000/​*
 +  wget ftp://​sidads.colorado.edu/​pub/​DATASETS/​nsidc0478_MEASURES_greenland_V01/​2005/​*
 +  wget ftp://​sidads.colorado.edu/​pub/​DATASETS/​nsidc0478_MEASURES_greenland_V01/​2006/​*
 +  wget ftp://​sidads.colorado.edu/​pub/​DATASETS/​nsidc0478_MEASURES_greenland_V01/​2007/​*
 +  wget ftp://​sidads.colorado.edu/​pub/​DATASETS/​nsidc0478_MEASURES_greenland_V01/​2008/​*
 +  ​
 +  # we've downloaded the measures vels with a slightly different directory structure...
 +  sed -i "​s@2000/​@@g"​ CreatDEM.m
 +  sed -i "​s@2005/​@@g"​ CreatDEM.m
 +  sed -i "​s@2006/​@@g"​ CreatDEM.m
 +  sed -i "​s@2007/​@@g"​ CreatDEM.m
 +  sed -i "​s@2008/​@@g"​ CreatDEM.m
 +  ​
 +  # then run the matlab script CreatDEM (I did this on a different machine as I 
 +  # didn't have matlab avialable)
 +  ​
 +  # then we can run the second example
 +  cd ../​Case1_Greenland
 +  make
  
courses/yamsnotes.txt ยท Last modified: 2014/03/07 04:10 by rgladstone
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