Hermes - HowTo

• How to test patches posted by someone somewhere
  Let say that David asks you to pull the branch called exodus-II from git://github.com/andrsd/hermes2d.git and review.
  First, add the remote link to David's repo by saying:
  git remote add david git://github.com/andrsd/hermes2d.git
  Then, create in your repo a new local branch where the patches will be tested.
  Assuming that you are in your master branch, type:
  git co -b test-david
  Then, fetch David's repo by typing:
  git fetch david
  Next, merge the branch of interest into your local branch:
  git merge david/exodus-II
  That's it. You can now type "cmake .", "make", and test if everything works.
• How to push into the repository on spilka
  git remote add write spilka.math.unr.edu:/home/git/repos/hermes2d.git
  git push --d write local_branch:master
  check that all is ok and then:
  git push write local_branch:master
  

• How to install Trilinos
  download the sources from the Trilinos page and unpack them in some temporary directory
  place this do-configure script into the trilinos source directory
  ./do-configure
  make
  make install (as root)
  (This places the installation into /opt/packages/trilinos dir. If you do not like this location, change
  the CMAKE_INSTALL_PREFIX variable to whatever you like.)
  go to the directory with hermes{2|3}d. In your CMake.vars, say:
  set(WITH_TRILINOS YES)
  set(TRILINOS_ROOT /opt/packages/trilinos) (or your modified CMAKE_INSTALL_PREFIX variable)
  cmake .
  make
  
• How to install ExoduxII and NetCDF libraries
  (necessary to real Cubit files in Hermes)
  For system-wide installation do (as a root):
  1) cd /
  2)
  wget http://spilka.math.unr.edu/~andrsd/exodusii-bin-amd64-4.81.tar.gz
  wget http://spilka.math.unr.edu/~andrsd/netcdf-bin-amd64-4.0.1.tar.gz
  3)
  tar xvzf exodusii-bin-amd64-4.81.tar.gz
  tar xvzf netcdf-bin-amd64-4.0.1.tar.gz
  4)
  rm exodusii-bin-amd64-4.81.tar.gz
  rm netcdf-bin-amd64-4.0.1.tar.gz
  
  This will unpack binary packages of netcdf and exodusii in to /opt/packages/netcdf
  and /opt/packages/exodusii, respectively. If you do not like the location you can
  change it to whatever you like, but you need to adjust the CMake variables accordingly
  (see below).
  

  To use exodusii support in Hermes2D:
  - clone the repo (is you have done it yet)
  - in CMake.vars, say:
  SET(WITH_EXODUSII YES)
  SET(EXODUSII_ROOT /opt/packages/exodusii)
  SET(NETCDF_ROOT /opt/packages/netcdf)
  
  cmake .
  make
  
  Note: the binary packages were prepared on Ubuntu 9.10 (64 bit).
  They might work on other 64 bit machines, but we did not test that.
  However, you can always build these packages by yourself if you are
  on a different architecture (both are available for free).

• How to install libstdc++5
  Add this to your /etc/apt/sources.list:
  deb http://ubuntu.osuosl.org/ubuntu/ jaunty main restricted universe multiverse
  apt-get update
  apt-get install libstdc++5 libg2c0
  Now you can remove that line from sources.list. Then
  tar xzf Cubit_LINUX64.12.0.tar.gz
  ./cubit
  

• How to update Sphinx on spilka
  ssh spilka
  sudo -i
  cd /var/www2/hermes2d/hermes2d
  git clean -dfx
  git pull
  cd doc
  make html