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Prerequisites for Ubuntu

To run MoFEM on Ubuntu Linux (e.g. Ubuntu 12.04LTS or Ubuntu 13.10), certain libraries have to be installed beforehand. A list of all the prerequisites is as follows:

Update software centre

$ sudo apt-get update

Pre-Requisite Libraries

$ sudo apt-get install wget
$ sudo apt-get install valgrind
$ sudo apt-get install git
$ sudo apt-get install vim
$ sudo apt-get install g++
$ sudo apt-get install m4
$ sudo apt-get install automake
$ sudo apt-get install libsigsegv2
$ sudo apt-get install build-essential
$ sudo apt-get install libibverbs-dev
$ sudo apt-get install gfortran
$ sudo apt-get install libatlas-dev
$ sudo apt-get install libatlas-base-dev
$ sudo apt-get install libjpeg-dev
$ sudo apt-get install libhdf5-openmpi-dev
$ sudo apt-get install libnetcdf-dev
$ sudo apt-get install graphviz
$ sudo apt-get install doxygen
$ sudo apt-get install cmake
$ sudo apt-get install blas-dev

Optional

$ sudo apt-get install aptitude
$ sudo apt-get install gnuplot
$ sudo apt-get install octave

Install PETSc, MOAB and BOOST Libraries

Login as root

$ sudo -s

Download, copy and extract the build directory in opt, containing Petsc 3.4.3, MOAB 4.6, BOOST 1.54

https://bitbucket.org/likask/mofem-joseph/wiki/downloads/build_for_ubuntu.tar.gz

Save and extract it in the opt directory

$ cd /opt
$ sudo tar -xvzf build_for_ubuntu.tar.gz

Configure, compile and install Boost 1.54.0

$ cd build_for_ubuntu
$ sudo tar -xvzf boost_1_54_0.tar.gz
$ cd boost_1_54_0/
$ sudo ./bootstrap.sh --prefix=/opt/local
$ sudo ./b2
$ sudo ./b2 install

Configure, compile and install PETSc 3.4.3

$ cd ..
$ sudo tar -xvzf petsc-3.4.3.tar.gz
$ cd petsc-3.4.3
$ sudo ./configure  --with-debugging=0 --with-fc=/usr/bin/mpif90 --with-cc=/usr/bin/mpicc --with-cxx=/usr/bin/mpicxx --download-superlu_dist=1 --download-metis=1 --download-parmetis=1 --download-umfpack=1 --download-hypre=1 --with-mumps=1 --download-mumps=1 --with-scalapack=1 --download-scalapack=1 --with-blacs=1 --download-blacs=1
$ sudo make PETSC_DIR=/opt/build_for_ubuntu/petsc-3.4.3 PETSC_ARCH=arch-linux2-c-opt all

Test PETSc

$ make PETSC_DIR=/opt/build_for_ubuntu/petsc-3.4.3 PETSC_ARCH=arch-linux2-c-opt test

Configure, compile and install MOAB 4.6.0

$ cd ..
$ cd moab-4.6.0
$ sudo make clean
$ sudo ./configure --with-mpi --prefix=/opt/local-moab-4.6.0
$ sudo make
$ sudo make install
$ sudo aclocal -I config

Install MoFEM

Create a directory for MoFEM in the HOME directory

$ mkdir ~/mofem
$ cd ~/mofem

Clone the MoFEM repository

$ git clone https://bitbucket.org/likask/mofem-joseph.git

Create a build directory for MoFEM

$ mkdir build-mofem
$ cd build-mofem

Build the build directory

$ cmake -DCMAKE_BUILD_TYPE=Release -DPETSC_DIR=/opt/build_for_ubuntu/petsc-3.4.3 -DPETSC_ARCH=arch-linux2-c-opt -DMOAB_DIR=/opt/local-moab-4.6.0/ -DCMAKE_CXX_FLAGS=-I/opt/build_for_ubuntu/boost_1_54_0 -DCMAKE_INSTALL_PREFIX=$HOME/local ../mofem-joseph/mofem_v0.1/

Compile and then check all tests

$ make
$ make install
$ ctest -VV -D Experimental

On your terminal you can see all the tests and whether they are executed successfully. CTest will submit this job to CDashTesting where you can see any errors, warnings and compare your test with others.

Download and install ParaView

Install from binaries at http://www.paraview.org/paraview/resources/software.php, or
Alternatively, build and install from source; see http://paraview.org/Wiki/ParaView:Build_And_Install

The easiest option is to install ParaView from binaries. ParaView can be run directly from the installed directory. Alternatively, you may want to to set an alias for it.

If you have any problems, feedback or would like to suggest corrections, please email to cmatgu@googlegroups.com.

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