How to install Moose

How to install MOOSE

Yanming Wang

June, 2017

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MOOSE, short for Multiphysics Object-Oriented Simulation Environment, is a finite-element multi-physics framework developed by Idaho National Laboratory. Here we briefly describe how to install MOOSE on the Certainty cluster.

System requirements

The installation of MOOSE requires Compiler: C++11 Compliant GCC 4.8.4, Clang 3.4.0, Intel20130607, and Python 2.7+. On Certainty, they are provided as modules, so you can simply type the following commands to load them,

module load gnu/4.7.2
module load clang/3.5.2
module load gnu/5.2
module load openmpi/1.10.2-gnu-5.2
module load cmake/2.8.12.2

Or you can copy and paste them in your ~/.bashrc file, which will load the modules automatically when you login to Certainty. Notice that on Certainty clang requires some libraries from gnu/4.7.2, so that you have to load gnu/4.7.2 first and update it later (to gnu/5.2 in this case) to satisfy the MOOSE requirement. Also, the version of openmpi compiler should be compatible with the gcc compiler.

Installation

The procedures of MOOSE installation is given in details on their official website.

PETSc

First, you need to install PETSc following the following steps. (mostly follow the official tutorial)

PREFIX Setup

export CLUSTER_TEMP=`mktemp -d /tmp/cluster_temp.XXXXXX`
export PACKAGES_DIR=$HOME/moose-compilers

Download Software

cd $CLUSTER_TEMP
curl -L -O http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.6.4.tar.gz

Extract Software

cd $CLUSTER_TEMP
tar -xf petsc-3.6.4.tar.gz

Create MOOSE Profile

Make note of your $PACKAGES_DIR:

echo $PACKAGES_DIR

Edit the following file:

$HOME/.moose-profile

Add the following content to that file:

export PACKAGES_DIR=INSERT-PACKAGES-DIR-HERE!!!!

export CC=mpicc
export CXX=mpicxx
export F90=mpif90
export F77=mpif77
export FC=mpif90

export ARCH=gcc
export PETSC_DIR=$PACKAGES_DIR/petsc/petsc-3.6.4/$ARCH-opt

And run,

source ~/.moose-profile

Build and Install PETSc

cd $CLUSTER_TEMP/petsc-3.6.4

./configure \
--prefix=$PETSC_DIR \
--download-hypre=1 \
--with-ssl=0 \
--with-debugging=yes \
--with-pic=1 \
--with-shared-libraries=1 \
--with-cc=mpicc \
--with-cxx=mpicxx \
--with-fc=mpif90 \
--download-fblaslapack=1 \
--download-metis=1 \
--download-parmetis=1 \
--download-superlu_dist=1 \
--download-scalapack=1 \
--download-mumps=1 \
CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif77 F90=mpif90 \
CFLAGS='-fPIC -fopenmp' \
CXXFLAGS='-fPIC -fopenmp' \
FFLAGS='-fPIC -fopenmp' \
FCFLAGS='-fPIC -fopenmp' \
F90FLAGS='-fPIC -fopenmp' \
F77FLAGS='-fPIC -fopenmp' \
PETSC_DIR=`pwd`

At the end of the configure step, the system will print out messages on your terminal window. The last printed section contains the make command you will need to enter on your terminal window. At the end of the make step, there will be another message about the make install commands. Just follow them to complete the setup. An example is the following. The specific folder you will need to enter will be different. Just copy and paste the printed out message.

make PETSC_DIR=/tmp/cluster_temp.wowSIm/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-debug all
make PETSC_DIR=/tmp/cluster_temp.wowSIm/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-debug install

Clone MOOSE

You can do exactly the same as suggested by their official tutorial.

mkdir ~/projects
cd ~/projects
git clone https://github.com/idaholab/moose.git
cd ~/projects/moose
git checkout master

Compile libMesh

This step is straight forward, but you may need some patience. The compilation may take up to an hour.

cd ~/projects/moose
scripts/update_and_rebuild_libmesh.sh

Test

cd ~/projects/moose/test
make -j8
./run_tests -j8

The test results should look like

Ran 1329 tests in 191.7 seconds
1328 passed, 51 skipped, 0 pending, 1 FAILED

You may receive one message regarding the failed item,

preconditioners/pbp.lots_of_variables....................................................... FAILED (TIMEOUT)

Don't worry about it. This is a timed test, which most likely indicates that the computer is running slow (or the machine is overburdened).

Phase field module

By default, MOOSE contains several modules, including one for phase field simulations. You can go to the corresponding folder and compile the code there

cd ~/projects/moose/modules/phase_field
make

If the compilation is successful, you expect to get the executable phase_field-opt. You can do a simple 3D grain growth simulation interactively.

 cd ~/projects/moose/modules/phase_field/examples/grain_growth
  ../../phase_field-opt -i grain_growth_3D.i

Alternatively, you can submit the job to Certainty using this sample pbs script phasefield_test_Moose.pbs.

cd ~/projects/moose/modules/phase_field/examples/grain_growth
qsub  phasefield_test_Moose.pbs

The results are saved in a series of files in .exodus format, which can be opened by Paraview, or Peacock (a GUI provided by MOOSE but not compatible with Certainty).

If you download the data and open them by Peacock, you expect to observe the 3D grain structures similar to what shown below.

MOOSE Installation on Mac

Installing MOOSE on Mac is straightforward. You can simply follow the below instructions online. http://mooseframework.org/getting-started/osx/

MOOSE GUI

Unfortunately, there are some issues about using Peacock on a cluster, but you are still able to use it to visualize your data or do some simple tests locally (e.g. on your Macbook). Assuming you are using a Mac OS, you can add the following line in your ~/.bash_profile to add Peacock to your PATH.

export PATH=~/projects/moose/gui:$PATH

Notice that you need to open Peacock in a directory that has your application's executable.

cd ~/projects/<your application directory>
peacock

And you can run a simulation with it from there.

cd ~/projects/trunk/<your application directory>/<your test directory>
peacock -i your_input_file.i

For detailed instructions, please refer to http://mooseframework.org/wiki/Peacock/.