SW:moose

Multiphysics Object-Oriented Simulation Environment - An open-source, parallel finite element framework

Building the MOOSE framework in your $SCRATCH

   cd $SCRATCH # where to install
   module purge # clear module environment
   module load MOOSE/moose-dev-gcc-ompi # load the MOOSE development module
   $EBROOTMOOSE/install-moose.sh build # get sources, update libmesh, finish build

This will download and build the MOOSE framework in $SCRATCH/moose. It runs a script called update_and_rebuild_libmesh.sh that takes the majority of the time. After that, it will switch to the $SCRATCH/moose/test directory and run 'make' and ./run_tests there to finish the build. In all, this will take about 100 minutes on ada and 80 minutes on terra (over an hour in either case).

Testing your MOOSE framework

The first tests to run were built at the end of the build process. To run them, do:

  ml MOOSE/moose-dev-gcc-ompi # make sure module is loaded
  cd $SCRATCH/moose/tests
  ./run_test.sh

That will run for nearly an hour (on terra) and will have output that ends in something like:

   time_integrators/convergence.implicit_astabledirk4_bootstrap/level1 ....................................... OK
   geomsearch/2d_moving_penetration.restart .................................................................. OK
   time_integrators/convergence.implicit_astabledirk4_bootstrap/level2 ....................................... OK
   geomsearch/2d_moving_penetration.restart2 ................................................................. OK
   samplers/distribute.scale/execute .................................................. [FINISHED] FAILED (CRASH)
   --------------------------------------------------------------------------------------------------------------
   Ran 2331 tests in 2768.0 seconds.
   2330 passed, 84 skipped, 0 pending, 1 FAILED

At this point, to do further testing of your installation you can build all the exercises with:

   ml MOOSE/moose-dev-gcc-ompi # make sure module is loaded
   cd $SCRATCH/moose/examples
   make -j 4 # build

For descriptions, and instructions on how to run the examples, see the MOOSE Examples page.

Using your MOOSE framework

(this needs more work... see the MOOSE web page for more details after the framework is installed)

Now you can build your model with the moose framework. Do as follows.

   ml MOOSE/moose-dev-gcc-ompi # make sure module is loaded
   cp -rp /path/to/my_module $SCRATCH/moose/modules # copy your module to framework
   cd $SCRATCH/moose/modules/my_module
   # MIGHT NEED A STEP HERE TO USE MOOSE TO CREATE A Makefile
   make

Sample job scripts on Terra

Sample 1

   #!/bin/bash
   ##ENVIRONMENT SETTINGS; CHANGE WITH CAUTION
   #SBATCH --get-user-env=L       #Replicate login environment
   #SBATCH -J moose-sample1       #Set the job name to "moose-sample1"
   #SBATCH -t 1:00:00             #Set the wall clock limit to 1hr 
   #SBATCH -N 20                  #Request 20 node
   #SBATCH --ntasks-per-node=28   #Request 28 tasks per node
   #SBATCH --mem=56G              #Request 56G per node
   #SBATCH -o moose-sample1.%j    #Send stdout/err to "Example1Out.[jobID]"
   
   module load MOOSE/moose-dev-gcc-ompi
   mpirun /path/to/moose-opt -i moose.i

Sample 2 Use half of the cores per node such that each core can have 2G*2=4G memory to use. This is useful for models that need large amount of memory.

   #!/bin/bash
   ##ENVIRONMENT SETTINGS; CHANGE WITH CAUTION
   #SBATCH --get-user-env=L       #Replicate login environment   
   #SBATCH -J  moose-sample2      #Set the job name to "moose-sample2"
   #SBATCH -t 1:00:00             #Set the wall clock limit to 1hr 
   #SBATCH -N 20                  #Request 20 node
   #SBATCH --ntasks-per-node=28   #Request 28 tasks per node
   #SBATCH --mem=56G              #Request 56G per node
   #SBATCH -o moose-sample2.%j    #Send stdout/err to "moose-sample2.[jobID]"
   
   module load MOOSE/moose-dev-gcc-ompi
   mpirun -np 280 -npernode 14 /path/to/moose-opt -i moose.i

Sample job script on Ada

Sample 1

   #BSUB -J moose-sample1
   #BSUB -o moose-sample1.%J
   #BSUB -e error.%J
   #BSUB -L /bin/bash
   #BSUB -W 20:00
   #BSUB -n 400
   #BSUB -M 2700
   #BSUB -R "span[ptile=20]"
   #BSUB -R "rusage[mem=2700]"
   
   module load MOOSE/moose-dev-gcc-ompi
   mpirun /path/to/moose-opt -i moose.i

Sample 2: Use half of the cores per node such that each core can have 2700x2=5400M memory to use. This is useful for models that need large amount of memory.

   #BSUB -J moose-sample2
   #BSUB -o moose-sample2.%J
   #BSUB -e error.%J
   #BSUB -L /bin/bash
   #BSUB -W 20:00
   #BSUB -n 400
   #BSUB -M 2700
   #BSUB -R "span[ptile=20]"
   #BSUB -R "rusage[mem=2700]"
   
   module load MOOSE/moose-dev-gcc-ompi
   mpirun -np 200 -npernode 10 /path/to/moose-opt -i moose.i