Hprc banner tamu.png

Difference between revisions of "SW:moose"

From TAMU HPRC
Jump to: navigation, search
(Using your MOOSE framework)
(Testing your MOOSE framework)
Line 16: Line 16:
 
At this point, to do further testing of your installation you can build all the exercises with:
 
At this point, to do further testing of your installation you can build all the exercises with:
  
 +
    ml purge
 
     ml MOOSE/moose-dev-gcc-ompi # make sure module is loaded
 
     ml MOOSE/moose-dev-gcc-ompi # make sure module is loaded
 
     cd $SCRATCH/moose/examples
 
     cd $SCRATCH/moose/examples
Line 24: Line 25:
 
Do do some very extensive, and lengthy, testing, you can build all the MOOSE modules and run their tests.
 
Do do some very extensive, and lengthy, testing, you can build all the MOOSE modules and run their tests.
  
 +
    ml purge
 
     ml MOOSE/moose-dev-gcc-ompi # make sure module is loaded
 
     ml MOOSE/moose-dev-gcc-ompi # make sure module is loaded
 
     cd $SCRATCH/moose/modules
 
     cd $SCRATCH/moose/modules

Revision as of 10:18, 18 August 2020

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
   time $EBROOTMOOSE/install-moose.sh build # get/build/test MOOSE

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' to finish the build.

Testing your MOOSE framework

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

   ml purge
   ml MOOSE/moose-dev-gcc-ompi # make sure module is loaded
   cd $SCRATCH/moose/examples
   make -j 8 # build

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

Do do some very extensive, and lengthy, testing, you can build all the MOOSE modules and run their tests.

   ml purge
   ml MOOSE/moose-dev-gcc-ompi # make sure module is loaded
   cd $SCRATCH/moose/modules
   make -j 8 # build
   ./run_tests -j 8 # run

Using your MOOSE framework

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

latest notes

See Create an Application and Compile and Test Your Application at the MOOSE Getting Started page. Replace all instances of ~/projects with $SCRATCH

old notes

(you should probably try the above first)

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