Difference between revisions of "MOOSE Configuration"

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== Configure and test your own "MOOSE" framework ==
 
== Configure and test your own "MOOSE" framework ==
 +
;Note: Make sure your .bashrc and .bash_profile shell initialization scripts are 'clean'. If you encounter errors while setting up MOOSE make sure there are no environment changes caused by those scripts.
 +
 
===Basic Steps===
 
===Basic Steps===
# mkdir projects
+
# mkdir projects (from a development session [[Development and Testing]])
 
# cd projects
 
# cd projects
# module load moose/12-aug-20
+
# module load moose/26-jul-21
 
# git clone https://github.com/idaholab/moose.git
 
# git clone https://github.com/idaholab/moose.git
 
# cd moose
 
# cd moose
 
# git checkout master
 
# git checkout master
 
# export VTKLIB_DIR=${HPC_VTK_LIB} VTKINCLUDE_DIR=${HPC_VTK_INC}
 
# export VTKLIB_DIR=${HPC_VTK_LIB} VTKINCLUDE_DIR=${HPC_VTK_INC}
# Run "./scripts/update_and_rebuild_libmesh.sh --enable-vtk-required"
+
# Run "./scripts/update_and_rebuild_libmesh.sh --enable-vtk-required --with-vtk-lib=${HPC_VTK_LIB} --with-vtk-include=${HPC_VTK_INC}" and allow it to complete.  It should finish without errors.
# Interrupt (''ctrl-c'') the above configure/build just after the ''git clone'' of libmesh is completed.
+
# cd test; make -j 4; ./run_tests -j 4 (from a login node)
# Patch the "configure" script using the accompanying patch file (see below).
 
# Rerun "./scripts/update_and_rebuild_libmesh.sh --enable-vtk-required" and allow it to complete.  It should finish without errors.
 
# cd test; run_tests -j 4
 
 
# Build and test the "phase field" module:
 
# Build and test the "phase field" module:
 
## cd moose/modules/phase_field
 
## cd moose/modules/phase_field
Line 21: Line 20:
 
## make -j 4
 
## make -j 4
 
##./run_tests -j 4
 
##./run_tests -j 4
=== Patch File ===
+
 
 +
===Additional Information===
 +
See [https://support.rc.ufl.edu/show_bug.cgi?id=43807 Bugzilla Request #43807]
 +
 
 +
==More Detailed Instructions==
 +
From a development session ([[Development and Testing]])
 +
===Load the MOOSE Module===
 +
There are multiple versions. Each version was built with different versions of the required libraries. In general, the latest version of the libraries will be used in the latest version of the module. The module listed below is good in general, but you may have specific reasons to use a different version.
 +
 
 +
module load moose/26-jul-21
 +
 
 +
 
 +
Check the module list, you should see something like:
 +
 
 +
<pre>
 +
module list
 +
 
 +
Currently Loaded Modules:
 +
  1) gcc/9.3.0
 +
  2) mkl/2020.0.166
 +
  3) openmpi/4.1.1
 +
  4) petsc/3.15.1
 +
  5) qt/5.12.9
 +
  6) vtk/8.2.0
 +
  7) moose/26-jul-21
 +
</pre>
 +
 
 +
===Clone MOOSE===
 +
<pre>
 +
mkdir ~/projects
 +
cd ~/projects
 +
git clone https://github.com/idaholab/moose.git
 +
cd moose
 +
git checkout master
 +
</pre>
 +
 
 +
===Export VTK paths===
 +
Make sure you export the VTK paths '''after''' the MOOSE module is loaded, otherwise the path may be empty.
 +
export VTKLIB_DIR=${HPC_VTK_LIB} VTKINCLUDE_DIR=${HPC_VTK_INC}
 +
 
 +
===Peacock===
 +
To use the [https://mooseframework.inl.gov/application_usage/peacock.html peacock] input file syntax front-end, add the path to the 'python' directory in your MOOSE install as peacock requires the mooseutils python module. E.g.
 +
export PYTHONPATH=/my/moose/dir/python:$PYTHONPATH
 +
 
 +
===Update and Build ''libmesh''===
 +
Run the update and build libmesh script. This step takes a while but should finish without errors (though you '''will''' see some warnings).
 +
<pre>
 +
cd ~/projects/moose
 +
./scripts/update_and_rebuild_libmesh.sh --enable-vtk-required --with-vtk-lib=${HPC_VTK_LIB} --with-vtk-include=${HPC_VTK_INC}
 +
</pre>
 +
 
 +
===Compile MOOSE Tests===
 +
Build the MOOSE test executables.
 +
<pre>
 +
cd ~/projects/moose/test
 +
make -j 4
 +
</pre>
 +
 
 +
===Run the Test Suites===
 +
Now run the tests. The test suite in moose/test is important to check if all libraries are correct. You need to exit the dev session to run the tests. If the build was successful, I would recommend building the module you are interested in and then exit and run both test scripts. Don’t forget that you may need to reload the moose module on the login node.
 +
<pre>
 +
cd ~/projects/moose/test
 +
./run_tests -j 4 (login node)
 +
</pre>
 +
 
 +
===Compile and Test Your Own Module===
 +
Build the executable and run the specific tests.
 +
<pre>
 +
cd ~/projects/moose/modules/combined
 +
make -j16 (dev session)
 +
./run_tests -j 4(login node)
 +
</pre>
 +
 
 +
===General suggestions===
 +
If you are not getting a fresh clone of MOOSE, it’s recommended to do a clean-up before you recompile your executables.
 +
<pre>
 +
cd ~/projects/moose/modules/combined
 +
make clobberall
 +
make -j 4
 +
</pre>
 +
 
 +
===MOOSE-based Applications===
 +
Perform all the previous steps related to the MOOSE installation. Then build your application and test it.
 +
<pre>
 +
cd ~/projects/YourAppName
 +
make clobberall
 +
make -j 4
 +
./run_tests -j 4 (login node)
 +
</pre>
 +
 
 +
===SLURM Job Script===
 +
This is an example of a slurm job script:
 +
<pre>
 +
#!/bin/sh
 +
#SBATCH --job-name=moose                #Job name
 +
#SBATCH --nodes=1                        #Number of nodes (servers, 32 proc/node)
 +
#SBATCH --ntasks=16                      #Number of tasks/MPI RankS
 +
#SBATCH --ntasks-per-node=16            #Tasks per node
 +
#SBATCH --ntasks-per-socket=8            #Tasks per socket
 +
#SBATCH --cpus-per-task=1                #Number of CPU per task
 +
#SBATCH --mem-per-cpu=3600mb            #Memory (120 gig/server)
 +
#SBATCH --distribution=cyclic:cyclic    #Distribute tasks cyclically
 +
#SBATCH --time=12:00:00                  #Walltime days-hh:mm:ss
 +
#SBATCH --output=moose-%j.out            #Output and error log
 +
#SBATCH --mail-type=END,FAIL            #When to email user
 +
#SBATCH --mail-user=your-email@ufl.edu  #Email address to send mail to
 +
#SBATCH --account=michael.tonks          #Allocation group name, add -b for burst job
 +
 
 +
srun --mpi=pmix_v3 ~/projects/moose/modules/combined-opt -i moose_input_file.i
 +
</pre>

Latest revision as of 23:34, 4 October 2022

Configure and test your own "MOOSE" framework

Note
Make sure your .bashrc and .bash_profile shell initialization scripts are 'clean'. If you encounter errors while setting up MOOSE make sure there are no environment changes caused by those scripts.

Basic Steps

  1. mkdir projects (from a development session Development and Testing)
  2. cd projects
  3. module load moose/26-jul-21
  4. git clone https://github.com/idaholab/moose.git
  5. cd moose
  6. git checkout master
  7. export VTKLIB_DIR=${HPC_VTK_LIB} VTKINCLUDE_DIR=${HPC_VTK_INC}
  8. Run "./scripts/update_and_rebuild_libmesh.sh --enable-vtk-required --with-vtk-lib=${HPC_VTK_LIB} --with-vtk-include=${HPC_VTK_INC}" and allow it to complete. It should finish without errors.
  9. cd test; make -j 4; ./run_tests -j 4 (from a login node)
  10. Build and test the "phase field" module:
    1. cd moose/modules/phase_field
    2. make -j 4
    3. ./run_tests -j 4
  11. Build and test the "combined" module:
    1. cd moose/modules/combined
    2. make -j 4
    3. ./run_tests -j 4

Additional Information

See Bugzilla Request #43807

More Detailed Instructions

From a development session (Development and Testing)

Load the MOOSE Module

There are multiple versions. Each version was built with different versions of the required libraries. In general, the latest version of the libraries will be used in the latest version of the module. The module listed below is good in general, but you may have specific reasons to use a different version.

module load moose/26-jul-21


Check the module list, you should see something like:

module list

Currently Loaded Modules:
  1) gcc/9.3.0
  2) mkl/2020.0.166 
  3) openmpi/4.1.1 
  4) petsc/3.15.1 
  5) qt/5.12.9 
  6) vtk/8.2.0 
  7) moose/26-jul-21

Clone MOOSE

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

Export VTK paths

Make sure you export the VTK paths after the MOOSE module is loaded, otherwise the path may be empty.

export VTKLIB_DIR=${HPC_VTK_LIB} VTKINCLUDE_DIR=${HPC_VTK_INC}

Peacock

To use the peacock input file syntax front-end, add the path to the 'python' directory in your MOOSE install as peacock requires the mooseutils python module. E.g.

export PYTHONPATH=/my/moose/dir/python:$PYTHONPATH

Update and Build libmesh

Run the update and build libmesh script. This step takes a while but should finish without errors (though you will see some warnings).

cd ~/projects/moose
./scripts/update_and_rebuild_libmesh.sh --enable-vtk-required --with-vtk-lib=${HPC_VTK_LIB} --with-vtk-include=${HPC_VTK_INC}

Compile MOOSE Tests

Build the MOOSE test executables.

cd ~/projects/moose/test
make -j 4

Run the Test Suites

Now run the tests. The test suite in moose/test is important to check if all libraries are correct. You need to exit the dev session to run the tests. If the build was successful, I would recommend building the module you are interested in and then exit and run both test scripts. Don’t forget that you may need to reload the moose module on the login node.

cd ~/projects/moose/test
./run_tests -j 4 (login node)

Compile and Test Your Own Module

Build the executable and run the specific tests.

cd ~/projects/moose/modules/combined
make -j16 (dev session)
./run_tests -j 4(login node)

General suggestions

If you are not getting a fresh clone of MOOSE, it’s recommended to do a clean-up before you recompile your executables.

cd ~/projects/moose/modules/combined
make clobberall
make -j 4

MOOSE-based Applications

Perform all the previous steps related to the MOOSE installation. Then build your application and test it.

cd ~/projects/YourAppName
make clobberall
make -j 4
./run_tests -j 4 (login node)

SLURM Job Script

This is an example of a slurm job script:

#!/bin/sh
#SBATCH --job-name=moose                 #Job name
#SBATCH --nodes=1                        #Number of nodes (servers, 32 proc/node)
#SBATCH --ntasks=16                      #Number of tasks/MPI RankS
#SBATCH --ntasks-per-node=16             #Tasks per node
#SBATCH --ntasks-per-socket=8            #Tasks per socket
#SBATCH --cpus-per-task=1                #Number of CPU per task
#SBATCH --mem-per-cpu=3600mb             #Memory (120 gig/server)
#SBATCH --distribution=cyclic:cyclic     #Distribute tasks cyclically 
#SBATCH --time=12:00:00                  #Walltime days-hh:mm:ss
#SBATCH --output=moose-%j.out            #Output and error log
#SBATCH --mail-type=END,FAIL             #When to email user
#SBATCH --mail-user=your-email@ufl.edu   #Email address to send mail to
#SBATCH --account=michael.tonks          #Allocation group name, add -b for burst job

srun --mpi=pmix_v3 ~/projects/moose/modules/combined-opt -i moose_input_file.i