Difference between revisions of "MOOSE Configuration"

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{|align=right
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  |__TOC__
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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.
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# 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 23:
 
## make -j 4
 
## make -j 4
 
##./run_tests -j 4
 
##./run_tests -j 4
−
=== Patch File (configure.patch) ===
 
−
The patch file below can be applied via the ''patch'' utility.
 
−
<source lang=bash>
 
−
  cd libmesh
 
−
  patch -p1 < configure.patch
 
−
</source>
 
−
 
−
<source lang=bash>
 
−
======================================configure.patch==========================================================
 
−
--- a/configure 2020-08-07 07:56:18.955696774 -0400
 
−
+++ b/configure 2020-08-07 08:00:45.329361095 -0400
 
−
@@ -38452,24 +38452,26 @@
 
−
                  VTK_LIBRARY_WITH_VERSION="-L$VTK_LIB -lvtkIOCore-$vtkmajorminor -lvtkCommonCore-$vtkmajorminor -lvtkCommonDataModel-$vtkmajorminor \
 
−
                                            -lvtkFiltersCore-$vtkmajorminor -lvtkIOXML-$vtkmajorminor -lvtkImagingCore-$vtkmajorminor \
 
−
                                            -lvtkIOImage-$vtkmajorminor -lvtkImagingMath-$vtkmajorminor \
 
−
-                                          -lvtkParallelMPI-$vtkmajorminor -lvtkParallelCore-$vtkmajorminor"
 
−
+                                          -lvtkParallelMPI-$vtkmajorminor -lvtkParallelCore-$vtkmajorminor \
 
−
+                                          -lvtkCommonExecutionModel-$vtkmajorminor"
 
−
 
−
                                                                    VTK_LIBRARY_NO_VERSION="-L$VTK_LIB -lvtkIOCore -lvtkCommonCore -lvtkCommonDataModel \
 
−
                                          -lvtkFiltersCore -lvtkIOXML -lvtkImagingCore \
 
−
                                          -lvtkIOImage -lvtkImagingMath \
 
−
-                                        -lvtkParallelMPI -lvtkParallelCore"
 
−
+                                        -lvtkParallelMPI -lvtkParallelCore -lvtkCommonExecutionModel"
 
−
 
−
else
 
−
 
−
                                                    VTK_LIBRARY_WITH_VERSION="-L$VTK_LIB -lvtkIOCore-$vtkmajorminor -lvtkCommonCore-$vtkmajorminor -lvtkCommonDataModel-$vtkmajorminor \
 
−
                                            -lvtkFiltersCore-$vtkmajorminor -lvtkIOXML-$vtkmajorminor -lvtkImagingCore-$vtkmajorminor \
 
−
                                            -lvtkIOImage-$vtkmajorminor -lvtkImagingMath-$vtkmajorminor -lvtkIOParallelXML-$vtkmajorminor \
 
−
-                                          -lvtkParallelMPI-$vtkmajorminor -lvtkParallelCore-$vtkmajorminor"
 
−
+                                          -lvtkParallelMPI-$vtkmajorminor -lvtkParallelCore-$vtkmajorminor \
 
−
+                                          -lvtkCommonExecutionModel-$vtkmajorminor"
 
−
 
−
                                                                    VTK_LIBRARY_NO_VERSION="-L$VTK_LIB -lvtkIOCore -lvtkCommonCore -lvtkCommonDataModel \
 
−
                                          -lvtkFiltersCore -lvtkIOXML -lvtkImagingCore \
 
−
                                          -lvtkIOImage -lvtkImagingMath -lvtkIOParallelXML \
 
−
-                                        -lvtkParallelMPI -lvtkParallelCore"
 
−
+                                        -lvtkParallelMPI -lvtkParallelCore -lvtkCommonExecutionModel"
 
−
 
−
fi
 
−
======================================================================================================
 
−
</source>
 
  
 
===Additional Information===
 
===Additional Information===
 
See [https://support.rc.ufl.edu/show_bug.cgi?id=43807 Bugzilla Request #43807]
 
See [https://support.rc.ufl.edu/show_bug.cgi?id=43807 Bugzilla Request #43807]
  
−
==More Detailed Instructions==
+
==Running MOOSE==
−
===Load a ''dev'' Session===
+
Now that Moose is configured, learn how to use it at [[Running MOOSE]]. Or from a development session ([[Development and Testing]]).
−
Build libmesh and the MOOSE executables in the dev session, but run the tests on the login node. This is an alias you can add to your ~/.bash_profile:
 
−
 
 
−
<source lang=bash>
 
−
vim ~/.bash_profile
 
−
alias devsess =’srundev --mem=32gb --ntasks=4 --cpus-per-task=4 --time=12:00:00’
 
−
</source>
 
−
 
 
−
===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.
 
−
<source lang=bash>
 
−
module load moose/12-aug-20
 
−
</source>
 
−
 
 
−
Check the module list, you should see something like:
 
−
 
 
−
<source lang=bash>
 
−
module list
 
−
 
 
−
Currently Loaded Modules:
 
−
1) ufrc
 
−
2) gui/2.0.0
 
−
3) python/3.8
 
−
4) gcc/8.2.0
 
−
5) openmpi/4.0.3
 
−
6) mkl/2020.0.166
 
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7) hypre/2.15.1
 
−
8) petsc/3.13.4
 
−
9) vtk/8.2.0
 
−
10) moose/12-aug-20
 
−
</source>
 
−
 
 
−
===Clone MOOSE===
 
−
<source lang=bash>
 
−
mkdir ~/projects
 
−
cd ~/projects
 
−
git clone https://github.com/idaholab/moose.git
 
−
cd moose
 
−
git checkout master
 
−
</source>
 
−
 
 
−
===Export VTK paths===
 
−
Make sure you export after the MOOSE module is loaded, otherwise the path may be empty.
 
−
<source lang=bash>
 
−
export VTKLIB_DIR=${HPC_VTK_LIB} VTKINCLUDE_DIR=${HPC_VTK_INC}
 
−
</source>
 
−
 
 
−
===Peacock===
 
−
To use [https://mooseframework.inl.gov/application_usage/peacock.html Peacock] input file syntax fron-end add the path to the 'python' directory in your MOOSE install as Peacock requires the mooseutils python module. E.g.
 
−
export PYTHOPATH=/my/moose/dir/python:$PYTHONPATH
 
−
 
 
−
===Update and Build ''libmesh'' – But Interrupt It===
 
−
Run the update and build libmesh script but interrupt (ctrl-c) the configure/build just after the git clone of libmesh is completed. The goal here is to simply populate the ''libmesh'' directory so that the associated ''configure'' script can be patched.
 
−
<source lang=bash>
 
−
cd ~/projects/moose/scripts
 
−
./scripts/update_and_rebuild_libmesh.sh --enable-vtk-required
 
−
(ctrl-c)
 
−
</source>
 
−
 
 
−
===Patch the ''libmesh'' configure script===
 
−
Patch the "configure" script according to the following command. The configure.patch file is available in the folder.
 
−
Note: in the future, this patch will be merged and distributed with MOOSE/libmesh.
 
−
<source lang=bash>
 
−
cd ~/projects/moose/libmesh
 
−
patch -p1 < configure.patch
 
−
</source>
 
−
 
 
−
===Update and Build ''libmesh''===
 
−
Run the update and build libmesh script again and let it complete. It should finish without errors.
 
−
<source lang=bash>
 
−
cd ~/projects/moose/scripts
 
−
./scripts/update_and_rebuild_libmesh.sh --enable-vtk-required
 
−
</source>
 
−
 
 
−
===Compile MOOSE Tests===
 
−
Build the MOOSE test executable.
 
−
<source lang=bash>
 
−
cd ~/projects/moose/test
 
−
make -j 4
 
−
</source>
 
−
 
 
−
===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.
 
−
<source lang=bash>
 
−
cd ~/projects/moose/test
 
−
./run_tests -j 4 (login node)
 
−
</source>
 
−
 
 
−
===Compile and Test Your Own Module===
 
−
Build the executable and run the specific tests.
 
−
<source lang=bash>
 
−
cd ~/projects/moose/modules/combined
 
−
make -j16 (dev session)
 
−
./run_tests -j 4(login node)
 
−
</source>
 
−
 
 
−
===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.
 
−
<source lang=bash>
 
−
cd ~/projects/moose/modules/combined
 
−
make clobberall
 
−
make -j 4
 
−
</source>
 
−
 
 
−
You may consider adding the module load and export steps to your ~/.bash_profile:
 
−
<source lang=bash>
 
−
vim ~/.bash_profile
 
−
 
 
−
module purge
 
−
module load moose/12-aug-20
 
−
export VTKLIB_DIR=${HPC_VTK_LIB} VTKINCLUDE_DIR=${HPC_VTK_INC}
 
−
</source>
 
−
 
 
−
===MOOSE-based Applications===
 
−
Perform all the previous steps related to the MOOSE installation. Then build your application and test it.
 
−
<source lang=bash>
 
−
cd ~/projects/your_app
 
−
make clobberall
 
−
make -j 4
 
−
./run_tests -j 4 (login node)
 
−
</source>
 
−
 
 
−
===Slurm Job Script===
 
−
This is an example of a slurm job script:
 
−
<source lang=bash>
 
−
#!/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
 
−
</source>
 

Latest revision as of 15:20, 5 May 2023

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

Running MOOSE

Now that Moose is configured, learn how to use it at Running MOOSE. Or from a development session (Development and Testing).

Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=MOOSE_Configuration&oldid=27887"