Difference between revisions of "MOOSE Configuration"

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  fi
 
  fi
 
======================================================================================================
 
======================================================================================================
 +
</source>
 +
 +
 +
===Load your dev session===
 +
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:
 +
 +
vim ~/.bash_profile
 +
 +
alias devsess =’srundev --mem=32gb --ntasks=16 --cpus-per-task=1 --time=12:00:00’
 +
 +
 +
===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 modules listed below is good in general, but you may have specific reasons to use a different version.
 +
 +
module load moose/12-aug-20
 +
 +
Check the module list, you should see something like:
 +
 +
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
 +
7) hypre/2.15.1
 +
8) petsc/3.13.4
 +
9) vtk/8.2.0
 +
10) moose/12-aug-20
 +
 +
===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 after the MOOSE module is loaded, otherwise the path may be empty.
 +
 +
export VTKLIB_DIR=${HPC_VTK_LIB} VTKINCLUDE_DIR=${HPC_VTK_INC}
 +
 +
===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.
 +
</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 -j10 (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 -j16
 +
</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 script===
 +
This is an example of a slurm 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>
 
</source>

Revision as of 15:14, 13 August 2020

Configure and test your own "MOOSE" framework

Basic Steps

  1. mkdir projects
  2. cd projects
  3. module load moose/12-aug-20
  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"
  9. Interrupt (ctrl-c) the above configure/build just after the git clone of libmesh is completed.
  10. Patch the "configure" script using the accompanying patch file (see below).
  11. Rerun "./scripts/update_and_rebuild_libmesh.sh --enable-vtk-required" and allow it to complete. It should finish without errors.
  12. cd test; run_tests -j 4
  13. Build and test the "phase field" module:
    1. cd moose/modules/phase_field
    2. make -j 4
    3. ./run_tests -j 4
  14. Build and test the "combined" module:
    1. cd moose/modules/combined
    2. make -j 4
    3. ./run_tests -j 4

Patch File (configure.patch)

The patch file below can be applied via the patch utility. 

   cd libmesh
   patch -p1 < configure.patch

======================================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
======================================================================================================


Load your dev session

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:

vim ~/.bash_profile

alias devsess =’srundev --mem=32gb --ntasks=16 --cpus-per-task=1 --time=12:00:00’


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 modules listed below is good in general, but you may have specific reasons to use a different version.

module load moose/12-aug-20

Check the module list, you should see something like:

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 7) hypre/2.15.1 8) petsc/3.13.4 9) vtk/8.2.0 10) moose/12-aug-20

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 after the MOOSE module is loaded, otherwise the path may be empty.

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

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. </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. 

cd ~/projects/moose/libmesh
patch -p1 < configure.patch

Update and build libmesh

Run the update and build libmesh script again and let it complete. It should finish without errors. 

cd ~/projects/moose/scripts
./scripts/update_and_rebuild_libmesh.sh --enable-vtk-required

Compile MOOSE Tests

Build the MOOSE test executable. 

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 -j10 (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 -j16

You may consider adding the module load and export steps to your ~/.bash_profile: 

vim ~/.bash_profile

module purge
module load moose/12-aug-20
export VTKLIB_DIR=${HPC_VTK_LIB} VTKINCLUDE_DIR=${HPC_VTK_INC}

MOOSE-based Applications

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

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

Slurm script

This is an example of a slurm 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
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