Difference between revisions of "TF MOOSE-MARMOT"

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=Running at INL=
 
=Running at INL=
 +
-- Remot login using VNC==
 +
 +
https://hpcview.inl.gov
  
 
==Remote login via ssh==
 
==Remote login via ssh==
  
ssh username@hpclogin.inl.gov
+
ssh username@hpclogin.inl.gov
  
 
A list of machines will appear in the login message
 
A list of machines will appear in the login message
  
ssh sawtooth1
+
ssh sawtooth1
  
 
You can use the installed version of moose using the module command
 
You can use the installed version of moose using the module command
  
module load pbs use.moose PETSc/3.11.4-GCC
+
module load pbs use.moose PETSc/3.11.4-GCC
  
  
Line 21: Line 24:
  
 
https://www.youtube.com/watch?reload=9&v=2tJwBsYaLaI
 
https://www.youtube.com/watch?reload=9&v=2tJwBsYaLaI
 +
 +
==Install MOOSE==
 +
 +
Use github to install MOOSE
 +
 +
<pre>
 +
git clone https://github.com/idaholab/moose.git
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cd moose
 +
git checkout master
 +
</pre>
 +
 +
if it is already installed then update your github version using
 +
 +
git fetch
 +
 +
 +
 +
now rebuild libmesh using the script
 +
 +
cd scripts
 +
 +
./update_and_rebuild_libmesh.sh
 +
 +
If this is successful, run the tests in the tests subdirectory
 +
 +
cd ../tests
 +
 +
make -j 6
 +
 +
. /run_tests
 +
 +
moose was not built correctly if this fails
 +
 +
 +
 +
 +
 +
Usually you need to build libmesh
 +
 +
cd libmesh
 +
 +
./configure --prefix=/home/foretony/src/MOOSE/projects/moose/libmesh
 +
 +
make
 +
 +
make install
  
 
==Setting up HPS uilities==
 
==Setting up HPS uilities==
Line 68: Line 117:
 
https://mooseframework.inl.gov/getting_started/installation/conda.html
 
https://mooseframework.inl.gov/getting_started/installation/conda.html
  
 +
==Install using conda==
 +
 +
 +
 +
 +
check install environment with
 +
 +
<pre>
 +
(moose) [foretony093457:~/src/MOOSE] foretony% which conda
 +
conda:  aliased to source /Users/foretony/miniconda3/etc/profile.d/conda.csh
 +
(moose) [foretony093457:~/src/MOOSE] foretony% conda info --envs
 +
# conda environments:
 +
#
 +
base                    /Users/foretony/miniconda3
 +
moose                *  /Users/foretony/miniconda3/envs/moose
 +
 +
</pre>
 +
 +
 +
'''updating conda'''
 +
 +
conda update -n base -c defaults conda
 +
 +
==On Linux==
 +
 +
 +
current script to install once conda is installed
 +
 +
 +
conda config --add channels conda-forge
 +
conda config --add channels idaholab
 +
 +
2. Create a new environment and install the moose libmesh
 +
 +
conda create --name moose moose-libmesh moose-tools
 +
 +
3. Activate the moose environment:
 +
 +
conda activate moose
 +
 +
 +
4. Clone MOOSE and [DON'T UPDATE LIBMESH, since it already compiled libmesh for you using conda]
 +
 +
mkdir ~/projects
 +
cd ~/projects
 +
git clone https://github.com/idaholab/moose.git
 +
cd moose
 +
git checkout master
 +
 +
 +
5. Compile and Test MOOSE
 +
 +
cd ~/projects/moose/test
 +
make -j 4
 +
./run_tests -j 4
 +
 +
'''useful commands'''
 +
 +
conda info --envs
 +
 +
conda config --remove channels https:/mooseframework.org/conda/moose
 +
 +
conda config --show channels
 +
 +
conda config --show-source
 +
 +
make clobberall
 +
 +
==PETSC==
 +
 +
needed to update petsc using file in scripts directory with a switch to get a new cmake version
 +
 +
cd scripts
 +
 +
./update_and_rebuild_petsc.sh --download-cmake
 +
 +
 +
set the environemntal variable for PETSC
 +
 +
export PETSC_DIR=/Users/foretony/src/MOOSE/projects/moose/petsc/
 +
 +
 +
PETSC_ARCH=arch-moose check
 +
 +
==LIBMESH==
 +
 +
After PETSC is build, build libmesh in the moose/scripts subdirectory
 +
 +
./update_and_rebuild_libmesh.sh
 +
 +
but I got the error
 +
 +
 +
configure: error: *** PETSc with Hypre was not found, but --enable-petsc-hypre-required was specified.
 +
make: *** No targets specified and no makefile found.  Stop.
 +
 +
so I attempted to compile without hypre
 +
 +
./update_and_rebuild_libmesh.sh --disable-petsc-hypre-required
 +
 +
 +
I got the next error
 +
 +
checking Whether MPI is available for Trilinos... yes
 +
checking Whether Real precision is compatible with Trilinos... yes
 +
<<< User requested thread model: openmp >>>
 +
checking for OpenMP flag of C++ compiler... unknown
 +
make: *** No targets specified and no makefile found.  Stop.
 +
 +
Installed an openmp library using
 +
 +
 +
brew install libopen-mpi
  
 +
brew install libopenmpt
  
 
=Daniel V's Binary collision Approx=
 
=Daniel V's Binary collision Approx=

Latest revision as of 00:41, 14 August 2020

User_talk:Foretony#INL

Running at INL

-- Remot login using VNC==

https://hpcview.inl.gov 

Remote login via ssh

ssh username@hpclogin.inl.gov

A list of machines will appear in the login message

ssh sawtooth1

You can use the installed version of moose using the module command

module load pbs use.moose PETSc/3.11.4-GCC


MOOSE Documentation:

MOOSE tutorial on Youtube

https://www.youtube.com/watch?reload=9&v=2tJwBsYaLaI

Install MOOSE

Use github to install MOOSE

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

if it is already installed then update your github version using

git fetch


now rebuild libmesh using the script

cd scripts
./update_and_rebuild_libmesh.sh

If this is successful, run the tests in the tests subdirectory

cd ../tests
make -j 6

. /run_tests

moose was not built correctly if this fails



Usually you need to build libmesh

cd libmesh
./configure --prefix=/home/foretony/src/MOOSE/projects/moose/libmesh
make
make install

Setting up HPS uilities

to list available modules type

module spider


MOOSE needs CMake and Python


the command

module spider cmake

will list all available cmake versions


below are the modules I loaded


module load intel-mpi/2019.0.117-intel-19.0.5-cydt
module load cmake/3.16.2-gcc-9.3.0-tza7
module load gcc/9.3.0-gcc-4.8.5-twls
module load python/3.7.4-gcc-9.3.0-ht2d

Loading packages using "module"

first load user modules

module load use.projects
module load use.spack
module load moose-dev/5.7.0-gmvolf-5.5.7



https://hpcsc.inl.gov/moose

local Moose

https://mooseframework.inl.gov/getting_started/installation/conda.html

Install using conda

check install environment with

(moose) [foretony093457:~/src/MOOSE] foretony% which conda
conda:   aliased to source /Users/foretony/miniconda3/etc/profile.d/conda.csh
(moose) [foretony093457:~/src/MOOSE] foretony% conda info --envs
# conda environments:
#
base                     /Users/foretony/miniconda3
moose                 *  /Users/foretony/miniconda3/envs/moose


updating conda

conda update -n base -c defaults conda

On Linux

current script to install once conda is installed


conda config --add channels conda-forge conda config --add channels idaholab

2. Create a new environment and install the moose libmesh

conda create --name moose moose-libmesh moose-tools

3. Activate the moose environment:

conda activate moose


4. Clone MOOSE and [DON'T UPDATE LIBMESH, since it already compiled libmesh for you using conda]

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


5. Compile and Test MOOSE

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

useful commands

conda info --envs

conda config --remove channels https:/mooseframework.org/conda/moose

conda config --show channels

conda config --show-source

make clobberall

PETSC

needed to update petsc using file in scripts directory with a switch to get a new cmake version

cd scripts
./update_and_rebuild_petsc.sh --download-cmake


set the environemntal variable for PETSC

export PETSC_DIR=/Users/foretony/src/MOOSE/projects/moose/petsc/


PETSC_ARCH=arch-moose check

LIBMESH

After PETSC is build, build libmesh in the moose/scripts subdirectory

./update_and_rebuild_libmesh.sh

but I got the error


configure: error: *** PETSc with Hypre was not found, but --enable-petsc-hypre-required was specified. make: *** No targets specified and no makefile found. Stop.

so I attempted to compile without hypre

./update_and_rebuild_libmesh.sh --disable-petsc-hypre-required


I got the next error

checking Whether MPI is available for Trilinos... yes checking Whether Real precision is compatible with Trilinos... yes <<< User requested thread model: openmp >>> checking for OpenMP flag of C++ compiler... unknown make: *** No targets specified and no makefile found. Stop.

Installed an openmp library using


brew install libopen-mpi
brew install libopenmpt

Daniel V's Binary collision Approx

Download

git clone https://github.com/vanwdani/GEANT_BCA.git

files are in

src/MOOSE/projects/GEANT_BCA

  see README file for installation instructions


need to install xerces

 brew install xerces-c


brew install jsoncpp

check the version number of json

  ls /usr/local/Cellar/jsoncpp/

and set your path to it


now setup your cloned version so it tracks the origin

foretony093457:GEANT_BCA foretony$ git remote -vv
origin  https://github.com/vanwdani/GEANT_BCA.git (fetch)
origin  https://github.com/vanwdani/GEANT_BCA.git (push)
foretony093457:GEANT_BCA foretony$ git fetch
foretony093457:GEANT_BCA foretony$ git fetch origin
foretony093457:GEANT_BCA foretony$ git remote -vv
origin  https://github.com/vanwdani/GEANT_BCA.git (fetch)
origin  https://github.com/vanwdani/GEANT_BCA.git (push)
foretony093457:GEANT_BCA foretony$ git checkout -b Freya origin/Freya
Branch 'Freya' set up to track remote branch 'Freya' from 'origin'.
Switched to a new branch 'Freya'


setup so you can update to your private repository call "MyBCA"  that is a fork of the original cloned repository
foretony093457:GEANT_BCA foretony$ git remote add MyBCA https://github.com/TonyForest/GEANT_BCA.git

foretony093457:GEANT_BCA foretony$ git remote -vv     
MyBCA   https://github.com/TonyForest/GEANT_BCA.git (fetch)
MyBCA   https://github.com/TonyForest/GEANT_BCA.git (push)
origin  https://github.com/vanwdani/GEANT_BCA.git (fetch)
origin  https://github.com/vanwdani/GEANT_BCA.git (push)



export PKG_CONFIG_PATH=/usr/local/Cellar/jsoncpp/1.9.3/lib/pkgconfig:$PKG_CONFIG_PATH


GitHUb install

Install petsc

git clone -b maint https://bitbucket.org/petsc/petsc petsc

cd petsc

./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-fblaslapack

make all test


export PETSC_DIR=$pwd/petsc

export PETSC_DIR=/Users/foretony/src/MOOSE/projects/moose/petsc/

export PETSC_ARCH=arch-darwin-c-debug check

Install libmesh

git clone git://github.com/libMesh/libmesh.git 

cd libmesh

make

make install

Install Moose

git clone https://github.com/idaholab/moose.git

cd moose

git checkout master


User_talk:Foretony#INL