TF MOOSE-MARMOT

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