TF MOOSE-MARMOT
Running at INL
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 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
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 --env # conda environments: # base /Users/foretony/miniconda3 moose * /Users/foretony/miniconda3/envs/moose
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