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==
 +
 +
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
 +
  
 
[http://mooseframework.org  MOOSE Documentation:]
 
[http://mooseframework.org  MOOSE Documentation:]
  
−
After following th MOOSE install directions I encountered the following error on the INL server
+
MOOSE tutorial on Youtube
 +
 
 +
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
 +
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==
 +
 
 +
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
  
−
python 2.7 is required to run the test harness
 
  
−
I need to tell the INL server to use python 2.7
+
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"==
 
==Loading packages using "module"==
Line 26: Line 111:
  
 
https://hpcsc.inl.gov/moose
 
https://hpcsc.inl.gov/moose
 +
 +
=local Moose=
 +
 +
 +
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=
 +
 +
==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
 +
 +
<pre>
 +
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'
 +
</pre>
 +
 +
 +
setup so you can update to your private repository call "MyBCA"  that is a fork of the original cloned repository
 +
 +
<pre>
 +
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)
 +
 +
</pre>
 +
 +
 +
 +
 +
export PKG_CONFIG_PATH=/usr/local/Cellar/jsoncpp/1.9.3/lib/pkgconfig:$PKG_CONFIG_PATH
  
  

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

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