File:Grain structure moose.png

2017-06-13T21:27:44Z

Yanmingw:

How to install Moose

2017-06-13T21:26:01Z

Yanmingw: /* Phase field module */

How to install MOOSE
<DIV>
Yanming Wang
June, 2017
 <HR>

[http://mooseframework.org MOOSE], short for Multiphysics Object-Oriented Simulation Environment, is a finite-element multi-physics framework developed by Idaho National Laboratory. Here we briefly describe how to install MOOSE on the [https://web.stanford.edu/group/hpcc/cgi-bin/certainty/index.php/Main_Page Certainty cluster].

== System requirements ==
The installation of MOOSE requires Compiler: C++11 Compliant GCC 4.8.4, Clang 3.4.0, Intel20130607, and Python 2.7+. On Certainty, they are provided as modules, so you can simply type the following commands to load them,

module load gnu/4.7.2
module load clang/3.5.2
module load gnu/5.2
module load openmpi/1.10.2-gnu-5.2
module load cmake/2.8.12.2

Or you can copy and paste them in your '''~/.bashrc''' file, which will load the modules automatically when you login to Certainty. Notice that on Certainty '''clang''' requires some libraries from '''gnu/4.7.2''', so that you have to load '''gnu/4.7.2''' first and update it later (to '''gnu/5.2''' in this case) to satisfy the MOOSE requirement. Also, the version of '''openmpi''' compiler should be compatible with the '''gcc''' compiler.

== Installation ==
The procedures of MOOSE installation is given in details on their [http://mooseframework.org/getting-started/ official website].
=== PETSc ===
First, you need to install PETSc following the following steps. (mostly follow the official tutorial)
==== PREFIX Setup ====
export CLUSTER_TEMP=`mktemp -d /tmp/cluster_temp.XXXXXX`
export PACKAGES_DIR=$HOME/moose-compilers
==== Download Software ====
cd $CLUSTER_TEMP
curl -L -O http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.6.4.tar.gz
==== Extract Software ====
cd $CLUSTER_TEMP
tar -xf petsc-3.6.4.tar.gz
==== Create MOOSE Profile ====
Make note of your $PACKAGES_DIR:

echo $PACKAGES_DIR
Edit the following file:

$HOME/.moose-profile
Add the following content to that file:

export PACKAGES_DIR=INSERT-PACKAGES-DIR-HERE!!!!

export CC=mpicc
export CXX=mpicxx
export F90=mpif90
export F77=mpif77
export FC=mpif90

export ARCH=gcc
export PETSC_DIR=$PACKAGES_DIR/petsc/petsc-3.6.4/$ARCH-opt

And run,
source ~/.moose-profile

==== Build and Install PETSc ====
cd $CLUSTER_TEMP/petsc-3.6.4

./configure \
--prefix=$PETSC_DIR \
--download-hypre=1 \
--with-ssl=0 \
--with-debugging=yes \
--with-pic=1 \
--with-shared-libraries=1 \
--with-cc=mpicc \
--with-cxx=mpicxx \
--with-fc=mpif90 \
--download-fblaslapack=1 \
--download-metis=1 \
--download-parmetis=1 \
--download-superlu_dist=1 \
--download-scalapack=1 \
--download-mumps=1 \
CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif77 F90=mpif90 \
CFLAGS='-fPIC -fopenmp' \
CXXFLAGS='-fPIC -fopenmp' \
FFLAGS='-fPIC -fopenmp' \
FCFLAGS='-fPIC -fopenmp' \
F90FLAGS='-fPIC -fopenmp' \
F77FLAGS='-fPIC -fopenmp' \
PETSC_DIR=`pwd`

At the end of the configure step, the system will print out messages on your terminal window. The last printed section contains the make command you will need to enter on your terminal window. At the end of the make step, there will be another message about the make install commands. Just follow them to complete the setup. An example is the following. The specific folder you will need to enter will be different. Just copy and paste the printed out message.

make PETSC_DIR=/tmp/cluster_temp.wowSIm/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-debug all
make PETSC_DIR=/tmp/cluster_temp.wowSIm/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-debug install

== Clone MOOSE ==
You can do exactly the same as suggested by their official tutorial.

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

== Compile libMesh ==
This step is straight forward, but you may need some patience. The compilation may take up to an hour.
cd ~/projects/moose
scripts/update_and_rebuild_libmesh.sh

== Test ==
cd ~/projects/moose/test
make -j8
./run_tests -j8

The test results should look like
Ran 1329 tests in 191.7 seconds
1328 passed, 51 skipped, 0 pending, 1 FAILED
You may receive one message regarding the failed item,
preconditioners/pbp.lots_of_variables....................................................... FAILED (TIMEOUT)
Don't worry about it. This is a timed test, which most likely indicates that the computer is running slow (or the machine is overburdened).

== Phase field module ==
By default, MOOSE contains several modules, including one for phase field simulations. You can go to the corresponding folder and compile the code there

cd ~/projects/moose/modules/phase_field
make

If the compilation is successful, you expect to get the executable '''phase_field-opt'''. You can do a simple 3D grain growth simulation interactively.

cd ~/projects/moose/modules/phase_field/examples/grain_growth
../../phase_field-opt -i grain_growth_3D.i

Alternatively, you can submit the job to Certainty using this sample pbs script[[Media:Phasefield_test_Moose.pbs.txt | phasefield_test_Moose.pbs]].
cd ~/projects/moose/modules/phase_field/examples/grain_growth
qsub phasefield_test_Moose.pbs

The results are saved in the .exodus format, which can be opened by Paraview, or [http://mooseframework.org/wiki/Peacock/ Peacock] (a GUI provided by MOOSE but not compatible with Certainty).

How to install Moose

2017-06-13T21:25:49Z

Yanmingw: /* Phase field module */

How to install MOOSE
<DIV>
Yanming Wang
June, 2017
 <HR>

[http://mooseframework.org MOOSE], short for Multiphysics Object-Oriented Simulation Environment, is a finite-element multi-physics framework developed by Idaho National Laboratory. Here we briefly describe how to install MOOSE on the [https://web.stanford.edu/group/hpcc/cgi-bin/certainty/index.php/Main_Page Certainty cluster].

== System requirements ==
The installation of MOOSE requires Compiler: C++11 Compliant GCC 4.8.4, Clang 3.4.0, Intel20130607, and Python 2.7+. On Certainty, they are provided as modules, so you can simply type the following commands to load them,

module load gnu/4.7.2
module load clang/3.5.2
module load gnu/5.2
module load openmpi/1.10.2-gnu-5.2
module load cmake/2.8.12.2

Or you can copy and paste them in your '''~/.bashrc''' file, which will load the modules automatically when you login to Certainty. Notice that on Certainty '''clang''' requires some libraries from '''gnu/4.7.2''', so that you have to load '''gnu/4.7.2''' first and update it later (to '''gnu/5.2''' in this case) to satisfy the MOOSE requirement. Also, the version of '''openmpi''' compiler should be compatible with the '''gcc''' compiler.

== Installation ==
The procedures of MOOSE installation is given in details on their [http://mooseframework.org/getting-started/ official website].
=== PETSc ===
First, you need to install PETSc following the following steps. (mostly follow the official tutorial)
==== PREFIX Setup ====
export CLUSTER_TEMP=`mktemp -d /tmp/cluster_temp.XXXXXX`
export PACKAGES_DIR=$HOME/moose-compilers
==== Download Software ====
cd $CLUSTER_TEMP
curl -L -O http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.6.4.tar.gz
==== Extract Software ====
cd $CLUSTER_TEMP
tar -xf petsc-3.6.4.tar.gz
==== Create MOOSE Profile ====
Make note of your $PACKAGES_DIR:

echo $PACKAGES_DIR
Edit the following file:

$HOME/.moose-profile
Add the following content to that file:

export PACKAGES_DIR=INSERT-PACKAGES-DIR-HERE!!!!

export CC=mpicc
export CXX=mpicxx
export F90=mpif90
export F77=mpif77
export FC=mpif90

export ARCH=gcc
export PETSC_DIR=$PACKAGES_DIR/petsc/petsc-3.6.4/$ARCH-opt

And run,
source ~/.moose-profile

==== Build and Install PETSc ====
cd $CLUSTER_TEMP/petsc-3.6.4

./configure \
--prefix=$PETSC_DIR \
--download-hypre=1 \
--with-ssl=0 \
--with-debugging=yes \
--with-pic=1 \
--with-shared-libraries=1 \
--with-cc=mpicc \
--with-cxx=mpicxx \
--with-fc=mpif90 \
--download-fblaslapack=1 \
--download-metis=1 \
--download-parmetis=1 \
--download-superlu_dist=1 \
--download-scalapack=1 \
--download-mumps=1 \
CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif77 F90=mpif90 \
CFLAGS='-fPIC -fopenmp' \
CXXFLAGS='-fPIC -fopenmp' \
FFLAGS='-fPIC -fopenmp' \
FCFLAGS='-fPIC -fopenmp' \
F90FLAGS='-fPIC -fopenmp' \
F77FLAGS='-fPIC -fopenmp' \
PETSC_DIR=`pwd`

At the end of the configure step, the system will print out messages on your terminal window. The last printed section contains the make command you will need to enter on your terminal window. At the end of the make step, there will be another message about the make install commands. Just follow them to complete the setup. An example is the following. The specific folder you will need to enter will be different. Just copy and paste the printed out message.

make PETSC_DIR=/tmp/cluster_temp.wowSIm/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-debug all
make PETSC_DIR=/tmp/cluster_temp.wowSIm/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-debug install

== Clone MOOSE ==
You can do exactly the same as suggested by their official tutorial.

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

== Compile libMesh ==
This step is straight forward, but you may need some patience. The compilation may take up to an hour.
cd ~/projects/moose
scripts/update_and_rebuild_libmesh.sh

== Test ==
cd ~/projects/moose/test
make -j8
./run_tests -j8

The test results should look like
Ran 1329 tests in 191.7 seconds
1328 passed, 51 skipped, 0 pending, 1 FAILED
You may receive one message regarding the failed item,
preconditioners/pbp.lots_of_variables....................................................... FAILED (TIMEOUT)
Don't worry about it. This is a timed test, which most likely indicates that the computer is running slow (or the machine is overburdened).

== Phase field module ==
By default, MOOSE contains several modules, including one for phase field simulations. You can go to the corresponding folder and compile the code there

cd ~/projects/moose/modules/phase_field
make

If the compilation is successful, you expect to get the executable '''phase_field-opt'''. You can do a simple 3D grain growth simulation interactively.

cd ~/projects/moose/modules/phase_field/examples/grain_growth
../../phase_field-opt -i grain_growth_3D.i

Alternatively, you can submit the job to Certainty using this sample pbs script[[Media:Phasefield_test_Moose.pbs.txt | Phasefield_test_Moose.pbs]].
cd ~/projects/moose/modules/phase_field/examples/grain_growth
qsub phasefield_test_Moose.pbs

The results are saved in the .exodus format, which can be opened by Paraview, or [http://mooseframework.org/wiki/Peacock/ Peacock] (a GUI provided by MOOSE but not compatible with Certainty).

How to install Moose

2017-06-13T21:25:30Z

Yanmingw: /* Phase field module */

How to install MOOSE
<DIV>
Yanming Wang
June, 2017
 <HR>

[http://mooseframework.org MOOSE], short for Multiphysics Object-Oriented Simulation Environment, is a finite-element multi-physics framework developed by Idaho National Laboratory. Here we briefly describe how to install MOOSE on the [https://web.stanford.edu/group/hpcc/cgi-bin/certainty/index.php/Main_Page Certainty cluster].

== System requirements ==
The installation of MOOSE requires Compiler: C++11 Compliant GCC 4.8.4, Clang 3.4.0, Intel20130607, and Python 2.7+. On Certainty, they are provided as modules, so you can simply type the following commands to load them,

module load gnu/4.7.2
module load clang/3.5.2
module load gnu/5.2
module load openmpi/1.10.2-gnu-5.2
module load cmake/2.8.12.2

Or you can copy and paste them in your '''~/.bashrc''' file, which will load the modules automatically when you login to Certainty. Notice that on Certainty '''clang''' requires some libraries from '''gnu/4.7.2''', so that you have to load '''gnu/4.7.2''' first and update it later (to '''gnu/5.2''' in this case) to satisfy the MOOSE requirement. Also, the version of '''openmpi''' compiler should be compatible with the '''gcc''' compiler.

== Installation ==
The procedures of MOOSE installation is given in details on their [http://mooseframework.org/getting-started/ official website].
=== PETSc ===
First, you need to install PETSc following the following steps. (mostly follow the official tutorial)
==== PREFIX Setup ====
export CLUSTER_TEMP=`mktemp -d /tmp/cluster_temp.XXXXXX`
export PACKAGES_DIR=$HOME/moose-compilers
==== Download Software ====
cd $CLUSTER_TEMP
curl -L -O http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.6.4.tar.gz
==== Extract Software ====
cd $CLUSTER_TEMP
tar -xf petsc-3.6.4.tar.gz
==== Create MOOSE Profile ====
Make note of your $PACKAGES_DIR:

echo $PACKAGES_DIR
Edit the following file:

$HOME/.moose-profile
Add the following content to that file:

export PACKAGES_DIR=INSERT-PACKAGES-DIR-HERE!!!!

export CC=mpicc
export CXX=mpicxx
export F90=mpif90
export F77=mpif77
export FC=mpif90

export ARCH=gcc
export PETSC_DIR=$PACKAGES_DIR/petsc/petsc-3.6.4/$ARCH-opt

And run,
source ~/.moose-profile

==== Build and Install PETSc ====
cd $CLUSTER_TEMP/petsc-3.6.4

./configure \
--prefix=$PETSC_DIR \
--download-hypre=1 \
--with-ssl=0 \
--with-debugging=yes \
--with-pic=1 \
--with-shared-libraries=1 \
--with-cc=mpicc \
--with-cxx=mpicxx \
--with-fc=mpif90 \
--download-fblaslapack=1 \
--download-metis=1 \
--download-parmetis=1 \
--download-superlu_dist=1 \
--download-scalapack=1 \
--download-mumps=1 \
CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif77 F90=mpif90 \
CFLAGS='-fPIC -fopenmp' \
CXXFLAGS='-fPIC -fopenmp' \
FFLAGS='-fPIC -fopenmp' \
FCFLAGS='-fPIC -fopenmp' \
F90FLAGS='-fPIC -fopenmp' \
F77FLAGS='-fPIC -fopenmp' \
PETSC_DIR=`pwd`

At the end of the configure step, the system will print out messages on your terminal window. The last printed section contains the make command you will need to enter on your terminal window. At the end of the make step, there will be another message about the make install commands. Just follow them to complete the setup. An example is the following. The specific folder you will need to enter will be different. Just copy and paste the printed out message.

make PETSC_DIR=/tmp/cluster_temp.wowSIm/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-debug all
make PETSC_DIR=/tmp/cluster_temp.wowSIm/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-debug install

== Clone MOOSE ==
You can do exactly the same as suggested by their official tutorial.

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

== Compile libMesh ==
This step is straight forward, but you may need some patience. The compilation may take up to an hour.
cd ~/projects/moose
scripts/update_and_rebuild_libmesh.sh

== Test ==
cd ~/projects/moose/test
make -j8
./run_tests -j8

The test results should look like
Ran 1329 tests in 191.7 seconds
1328 passed, 51 skipped, 0 pending, 1 FAILED
You may receive one message regarding the failed item,
preconditioners/pbp.lots_of_variables....................................................... FAILED (TIMEOUT)
Don't worry about it. This is a timed test, which most likely indicates that the computer is running slow (or the machine is overburdened).

== Phase field module ==
By default, MOOSE contains several modules, including one for phase field simulations. You can go to the corresponding folder and compile the code there

cd ~/projects/moose/modules/phase_field
make

If the compilation is successful, you expect to get the executable '''phase_field-opt'''. You can do a simple 3D grain growth simulation interactively.

cd ~/projects/moose/modules/phase_field/examples/grain_growth
../../phase_field-opt -i grain_growth_3D.i

Alternatively, you can submit the job to Certainty using this sample pbs script[[Media:Phasefield_test_Moose.pbs.txt | Phasefield_test_Moose.pbs]].
cd ~/projects/moose/modules/phase_field/examples/grain_growth
qsub Media:Phasefield_test_Moose.pbs

The results are saved in the .exodus format, which can be opened by Paraview, or [http://mooseframework.org/wiki/Peacock/ Peacock] (a GUI provided by MOOSE but not compatible with Certainty).

How to install Moose

2017-06-13T21:20:39Z

Yanmingw: /* Phase field module */

How to install MOOSE
<DIV>
Yanming Wang
June, 2017
 <HR>

[http://mooseframework.org MOOSE], short for Multiphysics Object-Oriented Simulation Environment, is a finite-element multi-physics framework developed by Idaho National Laboratory. Here we briefly describe how to install MOOSE on the [https://web.stanford.edu/group/hpcc/cgi-bin/certainty/index.php/Main_Page Certainty cluster].

== System requirements ==
The installation of MOOSE requires Compiler: C++11 Compliant GCC 4.8.4, Clang 3.4.0, Intel20130607, and Python 2.7+. On Certainty, they are provided as modules, so you can simply type the following commands to load them,

module load gnu/4.7.2
module load clang/3.5.2
module load gnu/5.2
module load openmpi/1.10.2-gnu-5.2
module load cmake/2.8.12.2

Or you can copy and paste them in your '''~/.bashrc''' file, which will load the modules automatically when you login to Certainty. Notice that on Certainty '''clang''' requires some libraries from '''gnu/4.7.2''', so that you have to load '''gnu/4.7.2''' first and update it later (to '''gnu/5.2''' in this case) to satisfy the MOOSE requirement. Also, the version of '''openmpi''' compiler should be compatible with the '''gcc''' compiler.

== Installation ==
The procedures of MOOSE installation is given in details on their [http://mooseframework.org/getting-started/ official website].
=== PETSc ===
First, you need to install PETSc following the following steps. (mostly follow the official tutorial)
==== PREFIX Setup ====
export CLUSTER_TEMP=`mktemp -d /tmp/cluster_temp.XXXXXX`
export PACKAGES_DIR=$HOME/moose-compilers
==== Download Software ====
cd $CLUSTER_TEMP
curl -L -O http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.6.4.tar.gz
==== Extract Software ====
cd $CLUSTER_TEMP
tar -xf petsc-3.6.4.tar.gz
==== Create MOOSE Profile ====
Make note of your $PACKAGES_DIR:

echo $PACKAGES_DIR
Edit the following file:

$HOME/.moose-profile
Add the following content to that file:

export PACKAGES_DIR=INSERT-PACKAGES-DIR-HERE!!!!

export CC=mpicc
export CXX=mpicxx
export F90=mpif90
export F77=mpif77
export FC=mpif90

export ARCH=gcc
export PETSC_DIR=$PACKAGES_DIR/petsc/petsc-3.6.4/$ARCH-opt

And run,
source ~/.moose-profile

==== Build and Install PETSc ====
cd $CLUSTER_TEMP/petsc-3.6.4

./configure \
--prefix=$PETSC_DIR \
--download-hypre=1 \
--with-ssl=0 \
--with-debugging=yes \
--with-pic=1 \
--with-shared-libraries=1 \
--with-cc=mpicc \
--with-cxx=mpicxx \
--with-fc=mpif90 \
--download-fblaslapack=1 \
--download-metis=1 \
--download-parmetis=1 \
--download-superlu_dist=1 \
--download-scalapack=1 \
--download-mumps=1 \
CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif77 F90=mpif90 \
CFLAGS='-fPIC -fopenmp' \
CXXFLAGS='-fPIC -fopenmp' \
FFLAGS='-fPIC -fopenmp' \
FCFLAGS='-fPIC -fopenmp' \
F90FLAGS='-fPIC -fopenmp' \
F77FLAGS='-fPIC -fopenmp' \
PETSC_DIR=`pwd`

At the end of the configure step, the system will print out messages on your terminal window. The last printed section contains the make command you will need to enter on your terminal window. At the end of the make step, there will be another message about the make install commands. Just follow them to complete the setup. An example is the following. The specific folder you will need to enter will be different. Just copy and paste the printed out message.

make PETSC_DIR=/tmp/cluster_temp.wowSIm/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-debug all
make PETSC_DIR=/tmp/cluster_temp.wowSIm/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-debug install

== Clone MOOSE ==
You can do exactly the same as suggested by their official tutorial.

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

== Compile libMesh ==
This step is straight forward, but you may need some patience. The compilation may take up to an hour.
cd ~/projects/moose
scripts/update_and_rebuild_libmesh.sh

== Test ==
cd ~/projects/moose/test
make -j8
./run_tests -j8

The test results should look like
Ran 1329 tests in 191.7 seconds
1328 passed, 51 skipped, 0 pending, 1 FAILED
You may receive one message regarding the failed item,
preconditioners/pbp.lots_of_variables....................................................... FAILED (TIMEOUT)
Don't worry about it. This is a timed test, which most likely indicates that the computer is running slow (or the machine is overburdened).

== Phase field module ==
By default, MOOSE contains several modules, including one for phase field simulations. You can go to the corresponding folder and compile the code there

cd ~/projects/moose/modules/phase_field
make

If the compilation is successful, you expect to get the executable '''phase_field-opt'''. You can do a simple test on 3D grain growth.

cd ~/projects/moose/modules/phase_field/examples/grain_growth
../../phase_field-opt -i grain_growth_3D.i

[[Media:Phasefield_test_Moose.pbs.txt | example pbs file]]

The results are saved in the .exodus format, which can be opened by Paraview, or [http://mooseframework.org/wiki/Peacock/ Peacock] (a GUI provided by MOOSE but not compatible with Certainty).

File:Phasefield test Moose.pbs.txt

2017-06-13T21:19:13Z

Yanmingw:

How to install Moose

2017-06-13T21:17:10Z

How to install deal.II
<DIV>
Yanming Wang
May, 2017
 <HR>

Deal.II is an open Finite Element Method (FEM) code. For detailed description of the code and tutorials, you can refer to their offical website http://www.dealii.org/. Here we explain how to install it on the [http://sherlock.stanford.edu/mediawiki/index.php/Main_Page Sherlock cluster].

==System Requirements==
The installation of Deal.II requires cmake 3.2 and up, openmpi/1.10.2/gcc and gcc/4.8.1. They have been pre-installed as modules on the cluster, to load them, you can type the following commands on your terminal.

module load cmake/3.2.2
module load gcc/4.8.1
module load openmpi/1.10.2/gcc

Or you can paste the above three lines into your ~/.bashrc file, and type

source ~/.bashrc

== Setup ==
Assuming you want to install the package in the home directory of group's shared space, you can firstly go to the folder by typing

cd /shared/PI/caiwei

From there, you can directly clone the package from Github.
git clone https://github.com/dealii/candi

Now you should have a folder called '''candi'''. The next step is to go into the folder and update the following two configuration files [[Media:candi.cfg.txt|candi.cfg]] and [[Media:dealii.package.txt|dealii.package]].
cd /shared/PI/caiwei/candi
wget -O candi.cfg http://micro.stanford.edu/mediawiki/images/1/1e/Candi.cfg.txt
cd /shared/PI/caiwei/candi/deal.II-toolchain/packages
wget -O dealii.package http://micro.stanford.edu/mediawiki/images/a/aa/Dealii.package.txt

Notice in '''candi.cfg''', there is one line that specifies the installation path,
PREFIX_PATH=/share/PI/caiwei/dealii/
This needs to be modified if you intend to install the package in other places.

== Installation ==
The installation is straight forward, but it may take up to 3 hours. To make sure it is not killed by the scheduler, you may submit a device allocation request for a relatively long time.

sdev -t 4:00:00 -p mc

When you get the node, the following automated script can guide you through the installation process.
cd /shared/PI/caiwei/candi
./candi.sh --platform=deal.II-toolchain/platforms/supported/centos7.platform

The program starts with a couple of checks, where you only need to press the '''Enter''' button to continue. Then, the [https://trilinos.org/ trilinos] library will be installed, which the Deal.II package depends on (Another choice is to use PETSc, but its installation is not demoed in this instruction).

If everything is installed successfully, at the end of the process, the following message will be popped up, which also contains the commands to load the Deall.II libraries.

dealii.git has now been installed in
/share/PI/caiwei/dealii/deal.II-v8.4.0
To update your environment variables, use the created modulefile:
/share/PI/caiwei/dealii/configuration/modulefiles/default
If you are not using modules, execute the following command instead:
source /share/PI/caiwei/dealii/configuration/deal.II-v8.4.0
To export environment variables for all installed libraries execute:
source /share/PI/caiwei/dealii/configuration/enable.sh
Build finished in 6377 seconds.

== Test ==
A simple example can be used to test if the package is successfully installed. Type the following commands to compile and run the example.

cd /share/PI/caiwei/dealii/deal.II-v8.4.0/examples/step-1
cmake .
make
make run

Once the program is finished, it generates the figures of two grids in .eps format. They look like

[[File:grid-1.jpg| grid-1.eps]]
[[File:grid-2.jpg| grid-2.eps]]

A comprehensive tutorial of Deal.II can be found on
https://www.dealii.org/8.4.0/doxygen/deal.II/Tutorial.html .

== Acknowledgement ==
We appreciate the great help from Xiaoxuan Zhang, who is a Ph.D. student in Prof. Christian Linder's group at Stanford University.

How to install deal.II

2017-05-30T20:18:41Z

Yanmingw: /* Test */

How to install deal.II
<DIV>
Yanming Wang
May, 2017
 <HR>

Deal.II is an open Finite Element Method (FEM) code. For detailed description of the code and tutorials, you can refer to their offical website http://www.dealii.org/. Here we explain how to install it on the [http://sherlock.stanford.edu/mediawiki/index.php/Main_Page Sherlock cluster].

==System Requirements==
The installation of Deal.II requires cmake 3.2 and up, openmpi/1.10.2/gcc and gcc/4.8.1. They have been pre-installed as modules on the cluster, to load them, you can type the following commands on your terminal.

module load cmake/3.2.2
module load gcc/4.8.1
module load openmpi/1.10.2/gcc

Or you can paste the above three lines into your ~/.bashrc file, and type

source ~/.bashrc

== Setup ==
Assuming you want to install the package in the home directory of group's shared space, you can firstly go to the folder by typing

cd /shared/PI/caiwei

From there, you can directly clone the package from Github.
git clone https://github.com/dealii/candi

Now you should have a folder called '''candi'''. The next step is to go into the folder and update the following two configuration files [[Media:candi.cfg.txt|candi.cfg]] and [[Media:dealii.package.txt|dealii.package]].
cd /shared/PI/caiwei/candi
wget -O candi.cfg http://micro.stanford.edu/mediawiki/images/1/1e/Candi.cfg.txt
cd /shared/PI/caiwei/candi/deal.II-toolchain/packages
wget -O dealii.package http://micro.stanford.edu/mediawiki/images/a/aa/Dealii.package.txt

Notice in '''candi.cfg''', there is one line that specifies the installation path,
PREFIX_PATH=/share/PI/caiwei/dealii/
This needs to be modified if you intend to install the package in other places.

== Installation ==
The installation is straight forward, but it may take up to 3 hours. To make sure it is not killed by the scheduler, you may submit a device allocation request for a relatively long time.

sdev -t 4:00:00 -p mc

When you get the node, the following automated script can guide you through the installation process.
cd /shared/PI/caiwei/candi
./candi.sh --platform=deal.II-toolchain/platforms/supported/centos7.platform

The program starts with a couple of checks, where you only need to press the '''Enter''' button to continue. Then, the [https://trilinos.org/ trilinos] library will be installed, which the Deal.II package depends on (Another choice is to use PETSc, but its installation is not demoed in this instruction).

If everything is installed successfully, at the end of the process, the following message will be popped up, which also contains the commands to load the Deall.II libraries.

dealii.git has now been installed in
/share/PI/caiwei/dealii/deal.II-v8.4.0
To update your environment variables, use the created modulefile:
/share/PI/caiwei/dealii/configuration/modulefiles/default
If you are not using modules, execute the following command instead:
source /share/PI/caiwei/dealii/configuration/deal.II-v8.4.0
To export environment variables for all installed libraries execute:
source /share/PI/caiwei/dealii/configuration/enable.sh
Build finished in 6377 seconds.

== Test ==
A simple example can be used to test if the package is successfully installed. Type the following commands to compile and run the example.

cd /share/PI/caiwei/dealii/deal.II-v8.4.0/examples/step-1
cmake .
make
make run

Once the program is finished, it generates the figures of two grids in .eps format. They look like

[[File:grid-1.jpg| grid-1.eps]]
[[File:grid-2.jpg| grid-2.eps]]

https://www.dealii.org/8.4.0/doxygen/deal.II/Tutorial.html

== Acknowledgement ==
We appreciate the great help from Xiaoxuan Zhang, who is a Ph.D. student in Prof. Christian Linder's group at Stanford University.

How to install deal.II

2017-05-30T20:13:49Z

Yanmingw:

How to install deal.II
<DIV>
Yanming Wang
May, 2017
 <HR>

Deal.II is an open Finite Element Method (FEM) code. For detailed description of the code and tutorials, you can refer to their offical website http://www.dealii.org/. Here we explain how to install it on the [http://sherlock.stanford.edu/mediawiki/index.php/Main_Page Sherlock cluster].

==System Requirements==
The installation of Deal.II requires cmake 3.2 and up, openmpi/1.10.2/gcc and gcc/4.8.1. They have been pre-installed as modules on the cluster, to load them, you can type the following commands on your terminal.

module load cmake/3.2.2
module load gcc/4.8.1
module load openmpi/1.10.2/gcc

Or you can paste the above three lines into your ~/.bashrc file, and type

source ~/.bashrc

== Setup ==
Assuming you want to install the package in the home directory of group's shared space, you can firstly go to the folder by typing

cd /shared/PI/caiwei

From there, you can directly clone the package from Github.
git clone https://github.com/dealii/candi

Now you should have a folder called '''candi'''. The next step is to go into the folder and update the following two configuration files [[Media:candi.cfg.txt|candi.cfg]] and [[Media:dealii.package.txt|dealii.package]].
cd /shared/PI/caiwei/candi
wget -O candi.cfg http://micro.stanford.edu/mediawiki/images/1/1e/Candi.cfg.txt
cd /shared/PI/caiwei/candi/deal.II-toolchain/packages
wget -O dealii.package http://micro.stanford.edu/mediawiki/images/a/aa/Dealii.package.txt

Notice in '''candi.cfg''', there is one line that specifies the installation path,
PREFIX_PATH=/share/PI/caiwei/dealii/
This needs to be modified if you intend to install the package in other places.

== Installation ==
The installation is straight forward, but it may take up to 3 hours. To make sure it is not killed by the scheduler, you may submit a device allocation request for a relatively long time.

sdev -t 4:00:00 -p mc

When you get the node, the following automated script can guide you through the installation process.
cd /shared/PI/caiwei/candi
./candi.sh --platform=deal.II-toolchain/platforms/supported/centos7.platform

The program starts with a couple of checks, where you only need to press the '''Enter''' button to continue. Then, the [https://trilinos.org/ trilinos] library will be installed, which the Deal.II package depends on (Another choice is to use PETSc, but its installation is not demoed in this instruction).

If everything is installed successfully, at the end of the process, the following message will be popped up, which also contains the commands to load the Deall.II libraries.

dealii.git has now been installed in
/share/PI/caiwei/dealii/deal.II-v8.4.0
To update your environment variables, use the created modulefile:
/share/PI/caiwei/dealii/configuration/modulefiles/default
If you are not using modules, execute the following command instead:
source /share/PI/caiwei/dealii/configuration/deal.II-v8.4.0
To export environment variables for all installed libraries execute:
source /share/PI/caiwei/dealii/configuration/enable.sh
Build finished in 6377 seconds.

== Test ==
To test if the package is successfully installed,

cd /share/PI/caiwei/dealii/deal.II-v8.4.0/examples/step-1
cmake .
make
make run

produces graphics of two grids (grid-1.eps and grid-2.eps). They look like this:

[[File:grid-1.jpg|grid-1.eps]]
[[File:grid-2.jpg|grid-2.eps]]

== Acknowledgement ==
We appreciate the great help from Xiaoxuan Zhang, who is a Ph.D. student in Prof. Christian Linder's group at Stanford University.

File:Grid-2.jpg

2017-05-30T20:11:27Z

Yanmingw:

2017-05-24T22:09:01Z

Yanmingw: