# Using moFEM on rdb-srv1 Server #

##SSH Connection

For a graphical client through SSH connection requires XQuartz on Mac or Xming for Windows

Execute in terminal

• untrusted X11 forwarding

$ ssh -X username@rdb-srv1.eng.gla.ac.uk

where username should be replaced by your username.

• Then enter the password when it is prompted.

#####Definition of untrusted X11 forwarding

The remote machine is treated as an untrusted client. When your local client sends a command to the remote machine and receives the graphical output. If your command violates some security settings you'll receive an error instead.

Compressed SSH connection

$ ssh -X -C username@rdb-srv1.eng.gla.ac.uk

##Setting up moFEM

create directory for moFEM

$ mkdir moFEM

cd in moFEM and execute the follow to obtain moFEM source

$ git clone https://username@bitbucket.org/likask/mofem-joseph.git

where username is your bitbucket username, and bicbucket password might be prompted.

create a build directory for moFEM

$ mkdir ~/build_moFEM

$ cd ~/buid_moFEM

cmake moFEM in build_moFEM

$ cmake -DCMAKE_BUILD_TYPE=Release -DPETSC_DIR=/opt/petsc-3.4.3 -DPETSC_ARCH=arch-linux2-c-opt -DMOAB_DIR=/opt/local-moab-4.6.0/ -DCMAKE_CXX_FLAGS="-I/opt/local_boost_1_54_0/include -L/opt/local_boost_1_54_0/include" -DCMAKE_INSTALL_PREFIX=$HOME/local ../moFEM/mofem-joseph/mofem_v0.1/

compile moFEM

$ make -j 4

where -j 4 is multi-processor compiling, using 4 processors

test compilation using ctest

$ ctest --http1.0 -D Experimental

and results are sent to our CDash Dashboard, where warnings and errors are shown.

for more compilation warnings, run the Continuous test

$ ctest --http1.0 -D Continuous

####Another way of installing moFEM

After running the cmake command in the build directory execute

$ make install
$ cd ~/local/bin

$ ./mofem_build.sh
$ ./mofem_update.sh
$ ./mofem_fast_check.sh 

##Working with moFEM

using git repository, allows you to work on several local branches and having several remote branches on bitbucket web page.

• to see which is the current branch

$ cd ~/moFEM/mofem-joseph/mofem_v0.1

$ git branch

• create new local branch, named newBranch1

  $ git branch newBranch1
  

• checkout in this newBranch1

  $ git checkout newBranch1
  

  PS: you cannot checkout to another branch if you've got changes in the current one, which you have not committed of stashed!!

• delete local master or other branches

  $ git branch -D master
  

• to pull a remote branch (ex. CDashTesting) in your current local branch

  $ git pull https://username@bitbucket.org/likask/mofem-joseph.git CDashTesting
  

• committing all changes of current local branch

  $ git commit -a -m "comment about the changes made"
  

• push changes to remote branch newBranch1_remote

  $ git push https://username@bitbucket.org/likask/mofem-joseph.git newBranch1_remote
  

• see status of changes

  $ git status
  

for more git commands visit Atlassian and gitref.org

one also can use git-cola as a gui of git.

Useful Stuff for the Server

###Colouring ssh -X connection

to view files and directories in different colours

execute this once when connected to the server

$ echo "alias ls='ls --color=always'" >> ~/.bashrc
$ source ~/.bashrc

• Created by Michael Cortis
• any difficulties or suggestions email cmatgu@googlegroups.com