Running on a Cluster

To run on the cluster, there are a number of steps you must follow in order to get it to work. Refer also to the instructions on how to check out Continuity with SVN (you will need to do this too).

Cluster configuration

  • Install the required software

  • Check out Continuity source using SVN

    • Don’t use g95 (use Intel Fortran Compiler 8.0)
    • Don’t bother trying to run the client
  • Set up all required environment variables. I like to put these in a .bashrc file like this: 
    • export PYTHONPATH=$PYTHONPATH:/home/lionetti/Cont6/pcty/MglToolsLib/i86Linux2/lib/python2.3/site-packages/Numeric
export PYTHONPATH=$PYTHONPATH:/home/lionetti/Cont6/pcty/MglToolsLib/i86Linux2/lib/python2.3/site-packages/f2py2e
export F2PY='/home/lionetti/F2PY-2.45.241_1926/f2py'
export IFC='/software/intel80/'
export IFC_LIB_PATH='/software/intel80/lib'
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/software/intel80/lib"

      • You will (of course) need to modify these depending upon your environment.

  • Change directory to the Continuity root directory (above both the pcty and src directories)

  • Type  autoconf 

  • Type  ./configure 

  • Type  make 

  • Type

    cd linuxlib
tar -xzvf mgltools.tar.gz
mv continuity/pcty/MglToolsLib/ ../pcty/MglToolsLib
cd ..

Additional cluster configuration

vim /etc/ssh/sshd_config
#change to yes
GatewayPorts yes

see https://nbcr.net/intranet/wiki/index.php?title=Installation_on_Kryptonite for more info.

Client configuration

  • These instructions assume that you are using Windows, although they should more or less work on Linux and MacOS X (PPC)
  • Install Continuity (source or binary version)

  • Install plink.exe, pageant.exe, and puttygen.exe from here

  • Use puttygen to generate key pairs, and load your private key into pageant.exe.
    • You need to add this key to your authorized keys on the cluster. (~/.ssh/authorized_keys)
      • More info is needed here–hopefully I’ll add it later.
  • Run Continuity client
    • Modify the Continuity client shortcut to have ” –no-threads” at the end of the “target” line.
  • Load a parallel problem

  • File->Start Remote Server

  • Fill out every item:

    • Server host = granite.ucsd.edu

    • Username = yourusername

    • Password = don’t use

    • Plink path = C:/…/plink.exe (of course use the actual path where you installed plink.exe on your system)

    • Location of pcty on host = /home/username/ContinuityDirectory/pcty

    • Port on frontend = favorite number between 9000 and 9990

    • Number of nodes = a number between 2 and 200

    • Parallel shared memory = use the default unless you get a memory error

    • Parallel executable = BM for biomechanics, puglisi or greenstein if electrophysiology

    • Server type = Parallel

  • Solve the problem