Computational Science Community Wiki

Man2

Further Help

Should this documentation not address an issue with Man2, users should email rcs@manchester.ac.uk stating that they have a problem on Man2, giving their username on the system (but not their password) and describing the problem.

What is the system most suitable for?

The system is suitable for:

What is the system not suitable for?

The system is not suitable for large-scale MPI jobs.

Available Software

The following software has been installed and tested on Man2:

Other software is available under /software but has not been tested.

Hardware

Man2 has a total of 27 compute nodes:

The system has a three TB disk array attached.

The North-West Grid

Man2 is part of the North-West Grid, which consists of HPC clusters from the University of Manchester, the University of Liverpool, Lancaster University and also Daresbury Laboratories.

Getting Access to Man2

University of Manchester academics, postdocs and postgraduates who wish to use Man2 should email rcs@manchester.ac.uk giving their IT Services username and describing briefly the nature of the nature of their computational work (e.g., serial or parallel, software needed, and, if possible, approximate memory and filesystem capacity requirements).

Those who wish to gain access to all North-West Grid HPC facilities should register via the North-West Grid Web site.

Logging into Man2; File Transfer; X-Windows

There are four things to consider when using Man2:

Network/VPN/Firewall Issues

Not all computers can connect to Man2:

Login Using SSH

Once network issues have been sorted out, as described above, you should be able to login using SSH. First, start the VPN if required.

Linux users will be able to login using OpenSSH, which comes with all popular distros, by typing

    ssh -l <username> man2.nw-grid.ac.uk
        # ...replace <username> with your username, cf. mpciish2...

at the command-line.

MS Windows users should download and install PuTTY, an SSH client.

File Transfer

It is likely that you will wish to upload files to Man2, or download them from Man2 to your desktop/laptop. Linux users can do this by using either scp or sftp, from the OpenSSH utilities suite (which comes will all popular distros), for example:

    scp myfile.txt <username>@man2.nw-grid.ac.uk:
        # ...to copy a file to Man2 --- don't forget the ":" at the end...

    scp <username>@man2.nw-grid.ac.uk:results.out results.copy
        # ...copy a file from Man2...

MS Windows users should download and install WinSCP, a GUI-based file-transfer client.

Using X-Windows: GUI-Based Applications

Using SSH on its own will enable you to login to Man2 and use the command-line. If you want to use GUI-based applications, such as gedit, a Notepad-like editor, or you want to use Matlab interactively, then you need to run an X11 server on your local desktop and enable X11-tunnelling in your SSH connection.

All popular Linux distros run an X11-based desktop (GNOME, KDE). The only remaining step is to enable X11-tunnelling when logging in:

    ssh -X -l <username> man2.nw-grid.ac.uk
        # ...that's an UPPERcase X...

MS Windows users will need to download and install an X11 server. The two obvious options are eXceed, for which the University has a site licence, and Xming, which is free to download and install. When connecting:

  1. Start the VPN, if necessary.
  2. Start eXceed or Xming, then
  3. start PuTTY, being careful to enable X11 tunnelling — click on "SSH" on the left-hand-side, then ensure the X11 tunnelling box is "checked", before starting a connection to Man2.

Where Everything Is: Filesystems and Backups

The three TB disk array is divided into three parts:

Running Jobs on Man2

All computational jobs lasting more than a few minutes must be submitted to one of the two batch systems on Man2: all parallel work (MPI and OpenMP) must be submitted to SGE; serial work can be submitted to either SGE or Condor.

Condor

Condor is available as an alternative means of submitting computational jobs to the cluster. It is suitable for serial jobs only; it is well-suited for large numbers of short jobs. Condor is used as backfill on the system; jobs submitted to SGE always have priority.

Compilers

The following compilers are installed on Man2: gcc, gfortran (GNU's Fortran 90/95 compiler); and Intel's Fortran 90/95 compiler, ifort. Usage details and example qsub scripts for running jobs under SGE are given on the dedicated page.

Parallel Work

MPI

Open MPI is installed on the system; OpenMPI is an open-source implementation of MPIv2, compiled with GCC (the GNU C compiler) and Ifort (the Intel Fortran compiler). OpenMPI is able to take advantage of multiple physical networks between compute nodes and works well with the batch system, SGE. Information regarding compilation and also submission of jobs to Man2's batch system can be found on the dedicated Man2 OpenMPI page.

N.B. OpenMPI should not be confused with OpenMP which is a shared-memory API, not an implementation of MPI. Libraries:

OpenMP

Now in testing...

Applications (Tested)

Stata v11

R

R 2.10.1 now available! (2010 March 08.)

Matlab

Castep

LAMMPS

Ox

Gauss

CFD: Fluent, Star-CD and Star CCM+

Amber

Lens

Applications (Not Fully Tested)

Free Surfer

  export PATH=$PATH:/software/FreeSurfer/bin/
  export FREESURFER_HOME=/software/FreeSurfer/
  source $FREESURFER_HOME/SetUpFreeSurfer.sh

then

  tkmedit bert orig.mgz

Applications (Not Yet Tested)

Intel MKL

The Intel Math Kernel Library is installed under

NAG Libraries

The NAG numerical libraries are installed under /opt/NAG. The current installation includes:

Usage details and examples can be found on the Man2 NAG Libs wiki page.