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r32 - 25 Sep 2013 - 11:02:58 - DavidAcremanYou are here: Astrophysics Wiki >  Zen Web  > ReadMeFirst

About Zen

If you are interested in using Zen for your research please see the page GettingAccessToZen

Zen consists of diskless compute nodes each with twelve cores and 24GiB of RAM. The compute nodes communicate over a high speed infiniband network, with a second infiniband network to connect the compute nodes to the storage.

There are two nodes you can log in to directly: a log in node called zen.astro.ex.ac.uk (with 2 cores and 8GiB of RAM) and a visualisation/post-processing node called zen-viz.astro.ex.ac.uk (with 8 cores and 32GiB of RAM).

Zen runs the Linux operating system. For more information on Linux/Unix see the LinuxResources page.

Code can be run in parallel using OpenMP or MPI. OpenMP can only be used within a node, as it requires all the threads to share the same memory. MPI can be used to parallelise code running on different nodes and can be combined with OpenMP in a hybrid configuration. There are two MPI implementations available on Zen: Intel MPI and SGI's MPT.

Logging in to Zen

You can log in to zen and zen-viz using ssh. To enable graphics to be displayed use a -X (Linux) or -Y (Mac OS) option. If you are connecting from outside the University of Exeter network you will need to use the VPN.

To connect to Zen from a Microsoft Windows PC you will need additional software to provide SSH capability. This capability can be provided by PuTTY. Graphics from Zen can be displayed on a Windows PC but this requires that you install an X server. An X server can be installed as part of cygwin.

Filestore

Each user has directories /home/username and /data/username. Directories in /home are backed up daily. More information file systems can be found on the FileSystems page.

Compilers

The system has the Intel Fortran and C/C++ compilers, ifort and icc, MPI compiler/linker, mpif90/mpiicc. For more more information on compilers see CompilingAndLinking.

Running Jobs

Work is submitted to compute nodes using the Torque Resource Manager. See the RunningJobs page for details of how this works.

Any intensive work should not be run on the main log in node (the one called zen) as it is not sufficiently powerful. Intensive interactive work can be run on zen-viz or using an interactive session on a compute node (see the RunningJobs page for details of how to do this).

Publications

When you write a publication which has made use of Zen please include the appropriate acknowledgement (see AcknowledgingZen). Please also notify Matthew Bate, so that the publication can be added to the Zen publications list.

Policies

  • Run intensive post-processing, visualisation and interactive work on zen-viz. The other log in node is much less powerful and may not cope.

  • There is no local file-store on the nodes, so be aware that reading and writing files is done over a network and your actions can affect other users.

  • Write large files to your /data directory, reserving the /home directory for files that need out-of-building backup. (Directories within /home that don't need backing up should be called SCRATCH)

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Zen.ReadMeFirst moved from Zen.SystemOverview on 28 Jan 2008 - 16:51 by JohnRowe - put it back

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