Get Started - Sciama - University of Portsmouth

Page 1 of 12 High Performance Compute (HPC) Cluster Getting Started with SCIAMA ( pro: Shama ) Author: G.Burton Version: Version 1.5 Date: Aug 15 http://www.sciama.icg.port.ac.uk Page 2 of 12 INTRODUCTION
Sciama (pronounced Shama) is a High Performance Compute (HPC) cluster. Sciama, named after Dennis Sciama, stands for:-­‐ SEPNet Computer Infrastructure for Astrophysical Modeling and Analysis The environment comprises of:-­‐ •
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Sciama is a +4000 core, distributed memory cluster. It uses 2.66GHz Intel Xeon processors. It has 2 or 4Gbytes of memory per core It has 650 Tbytes of fast parallel storage. It has 145 Tbytes of NFS storage. It has three networks: 100bT, Gigabit, Infiniband. It uses an Open Source software stack. To use the environment:-­‐ 1.
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Request an account. Download a connection client (if necessary) Use the connection client to log into a designated Login Server. Copy any data from your home environment. Prepare your job. Submit your job(s) to the compute pool. Copy results to your home environment. Page 3 of 12 GETTING STARTED WITH SCIAMA This document describes how you get started in the Sciama HPC environment. 1.
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Applying for a login account. Accessing the Sciama environment. Installing an appropriate “access” application. Configuring access to the environment with X2go. The Sciama desktop. Important: Changing your password Disconnecting and reconnecting to a session. How to copy data to and from the environment. Where to get help. Page 4 of 12 1. APPLYING FOR A LOGIN ACCOUNT Accounts will be granted to the following bodies : •
Members of the University of Portsmouth. •
University of Portsmouth collaborators. •
Others at discretion of Computer management. Accounts need to be applied for online at :-­‐ http://www.sciama.icg.port.ac.uk/accrequest.htm You will need to do the following:-­‐ 1.
Read and accept the UoP computer code of conduct. 2.
Supply a valid University email address. 3.
Supply a full name. 4.
Supply a preferred “username” (8 chars). 5.
The IP address of your desktop. Once you have completed and submitted the online form you will be emailed further details. Page 5 of 12 2. ACCESSING THE SCIAMA ENVIRONMENT The SSH protocol is used to access the Sciama environment. The environment is reachable from both the University networks and the Internet. Page 6 of 12 3. INSTALLING AN APPROPRIATE “ACCESS” APPLICATION The environment can be reached in one of two ways:-­‐ •
Via an SSH command line client . A list of common SSH clients can be found here :-­‐ http://en.wikipedia.org/wiki/Comparison_of_SSH_clients An example of such a client is Putty:-­‐ •
Via a remote Linux desktop client called X2go. This will give you a desktop in the Sciama environment:-­‐ The X2go client can be downloaded from here:-­‐ http://wiki.x2go.org/doku.php Page 7 of 12 4. CONFIGURING ACCESS TO THE ENVIRONMENT WITH X2GO The following screen shots are taken from a Windows installation, Linux and MAC will be similar. From the X2go client select Sessions -­‐> new Type in the fully qualified domain name of the Login server you have been assigned and set an appropriate network connection speed. Select GNOME as the desktop type and an appropriate desktop size:-­‐ Page 8 of 12 5. THE SCIAMA DESKTOP Sciama uses the default Gnome desktop that comes with Scientific Linux:-­‐ Please note that the Sciama desktop is made available to make it easier to set up your HPC jobs, it is not intended to replace your day to day working environment. For security reasons internet access is restricted as is the number of applications installed. There are two text editors available Nedit or Gedit . Nedit is context sensitive so probably better for code writing. Emacs is also available. Page 9 of 12 6. IMPORTANT – CHANGING YOUR PASSWORD The first time you login make sure you change your password using the yppasswd command:-­‐ Page 10 of 12 7. DISCONNECTING AND RECONNECTING TO A SESSION Whether you are accessing the environment via a command line terminal or by the remote desktop client you will be able to create “sessions” which can be disconnected and reconnected. To create a terminal session use the Linux command “screen”. A short “screen” tutorial can be found here:-­‐ http://www.rackaid.com/resources/linux-­‐screen-­‐tutorial-­‐and-­‐how-­‐to/ Full details can be found here:-­‐ http://www.manpagez.com/man/1/screen/ Using the X2go client closing the window by clicking the top right “x” . Reconnection is done via the X2go client. Page 11 of 12 8. HOW TO COPY DATA TO AND FROM THE ENVIRONMENT From the command line “scp” or “sftp” should be used to transfer data from your local environment to the Sciama cluster. It should be noted that DATA WILL NOT BE BACKED UP ON SCIAMA . When using a remote desktop a graphical file manager like Nautilus can be used :-­‐ For UoP users you can mount your N: drive using myfiles.port.ac.uk . This should be used to transfer files to and from your home environment. See:-­‐ http://www.is.port.ac.uk/staff/workanywhere/fileaccess/connecttoserverlinux Your Home account will be limited to 10Gbytes. If you have large datasets then a separate Project area can be created on the Lustre parallel file system. Project data area usage will be monitored. Any data not referenced for a defined period will be deleted. Full details on how to transfer data can be found here:-­‐ http://www.sciama.icg.port.ac.uk/copyingdata.pdf Page 12 of 12 9. WHERE TO GET HELP Firstly please refer to the “How To” section on the website at:-­‐ http://www.sciama.icg.port.ac.uk else via email to :-­‐ mailto:[email protected] Institute of Cosmology and Gravitation (ICG), Dennis Sciama Building, Burnaby Road, Portsmouth, PO1 3FX +44 (0)23 9284 5540 (office)