Phoenix Introduction

Hardware and Architecture

The HWW Opteron Cluster phoenix platform consists of one front node for interactive access (phoenix.hww.de), serveral compute nodes for execution of parallel programs and some service nodes.

Different compute node types are installed:

• AMD Opteron dual core, 2GHz, 4GB memory, myrinet
• AMD Opteron quad core, 2.8GHz, 8GB memory, GigE
• AMD Opteron quad core, 2.6GHz, 8GB memory, Infinipath

Features

• Operating System: ScientificLinux 5 on AMD Opteron based nodes, diskless
• Batchsystem: Torque/Maui
• node-node interconnect: Infinipath, GigE, Myrinet
• Local Disk for scratch on some nodes
• Disk > 17 TB
• GPFS

Short overview of installed compute nodes

Type	memory	Freq	cores	Disk	PBS properties	Interconnect	nodes	number
1	4GB	2.0 GHz	2	30GB	old	GigE/Myrinet	c3-05, c3-17 - c3-31	16
2	8GB	2.8 GHz	4	-	asus	GigE	c4-01 - c4-08	8
3	8GB	2.8 GHz	4	-	rs161e4	GigE	c4-09 - c4-16	8
4	8GB	2.6 GHz	4	70GB	hp	GigE, Infinipath	c5-01 - c5-10	10

Access

The only way to access phoenix.hww.de (frontend node of HWW Opteron Cluster phoenix) from outside is through ssh

Usage

The frontend node

phoenix.hww.de

is intended as single point of access to the entire cluster. Here you can set your environment, move your data, edit and compile your programs and create batch scripts. Any interactive usage of the frontend node which causes a high cpu/memory load are NOT allowed (production runs).

The compute nodes for running parallel jobs are available only through the Batch system on the frontend node.

HOME Directories

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All user HOME directories for every compute node of the cluster are located on the I/O Servers. The compute nodes and login node (frontend) have the HOME directories mounted via NFS. On every node of the cluster the path to your HOME is the same. The filesystem space on HOME is limited by a quota of 50MB! Please note the Filesystem Policy!

SCRATCH directories

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Local Scratch

When allocating nodes with local disks (see table) using the batch queuing system (Torque), the /tmp on the compute nodes can be used as scratch. After your batch jobs are finished, the /tmp will be cleaned automatically.

Global Scratch

Another scratch you can get are global space on shared filesystems. There are 3 globel shared filesystems available on phoenix:

default It's a filesystem which is available via NFS on all phoenix compute nodes and on the phoenix frontend system gpfs 1.3.2 IBM GPFS filesystem shared globaly on different HWW Clusters To use it on cacau compute nodes, you need to create a file named '.gpfs' in your HOME directory (touch $HOME/.gpfs). The GPFS filesystem need some of the compute nodes memory. If you are short in memory on those nodes and you didn't need this filesystem, then please delete $HOME/.gpfs. If no such file found in your HOME, then the GPFS modules will not be loaded on the compute nodes. You are responsible to obtain it from the system. To get access to this global scratch filesystems you have to use the workspace mechanism 1.3.2.

Environment Settings

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In order to use some software features like special MPI versions, or Compilers, you have to perform some environmental settings. To modify the default HLRS DGRID environmental settings on login, you can create a file $HOME/.profile which contains your own envirenmental settings. The login shell is a bash shell which reads $HOME/.profile during login!

Environment Settings using command module

The environmental setting using this methode will not be saved and will be lost for a new session. A new session (login, new job) will have the default HLRS DGRID environment. The Cluster system uses modules in the user environment to support multiple versions of software, such as compilers, and to create integrated software packages. As new versions of the supported software become available, they are added automatically to the programming environment, while earlier versions are retained to support legacy applications. By specifying the module to load, you can choose the default version of an application, or another version. Modules also porvide a simple mechanism for updating certain environment variables, such as PATH, MANPATH, and LD_LIBRARY_PATH. The following topics describe the fundamentals of using the modules environment.

• to invoke the module command, type:

  module option args

module help modulecommand

The help command will provide more detailed information on the specified module. Without argument modulecommand you will get online help for the module command.

module avail

The avail option displays all the modules that are available on the system. Where there is more than one version of a module, the default version is denoted by (default).

module list

The list option displays all the modules that are currently loaded into your user environment.

module add / module load modulename

The add option and the load option have the same function - to load the specified module into your user environment.

module rm / module unload modulename

The rm option and the unload option have the same function - to unload the specified module from your user environment. Before loading a module that replaces another version of the same package, you should always unload the module that is to be replaced.

module display modulename

The display option shows the changes that the specified module will make in your environment, for example, what will be added to the PATH and MANPATH environment variables.

module switch modulename/currentversionmodulename/newversion

The switch option replaces the currently loaded version of a module with a different version. When the new verion is loaded, the man page for the specified software will also be updated.

• using $HOME/.modulerc

This file can be used to load or to define your own environment during each login. An example looks like this:

#%Module1.0#

set version 1.0
module load use.own

Filesystem Policy

IMPORTANT! NO BACKUP!! There is NO backup done of any user data located on HLRS DGRID systems. The only protection of your data is the redundant disk subsystem. This RAID system (Raid5) is able to handle a failure of one component (e.g. a single disk or a controller). There is NO way to recover inadvertently removed data. Users have to backup critical data on their local site!

Support / Feedback

Please report all problems to:

• System Administrators

1. Thomas Beisel
2. Bernd Krischok
3. H. Ohno

• Applications

1. Martin Bernreuther