1.2 Operating system and shell environment

Sisu is a Linux cluster. The login nodes of Sisu are based on the SUSE Linux Enterprise Server 11.3 (SLES11.3) distribution. The system software set installed on the login nodes offers a wide selection of libraries and development packages to compile your own software.

The computing nodes use a run-time environment provided by Cray, called Compute Node Linux (CNL).  Compute Node Linux, is a run-time environment based on SLES as well, but it includes only drivers, libraries and compilers required to run high-performance computing applications and a minimal amount of user-level commands (see http://www.busybox.net/). In general, all libraries available on the computing nodes are also available on the login nodes. You can inspect which packages are installed on SLES based servers using the following command:

 rpm -qa
This command is also useful in finding out what is the version of an installed package. Other options can be given to the rpm command to inspect the system configuration. Alternatively, locate and find are also good tools for inspecting the software configuration of a system. Note that users can't use the rpm command to install software to Sisu.

During the lifetime of the cluster, CSC aims to keep the software packages up to date following the minor releases of the operating system, as long as this preserves the necessary compatibility with previous versions. The computing nodes have an identical software configuration. The same applies to the login nodes.

As the system packages will be updated without any previous notification, we suggest to use the module environmnet to load specific library versions and software supported by CSC, or to install your own version in $USERAPPL directory. In this way your software dependencies will be safely preserved.

As a general rule, x86-64 binaries should be used for software installed on Sisu. x86-64 is the 64-bit extension of the x86 instruction set.

The default and recommended command shell in Sisu is bash. Previously CSC has been using tcsh as the default command shell and you can still continue to use tcsh shell in Sisu too. The chsh command can be used to change the default shell.

When a user logs into Sisu, the bash startup script defines a set of CSC specific variables defining the location of the user specific directories: $WRKDIR, $HOME, $TMPDIR and $USERAPPL. Further, rm, cp and mv commands are aliased so that by default they ask for permission before removing or overwriting existing files. Also the clobber options are set up so that output forwarding does not overwrite an existing file.

If you wish to add more settings or aliases that are automatically set up when you log in, you should add the corresponding Linux commands to the end of the bash set-up file .bashrc which is located in your home directory.

The Sisu system supports the UTF-8 character encoding, which makes it possible to represent every character in the Unicode character set. UTF-8 was not supported on older CSC systems, so care should be taken when sharing files with other systems.

User specific software should be compiled in the $TMPDIR, which resides on the login nodes, instead of $WRKDIR or $HOME which reside on the Lustre file system. Compilation in $TMPDIR is much faster as it runs on local login node's disk instead of Lustre.

 

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