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Logging on to JUGENE

Dispatch

Prerequisite for using the JUGENE system is to successfully pass through the application process. All details can be found at the website Allocation of computing time for the central computing systems (english version).

Login Nodes

The IBM Blue Gene/P uses so called front-end nodes or login nodes for interactive access and the submission of batch jobs.

JUGENE has two different login nodes (jugene3 and jugene4) which may be addressed as:

jugene.fz-juelich.de

The front-end nodes have an identical environment, but multiple sessions of one user may reside on different nodes which must be taken into account when killing processes.

Access with ssh

Generating a key

The access is only possible by using ssh connections with keys.

The public ssh key has to be generated on the system from which you want to access JUGENE and stored in the $HOME directory, e.g.

ssh-keygen -t [dsa|rsa]

Please protect the ssh key with a non-trivial pass phrase to fulfill the FZJ security policy. (For further details on ssh key generation see FAQ: How to generate ssh keys)

The contents of the files id_dsa.pub or id_rsa.pub key must be uploaded through the JSC WEB interface when initially applying for a userid and will be appended to $HOME/.ssh/authorized_keys.

Note: Please make sure that your home directory on JUGENE is not open for write access for other users or user groups, otherwise .ssh will not work.

Make sure there is no write access for group or world on the $HOME directory, otherwise .ssh does not work.

Login

After that a typical login looks like

ssh <userid>@jugene.fz-juelich.de

jugene is a generic name which will either establich a connection to jugene3 or jugene4.

Comment: Too many accesses (ssh or scp) within a short amount of time will be interpreted as intrusion and leads to automatic disabling the origin system at the FZJ firewall.
For transferring multiple files in a single scp session the -r option can be used, which allows to transfer a whole directory.

X11 Forwarding

If a login is done via multiple machines, the X11 forwarding must be enabled in the file .ssh/config with:

PubkeyAuthentication yes
ForwardAgent yes
ForwardX11 yes

Home Data

JUGENE users have access to their home data in a common General Parallel File System (GPFS). For organization of the home data in respect to using multiple systems it is strongly recommended to add a new subdirectory in $HOME and to store the Blue Gene data there.

Attention: Please do NOT rename or reorganize the directory structure of the existing directories because this will cause recall and backup activities for every changed file due to path or name modifications.

Login Shell

The Login Shell on each system points to system's favored shell:

JUGENE -> bash

Users are not allowed to change the Login Shell but they can switch to a personal shell within the login process. User's will find a template within the initial FZJ .profile in $HOME.

To avoid mismatches when logging on to different systems, which share the $HOME, it is recommended to do special settings within the .profile in respect to the system

if [ `uname` = "AIX" ]; then
... do JUMP stuff
elif [ `uname` = "Linux" ]; then
... do JUGENE stuff
fi

Memory Limit

The Linux system of the front-end nodes has 32 GB of main memory.
Default user limit: To prevent overloading the memory, the sessions have a hardlimit of 1 GB each.

Limits can be checked with the command:

ulimit -v or ulimit -a

Check for: virtual memory (kbytes, -v)
The limit specification is in KBytes.

Programming environment, modules and libraries

The persistent settings of the shell environment are governed by the content of .bashrc , .profile or scripts sourced from within these files. Please use these files for storing your personal settings.

The common programming environment is maintained with the concept of software modules in directory /usr/local and /bgsys/local. The framework provides a set of installed libraries and applications (including multiple-version support) and an easy to use interface (module command) to set up the correct shell environment (see also the slides: module setup and compiler).


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