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Welcome to the High Performance Computing Cluster BIOcrunch Wiki at ZSM Munich.



The cluster was upgraded in June 2013. It is up and running at See the ClusterUpgradeEmail



The BIOCrunch cluster at ZSM is a centrally administered cluster composed of compute nodes owned by ZSM.

The cluster runs 64-bit linux and is accessible at to users with accounts.

There is an BIOCrunch Advisory Committee that oversees the cluster. Day-to-day management of the cluster falls to Gerhard Recher.

Send emails to if you have a technical question or problem that cannot be addressed by the documentation below.

If you are new to the cluster, please check scheduler and resource manager tutorials and go through FAQs. Thanks.


We will attempt to provide all necessary information to use BIOCrunch effectively here in this website.


Submitting jobs

  • Prepare job on local machine PrepareJob
  • Starting job on the cluster with qsub ? Qsub

Executables and Libraries

Can you install programs for me ? Where is python 2.5 ? Information on Libraries and Interfaces installed on the cluster.


BIOCrunchC GPU computing How to check if my program is using threads Please Contact for problems,requests,etc...

Older News

Best practices

Our aim is to publish best practices and experiences about research and cluster computing. What is a "project"? Software development Data collection Data processing

Technical/administration information

This section is for documenting the technical and administration side of BIOCrunch. BIOCrunch's blueprint? How to add a user? How to add a node? How to add a file server? rocks sync config hangs! Configuration of master node Configuration of gridengine How to install different compilers? Syslog Notes Monitoring Issues - to be resolved eventually Unpacking Nodes Software tips, tricks, howtos Hardware tips, tricks, howtos Testing ground

Gerhard W. Recher / Matthias Müller

Personal tools