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

Contents

News

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


Introduction

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 cluster.zsm-intra.net 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 administrator@zsm.mwn.de 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.

FAQs

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

Basics

How to get an account ? Some guidelines What are my responsibilities ? How to login ? How to do file transfers Link-Text? What about Disk Storage ? How to observe the Cluster Status

Submitting jobs

How do I open an interactive session on a compute node? What is qsub ? What is qrsh? How to run single jobs ? How to run parallel jobs ? How to run many, many jobs at once: use array jobs Requesing memory for a job with large RAM requirements

Executables and Libraries

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

Other

BIOCrunchC GPU computing How to check if my program is using threads Please Contact administrator@zsm.mwn.de 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

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