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# Welcome to Wiki Shark cluster
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## Introduction
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In this wiki, we will introduce the Shark cluster. We assume you know your way around in the terminal and that you will use the cluster in a responsible way and respect the available resources. Remember that a cluster runs many different processes submitted by many different users. If you are not sure what you are doing, ask your administrator before submitting very intensive jobs! For more examples and useful commands you can use our svn repository https://humgenprojects.lumc.nl/svn/shark/
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Shark cluster runs with [Open Grid Scheduler/Grid Engine](http://gridscheduler.sourceforge.net/) this is a free and open-source batch-queuing system for distributed resource management. OGS/GE is based on Sun Grid Engine, and maintained by the same group of external (i.e. non-Sun) developers who started contributing code to Sun Grid Engine since 2001.
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**Current release of Open Grid Scheduler** : *Grid Engine 2011.11p1*
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## Introduction and interesting starting points
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The following links contain the minimal information you need to get started on the shark cluster. When using the cluster you acknowledge that you have read and understand the following articles.
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* [Guidelines] -- what you can and can't do on this cluster
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* [function of the Shark cluster](Primairy) -- Primary usage Shark cluster
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* [network shares](Network_shares) -- where to put your data
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* [Queues] -- which queue is for what
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* [Batch queuing commands](qsubCommands) -- explanation of the qsub command
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* [Examples] -- examples how to qsub your jobs
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* [Makefile] -- Howto use qmake with a Makefile
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* [SGE state symbol codes](StateCode) -- Sun Grid Engine SGE state letter symbol codes meanings
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* [FAQ] -- Frequently asked questions and answers
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* [Presentations] -- Interesting presentations
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* [testsets] -- Featured test data
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* [Using the checkpointing queue](CheckpointingQueue) -- how/when to use the checkpointing queue
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----
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## The new SHARK cluster in the resource/research network
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* [What is new](new)
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* [How to Connect](Howtoconnect)
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* [How to get a Research account](RresearchAccount)
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* [ How to use the Evironment Modules](EnvironmentModules)
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* [How to access grid storage](AccessingGridStorage)
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* [Using the fsl analysis tools for FMRI, MRI and DTI brain imaging data](UsingFSL)
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* [Graphical access SHARK cluster](Graphical)
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----
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## Configuration Shark cluster
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* [configuration Type of headnode and blade servers](Configuration)
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* [Graphical representation of the shark cluster](Graphicalview)
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* [Description of the execute nodes](DescriptionExenode)
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## Getting started
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* [How to get a user account on the Shark Cluster](UserAccount)
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* [How to connect to the Shark Cluster](GetConnected)
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* [How to configure public key authentication](PublicKeyAuth)
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* [Short intro course for new Shark users](Intro_course)
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* [Forking an input stream to several programs](StreamForking)
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* [How to submit a R-script with qsub](qsub_R-script)
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* [How to submit a MPICH2 job](MPICH2)
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* [How to start an IPython Notebook session](IPythonNotebook)
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* [How to correct long PacBio reads using pacBioToCA](pacBioToCA)
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* [How to change your researchlumc password](ChangePasswd)
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## Limitations
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* [How to use more then the default memory allocation for my job](MemoryLimitations)
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## Support
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* [Contact Information](Contact_info_shark)
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* [Ganglia Shark cluster monitor](http://shark.lumcnet.prod.intern/ganglia/?c=Shark%20Cluster&m=load_one&r=hour&s=descending&hc=4&mc=2) -- view the load, disk space etc. on the Shark cluster
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* [Grid Engine HOWTOs](http://arc.liv.ac.uk/SGE/howto/).
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* [SVN repository (for course material and example scripts).](https://humgenprojects.lumc.nl/svn/shark/)
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## Usage Statistics
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* [Shark Usage 2012](http://shark.lumcnet.prod.intern/stats/SharkStats2012.html)
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* [Projects from LGTC people that need cleanup](ProjectsCleanup)
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## Usefull Links
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* [Wiki gridengine](http://wiki.gridengine.info/wiki/index.php/Main_Page)
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* [This is an archive of Stephan Grell's blog posts.](http://wiki.gridengine.info/wiki/index.php/StephansBlog)
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* [DanT's Grid Blog, Sun Grid Engine for dummies](https://blogs.oracle.com/templedf/entry/sun_grid_engine_for_dummies)
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* [sge_intro(1) - Linux man page](http://linux.die.net/man/1/sge_intro)
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## Documentation
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* Setup and install the [Shark](Shark_setup) head node with Ubuntu 10.04.04 LTS and Open Grid Scheduler
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* Setup [LDAP/Kerberos authentication](Ubuntu) within a Microsoft Windows 2008 Domain
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* Open Grid Scheduler [FineTune and solutions](FineTune/Solutions)
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For a complete list of local wiki pages, see TitleIndex.
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\ No newline at end of file |
