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# Welcome to Wiki Shark cluster # Welcome to Wiki Shark cluster
## Introduction ## Introduction
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/ 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!
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. 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.
...@@ -22,25 +22,18 @@ The following links contain the minimal information you need to get started on t ...@@ -22,25 +22,18 @@ The following links contain the minimal information you need to get started on t
* [testsets](testsets)-- Featured test data * [testsets](testsets)-- Featured test data
* [Using the checkpointing queue](CheckpointingQueue) -- how/when to use the checkpointing queue * [Using the checkpointing queue](CheckpointingQueue) -- how/when to use the checkpointing queue
---- ----
## The new SHARK cluster in the resource/research network
* [What is new](new)
* [How to Connect](Howtoconnect)
* [How to get a Research account](RresearchAccount)
* [ How to use the Evironment Modules](EnvironmentModules)
* [How to access grid storage](AccessingGridStorage)
* [Using the fsl analysis tools for FMRI, MRI and DTI brain imaging data](UsingFSL)
* [Graphical access SHARK cluster](Graphical)
----
## Configuration Shark cluster ## Configuration Shark cluster
* [configuration Type of headnode and blade servers](Configuration) * [configuration Type of headnode and blade servers](Configuration)
* [Graphical representation of the shark cluster](Graphicalview) * [Graphical representation of the shark cluster](Graphicalview)
* [Description of the execute nodes](DescriptionExenode) * [Description of the execute nodes](DescriptionExenode)
## Getting started ## Getting started
* [How to get a user account on the Shark Cluster](UserAccount) * [How to get a user account on the Shark Cluster](RresearchAccount)
* [How to connect to the Shark Cluster](GetConnected) * [How to connect to the Shark Cluster](Howtoconnect)
* [How to configure public key authentication](PublicKeyAuth) * [How to configure public key authentication](PublicKeyAuth)
* [How to use the Evironment Modules](EnvironmentModules)
* [How to access grid storage](AccessingGridStorage)
* [Graphical access SHARK cluster](Graphical)
* [Short intro course for new Shark users](Intro_course) * [Short intro course for new Shark users](Intro_course)
* [Forking an input stream to several programs](StreamForking) * [Forking an input stream to several programs](StreamForking)
* [How to submit a R-script with qsub](qsub_R-script) * [How to submit a R-script with qsub](qsub_R-script)
...@@ -48,6 +41,7 @@ The following links contain the minimal information you need to get started on t ...@@ -48,6 +41,7 @@ The following links contain the minimal information you need to get started on t
* [How to start an IPython Notebook session](IPythonNotebook) * [How to start an IPython Notebook session](IPythonNotebook)
* [How to correct long PacBio reads using pacBioToCA](pacBioToCA) * [How to correct long PacBio reads using pacBioToCA](pacBioToCA)
* [How to change your researchlumc password](ChangePasswd) * [How to change your researchlumc password](ChangePasswd)
* [Using the fsl analysis tools for FMRI, MRI and DTI brain imaging data](UsingFSL)
## Limitations ## Limitations
* [How to use more then the default memory allocation for my job](MemoryLimitations) * [How to use more then the default memory allocation for my job](MemoryLimitations)
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