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====== Mogon I & II ======

===== News =====

News from our group and our "mogon ticker" with software / work related news can be found at [[https://hpc.uni-mainz.de/|our webpage.]] The easiest way to get informed about our news is to [[https://hpc.uni-mainz.de/feed/rss/|subscribe to our rss-feed.]]


===== Training & Outreach =====

  * [[training_and_outreach:courses|Courses]]
  * [[training_and_outreach:workshop|HPC-Workshop]]
  * [[training_and_outreach:ticket_system|Getting Support]]
  * [[training_and_outreach:FAQ|FAQ]]

===== Documentation =====


==== Policies ====

The [[https://www.en-zdv.uni-mainz.de/regulations-for-use-of-the-data-center/|regulations for use of the data center (ZDV)]] apply at all times. Further Policies are listed per item:
  * [[policies_loginnodes|Login-Nodes]]
  * [[policies_home_directory|Home directory]]
  * [[accounts|Accounts & Accounting]]
  * [[thirdpartycourses|Conducting courses on Mogon I or II]]
  * For **software install requests**, please answer the questions of our **[[https://hpc.uni-mainz.de/high-performance-computing/service-angebot/softwareinstallation/|form]]**.

==== Mogon - Cluster Odds & Ends ====

  * [[access|How to access the mogon clusters I & II]]
  * [[nodes|Compute nodes with technical description]]

==== Working on Mogon / Using our job scheduler  ====
  * [[slurm_submit|Submit jobs on Mogon]]
  * [[partitions|General Notes on Partitions (a.k.a. batch queues)]]
  * [[slurm_manage|Manage and monitor jobs, pending reasons, information on job failures]]
  * [[memory_reservation|Memory reservation]]
  * [[io_odds_and_ends|Managing I/O issues]]:
    * [[slurm_localscratch|Node local scratch]] 
    * [[ramdisk|Ramdisk reservation]]
    * Special/Dedicated File Systems:  
      * [[etap|EtapFS]]
      * [[io_reservation|I/O bandwidth reservation (ATLAS)]]
  * Workflow Organization:
    * [[setting_up_environment_modules|Setting up the environment (Modules)]]    
    * [[job_dependeny|Job Dependency]]
    * [[job_arrays|Job Arrays]]
    * [[node_local_scheduling|Script Based Parallelisation (a.k.a Node-local scheduling)]] 
    * [[checkpoint_restart|Checkpoint Restarting]]
  * Using Accelerators:
    * [[gpu|Using GPU Nodes]]
  * Evaluation
    * [[job_evaluation|Evaluation of Jobs]]
    * [[accounting_status|Evaluate Accounting Status]]


==== Filesystems and Data Management ====

  * [[Filesystems:Overview|Filesystems Overview]] 
    * [[Filesystems:Transfer|Data Transfer Options]] 
    * [[Filesystems:Quotas|Quotas]] 
    * [[Filesystems:Backup|Backup]] (currently only for Mogon I)
  * Archiving Data
    * [[archiving:preparation|Preparation Steps prior to Archiving]]
    * [[archiving:tsm|Archiving Data with TSM]] 
  * [[data_management:irods|Data Management with iRODS]]




===== Installed Software and Software Installation Requests =====

Here you will find information about specific software installed on Mogon along with several usage instructions. More information on how we [[software|build software and how to request installations can be found under this link]]. However, the direct link for install requests is [[https://hpc.uni-mainz.de/high-performance-computing/service-angebot/softwareinstallation/|here]].

==== Topical Software ====

  * [[software:topical:lifescience|Life Sciences]]
  * [[software:topical:physics|Physical Simulation and Analytics Software]]

==== Scripting Languages ====

  * [[java|JAVA]]
  * [[software:matlab|MATLAB]]
  * [[software:mathematica|Mathematica]]
  * [[software:perl|Perl]]
  * [[software:python|Python]] 
    * [[software:python#Your_Personal_Environment_(Additional_Packages)|Your Personal Environment (Additional Packages)]]
    * [[software:python#job_submission|Job Submission]]
    * [[software:python#performance_hints|Performance Hints]]
  * [[software:R|R]]
  * [[software:Shell|Shells (with a focus on Bash)]]

=== Odds and Ends ====

    * [[mpi|MPI]]
    * [[visualize_queue:paraview|Paraview]]
    * [[spark|Apache Spark]]

==== ATLAS specific usage ====

  * [[lhcgrid|LHC Grid documentation]]

==== Development Tools ====


=== Performance Analysis Tools and Optimization Tools / Aspects ===

  * Scalasca [[http://www.scalasca.org/]]
  * OpenSpeedShop  [[http://www.openspeedshop.org/wp/]] (further information soon)
  * [[profiling|Profiling]]
  * [[debugging|Debugging]]
  * [[unittests|Unit Testing]]


==== Monitoring Systems ====

  * [[Ganglia]]
    * [[http://ganglia.sourceforge.net|Official Ganglia web page]]
    * [[http://m2monitor.zdv.uni-mainz.de/ganglia|MOGON ganglia monitoring report]]
    * [[Specific parameter and monitoring for MOGON|Specific parameters and monitoring for MOGON]]
  * [[Shell Based Monitoring]]

==== Editors / IDEs ====

  * [[Editors]]
  * [[IDEs]]
    
===== How to acknowledge Mogon =====

When preparing a journal publication please reference Mogon. We prepared a basic [[https://hpc.uni-mainz.de/high-performance-computing/publikationen/|acknowledgement]].
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