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start [2019/06/11 11:01]
meesters [Editors / IDEs]
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jrutte02
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-====== Mogon I & II ======+<grid> 
 +<col xs="12" sm="12" md="6" lg="6"> 
 +<jumbotron> 
 +====== WELCOME======
  
-===== News =====+... to the MOGON Wiki 
 +</jumbotron> 
 +</col> 
 +<col xs="12" sm="12" md="6" lg="6"> 
 +<callout color="#c1002a" icon="fa fa-hand-spock-o" title="Dear User,"> 
 +welcome to our Wiki. We hope it will make your research on MOGON more comfortable! 
  
-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.]]+If you miss pages or discover mistakes, please do not hesitate to [[hpc@uni-mainz.de|contact us]] or to <button type="info" icon="fa fa-pencil" size="xs">[[:start:training_and_outreach:faq#may_i_contribute_to_this_wiki|become active]]</button> yourself.
  
 +</callout>
  
-===== 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 ===== 
  
 +</col>
 +</grid>
 +<grid>
  
-==== Policies ====+<col xs="12" sm="6" md="4" lg="3"> 
 +<panel type="default" title="Help and Service"> 
 +<nav type="pills" stacked="true"> 
 +  * [[:start:training_and_outreach:courses|Courses]] 
 +  * [[:start:training_and_outreach:workshop|HPC Workshop]] 
 +  * [[:start:training_and_outreach:ticket_system|Getting Support]] 
 +  * [[:start:training_and_outreach:faq|FAQ]] 
 +</nav> 
 +</panel> 
 +<panel type="default" title="Policies"> 
 +<nav type="pills" stacked="true"> 
 +  * [[:start:policies:loginnodes|Login-Nodes]] 
 +  * [[:start:policies:home_directory|Home directory]] 
 +  * [[:start:policies:accounts|Accounts & Accounting]] 
 +  * [[:start:policies:thidpartycourses|MOGON Courses]] 
 +  * [[:start:policies:software_installation|Software request]] 
 +  * [[:start:policies:data_management|Data Management]] 
 +</nav> 
 +</panel> 
 +<panel type="default" title="MOGON-Cluster"> 
 +<nav type="pills" stacked="true"> 
 +  * [[:start:mogon_cluster:access|Accessing MOGON]] 
 +  * [[:start:mogon_cluster:basic_authentication|Basic Authentication]] 
 +  * [[:start:mogon_cluster:access_from_outside_windows|Access MOGON using Windows]] 
 +  * [[:start:mogon_cluster:access_from_outside_unix|Access MOGON using Linux/macOS]] 
 +  * [[:start:mogon_cluster:nodes|Hardware and Architecture]] 
 +</nav> 
 +</panel> 
 +</col> 
 +<col xs="12" sm="6" md="4" lg="3"> 
 +<panel type="default" title="Working on MOGON"> 
 +<panel-body> 
 +<nav type="pills" stacked="true"> 
 +  * [[:start:working_on_mogon:slurm_submit|Submit Jobs to MOGON]] 
 +  * [[:start:working_on_mogon:partitions|Partitions / Batch Queues]] 
 +  * [[:start:working_on_mogon:slurm_manage|Manage and Monitor Jobs]] 
 +  * [[:start:working_on_mogon:memory_reservation|Memory Reservation]] 
 +  * Managing I/O Issues 
 +    * [[:start:working_on_mogon:io_odds_and_ends:slurm_localscratch|Node Local Scratch]]     
 +    * [[:start:working_on_mogon:io_odds_and_ends:ramdisk|Ramdisk Reservation]] 
 +    * [[:start:working_on_mogon:io_odds_and_ends:special_fs|Special File Systems]] 
 +  * Workflow Organization 
 +    * [[:start:working_on_mogon:workflow_organization:setting_up_environment_modules|Setting up the environment (Modules)]]   
 +    * [[:start:working_on_mogon:workflow_organization:job_dependeny|Job Dependency]] 
 +    * [[:start:working_on_mogon:workflow_organization:job_arrays|Job Arrays]] 
 +    * [[:start:working_on_mogon:workflow_organization:node_local_scheduling|Script Based Parallelization]] 
 +    * [[:start:working_on_mogon:workflow_organization:spark|Apache Spark]] 
 +    * [[:start:working_on_mogon:workflow_organization:checkpoint_restart|Checkpoint Restarting]]  
 +  * [[:start:working_on_mogon:gpu|Using GPU Nodes]] 
 +  * [[:start:working_on_mogon:evaluation|Evaluating Jobs]] 
 +</nav> 
 +</panel-body> 
 +</panel> 
 +<panel type="default" title="Filesystems"> 
 +<nav type="pills" stacked="true"> 
 +  * [[:start:fs_dm:filesystems:overview|Filesystems Overview]] 
 +  * [[:start:fs_dm:filesystems:transfer|Data Transfer Options]] 
 +  * [[:start:fs_dm:filesystems:quotas|Quotas]] 
 +  * [[:start:fs_dm:filesystems:backup|Backup]] 
 +  * [[:start:fs_dm:filesystems:access_fs_windows|Access w/ Windows]] 
 +  * [[:start:fs_dm:filesystems:access_fs_mac|Access w/ Mac]] 
 +  * [[:start:fs_dm:filesystems:access_fs_linux|Access w/ Linux]] 
 +</nav> 
 +</panel> 
 +</col> 
 +<col xs="12" sm="6" md="4" lg="3"> 
 +<panel type="default" title="Data Management"> 
 +<nav type="pills" stacked="true"> 
 +  * [[:start:fs_dm:download|Downloading Scientific Data]] 
 +  * [[:start:fs_dm:archiving:preparation|Preparation Steps]] 
 +  * [[:start:fs_dm:archiving:irods|Data Management with iRODS]] 
 +</nav> 
 +</panel> 
 +<panel type="default" title="Software">
  
-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: +=== General ===
-  * [[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 ====+<nav type="pills" stacked="true"> 
 +  * [[:start:software:installation_remarks|How we build and how you can use Software]]  
 +</nav>
  
-  * [[access|How to access the mogon clusters I & II]] +=== Containers ===
-  * [[nodes|Compute nodes with technical description]]+
  
-==== Working on Mogon / Using our job scheduler  ==== +<nav type="pills" stacked="true"> 
-  * [[slurm_submit|Submit jobs on Mogon]] +  * [[:start:software:containers:singularity|Singularity]]  
-  * [[partitions|General Notes on Partitions (a.k.a. batch queues)]] +</nav>
-  * [[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]]+
  
 +=== Topical ===
  
-==== Filesystems and Data Handling beyond Compute Jobs ====+<nav type="pills" stacked="true"> 
 +  * LifeSciences 
 +    * [[:start:software:topical:lifesciences:r_bio|R and BioConductor]] 
 +    * [[:start:software:topical:lifesciences:ngs|NGS & Co.]] 
 +    * [[:start:software:topical:lifesciences:evol_soft|Evolutionary & Phylogenetics Software Tools]] 
 +    * [[:start:software:topical:lifesciences:molecular_docking|Molecular Docking Tools]] 
 +    * [[:start:software:topical:lifesciences:molecular_dynamics|Molecular Dynamics Simulations]] 
 +    * [[:start:software:topical:lifesciences:single_particle_analysis|Single Particle Processing / Analysis]] 
 +  * Physical and Chemical Simulation Software 
 +    * [[:start:software:topical:physics:cp2k|CP2K]] 
 +    * [[:start:software:topical:lifesciences:molecular_dynamics|VMD and NAMD]] 
 +    * [[:start:software:topical:physics:orca|ORCA]] 
 +    * [[:start:software:topical:physics:eulag|Simulations using EULAG]] 
 +    * [[start:software:topical:physics:hoomd-plugins|Installation of HOOMD-plugins]] 
 +    * [[https://gaussian.com|Gaussian]] 
 +    * [[https://www.plumed.org/|PLUMED]] 
 +    * [[https://sunqm.github.io/pyscf/|PySCF]] 
 +    * [[http://www.espresso-pp.de/|ESPResSo++]] 
 +</nav> 
 +=== Visualization ===
  
-  * [[Filesystems:Overview|Filesystems Overview]]  +<nav type="pills" stacked="true"> 
-    * [[Filesystems:Transfer|Data Transfer Options]]  +  * [[:start:software:visualization:paraview|Paraview]]  
-    * [[Filesystems:Quotas|Quotas]]  +</nav> 
-    * [[Filesystems:Backup|Backup]] (currently only for Mogon I) +</panel> 
-  * Archiving Data +</col> 
-    * [[archiving:preparation|Preparation Steps prior to Archiving]] +<col xs="12" sm="6" md="4" lg="3"> 
-    * [[archiving:tsm|Archiving Data with TSM]] +<panel type="default" title="Development"> 
 +<nav type="pills" stacked="true"> 
 +  * Scripting Languages 
 +    * [[:start:development:scripting_languages:java|Java]] 
 +    * [[:start:development:scripting_languages:matlab|Matlab]] 
 +    * [[:start:development:scripting_languages:mathematica|Mathematica]] 
 +    * [[:start:development:scripting_languages:julia|Julia]] 
 +    * [[:start:development:scripting_languages:perl|Perl]] 
 +    * [[:start:development:scripting_languages:python|Python]] 
 +    * [[:start:development:scripting_languages:r_bio|R]] 
 +    * [[:start:development:scripting_languages:shells|Shells]] 
 +  * [[:start:development:ides_and_editors|Editors and IDEs]] 
 +  * [[:start:development:monitoring|Monitoring]] 
 +  * [[:start:development:source_code_management|Source Code Management]] 
 +  * Parallelization Libraries 
 +    * [[:start:development:parallelization:parallel_io|Parallel File I/O]] 
 +    * [[:start:development:parallelization:mpi|MPI]] 
 +  * [[:start:development:analysis_and_optimization|Performance Optimization Tools]] 
 +  * [[:start:development:debugging|Debugging Tools]] 
 +</nav> 
 +</panel> 
 +</col> 
 +</grid>
  
  
  
 + 
  
-===== 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]] 
-  * Optimization 
-    * [[vectorization|Vectorization with regard to GCC]] 
- 
-==== 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]]. 
  
  • start.1560243672.txt.gz
  • Last modified: 2019/06/11 11:01
  • by meesters