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start [2019/06/11 11:01]
meesters [Editors / IDEs]
start [2020/04/17 12:05]
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 redesigned 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>​
 +</​col>​
 +</​grid>​
 +<​grid>​
  
-===== Training ​Outreach ​=====+<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]] 
 +</​nav>​ 
 +</​panel>​ 
 +<panel type="​default"​ title="​MOGON-Cluster">​ 
 +<nav type="​pills"​ stacked="​true">​ 
 +  * [[:​start:​mogon_cluster:​access|Access MOGON]] 
 +  * [[:​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|Evaluation]] 
 +</​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]] 
 +</​nav>​ 
 +</​panel>​ 
 +</​col>​ 
 +<col xs="​12"​ sm="​6"​ md="​4"​ lg="​3">​ 
 +<panel type="​default"​ title="​Archiving Data">​ 
 +<nav type="​pills"​ stacked="​true">​ 
 +  * [[:​start:​fs_dm:​archiving:​preparation|Preparation Steps]] 
 +  * [[:​start:​fs_dm:​archiving:​tsm|Archiving Data with TSM]] 
 +  * [[:​start:​fs_dm:​archiving:​irods|Data Management with iRODS]] 
 +</​nav>​ 
 +</​panel>​ 
 +<panel type="​default"​ title="​Software">​ 
 +<callout type="​default"​ title="​General">​ 
 +<nav type="​pills"​ stacked="​true">​ 
 +  * [[:​start:​software:​installation_remarks|How we build Software]]  
 +</​nav>​ 
 +</​callout>​ 
 +<callout type="​default"​ title="​Topical">​ 
 +<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]] 
 +    * [[https://​gaussian.com|Gaussian]] 
 +    * [[https://​www.plumed.org/​|PLUMED]] 
 +    * [[https://​sunqm.github.io/​pyscf/​|PySCF]] 
 +    * [[http://​www.espresso-pp.de/​|ESPResSo++]] 
 +</​nav>​ 
 +</​callout>​ 
 +<callout type="​default"​ title="​Visualization">​ 
 +<nav type="​pills"​ stacked="​true">​ 
 +  * [[:​start:​software:​visualization:​paraview|Paraview]]  
 +</​nav>​ 
 +</​callout>​ 
 +</​panel>​ 
 +</​col>​ 
 +<col xs="​12"​ sm="​6"​ md="​4"​ lg="​3">​ 
 +<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:​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>​
  
-  * [[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 Handling beyond Compute Jobs ==== 
- 
-  * [[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]]  
- 
- 
- 
- 
-===== 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.txt
  • Last modified: 2020/08/05 12:53
  • by jrutte02