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start [2019/10/18 11:44]
meesters [Development on the JGU HPC System(s)]
start [2020/09/08 15:30] (current)
jrutte02
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-====== ​Mogon I & II ======+<callout color="#​c1002a"​ icon="fa fa-power-off"​ title="MOGON I End Of Life">​ 
 +MOGON I will be shut down at 31th September 2020 
 +</​callout>​ 
 +<​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>​
  
-===== Training & Outreach ===== 
  
-  ​[[training_and_outreach:​courses|Courses]] +<alert type="​danger"​ dismiss="​true"​ icon="​fa fa-warning">​**Warning!** Due to changed settings on MOGON as a result of the security incident, many articles may need to be revised.</​alert>​
-  ​[[training_and_outreach:​workshop|HPC-Workshop]] +
-  ​[[training_and_outreach:​ticket_system|Getting Support]] +
-  ​[[training_and_outreach:​FAQ|FAQ]]+
  
-===== Documentation =====+</​col>​ 
 +</​grid>​ 
 +<​grid>​
  
 +<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|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|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]]
 +  * [[:​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">​
 +<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>​
  
-==== 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 Parallelization]] ​ 
-    * [[spark|Apache Spark]] 
-    * [[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]] 
- 
-==== Visualization ==== 
- 
-    * [[visualize_queue:​paraview|Paraview]] 
- 
- 
- 
- 
-===== Development on the JGU HPC System(s) ===== 
- 
-The JGU HPC group supports all kind of HPC development efforts on its systems. For this we provide a variety of tools and services: 
- 
-  * [[development|Overview on Development Tools and Services]] (from Editors over Monitoring to Debugging Tools) 
-  * shortcut -> [[development:​scripting_languages|Scripting Languages]] 
- 
- 
- 
- 
- 
- 
- 
- 
-    ​ 
-===== 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.1571391876.txt.gz
  • Last modified: 2019/10/18 11:44
  • by meesters