diff --git a/Dockerfile b/Dockerfile
index 0999141870c48b88e0f983a51a9e5eec43b38d09..160c23dce89c29cae241af83a6d7b2cde2f2743b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -6,7 +6,7 @@ SHELL ["/bin/bash", "-c"]
# Base #
########
-RUN pip install mkdocs>=1.1.2 mkdocs-material>=7.1.0
+RUN pip install mkdocs>=1.1.2 mkdocs-material>=7.1.0 mkdocs-htmlproofer-plugin==0.8.0
##########
# Linter #
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diff --git a/doc.zih.tu-dresden.de/docs/application/overview.md b/doc.zih.tu-dresden.de/docs/application/overview.md
index ac8a94a3c78eadbd1e18fa5b104169ceb05f5816..df98127158af3af36724cb3f9d20acf483eeb8af 100644
--- a/doc.zih.tu-dresden.de/docs/application/overview.md
+++ b/doc.zih.tu-dresden.de/docs/application/overview.md
@@ -14,14 +14,14 @@ To learn more about applying for a project or a course, check the following page
### Get Access without an existing ZIH Login
-To use the resources, you need a [valid ZIH login][2]. To get a ZIH login and the access to HPC,
-please use the [HPC login application form][3].
+To use the resources, you need a valid ZIH login. To get a ZIH login and the access to HPC,
+please use the [HPC login application form][2].
### Get Access with a valid ZIH Login
When you have a valid ZIH login, there are two possibilities for you: Either the manager or
administrator of a HPC project needs to add you as a member of this project via the
-[manager view](project_management.md#manage-project-members-dis-enable), or you have to
+[manager view](project_management.md), or you have to
[apply for a project](project_request_form.md).
## Acknowledgment in Publications
@@ -33,5 +33,5 @@ publications that are based on granted HPC resources of the TU Dresden.
We provide some [acknowledgment examples](acknowledgement.md) that show you how to do that.
[1]: https://tu-dresden.de/zih/hochleistungsrechnen/zugang
-[2]: https://tu-dresden.de/zih/dienste/service-katalog/zugangsvoraussetzung
+[2]: https://selfservice.zih.tu-dresden.de/index.php/hpclogin/noLogin
[3]: https://selfservice.zih.tu-dresden.de/l/index.php/hpclogin
diff --git a/doc.zih.tu-dresden.de/docs/application/project_request_form_jards.md b/doc.zih.tu-dresden.de/docs/application/project_request_form_jards.md
new file mode 100644
index 0000000000000000000000000000000000000000..0f4d58c82ec000a883b753f924481206784d315b
--- /dev/null
+++ b/doc.zih.tu-dresden.de/docs/application/project_request_form_jards.md
@@ -0,0 +1,431 @@
+# Project Request Form Jards
+
+This page describes the steps to fill the form on
+[https://hpcprojekte.zih.tu-dresden.de/](https://hpcprojekte.zih.tu-dresden.de/application/).
+
+Please be aware of, with the changeover to JARDS, the approval
+period lasts between 4 and 8 weeks. Except for trial projects and courses,
+regular projects are only approved after a positive review.
+
+If you have not already reached the login form through a specialized page,
+here you have an overview of the possible project applications.
+There are technical and scientific reviews of the project applications,
+which vary depending on the type of application.
+
+Since 2021, HPC at universities has been restructured by the NHR network.
+The network consists of nine centers, which operate the systems and offer
+a coordinated consulting service on the methodological competence of scientific HPC.
+The aim is to provide scientists at German universities with computing capacity
+for their research and to strengthen their skills in the efficient use of this resource.
+
+Due to the structuring there are different ways to access [HPC resources](https://doc.zih.tu-dresden.de/jobs_and_resources/hardware_overview/).
+
+## Workflow
+
+There are several steps for a project application ...
+
+- Selection which kind of project proposal is applicable → [Kind of Application](#kind-of-application)
+- Login to the application portal → [Login](#login)
+- Managing one or several applications in the application portal → [Jards Frontend](#jards-frontend)
+- Details for each project application → [Application](#application)
+- Finalize and submit your application → [Finalized Application](#finalized-application)
+
+Afterwards, the submitted application undergoes a technical and scientific
+review and you will be informed about the result in 1 to N work days.
+If a project is granted, you can use the project management portal
+[https://hpcprojekte.zih.tu-dresden.de/](https://hpcprojekte.zih.tu-dresden.de/application/).
+
+All steps for an application are documented in detail below.
+
+### Kind of Application
+
+Since January 2021 ZIH, TU Dresden is a NHR-center (Nationales Hochleistungsrechnen).
+More details can be found in [https://tu-dresden.de/zih/hochleistungsrechnen/nhr-center](https://tu-dresden.de/zih/hochleistungsrechnen/nhr-center).
+
+At ZIH, TU Dresden we have 3 different kinds of application
+for applying for HPC resources: NHR, Saxony and TUD/TIER3.
+
+- [NHR](https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=nhr)
+- [Saxony](https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=saxony)
+- [TUD/Tier3](https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=tier3)
+
+![HPC Project Application][37]
+
+??? abstract "National NHR Application:"
+
+ #### NHR
+
+ This application kind is recommended for:
+
+ * for researchers from all over Germany there is the possibility
+ to apply for HPC resources at the NHR Center of the TU Dresden
+ * for all research projects related to our focus topics
+ * Life Sciences
+ * Earth System Science
+ * Methods for big data and data analysis and management
+ * Machine Learning
+ * Tiered storage architectures and I/O optimization
+ * Performance and energy efficiency analysis and optimization
+ * Further information can be found in [https://tu-dresden.de/zih/hochleistungsrechnen/nhr-center](https://tu-dresden.de/zih/hochleistungsrechnen/nhr-center).
+ If your research topic fits the above focus topics, the application kind 'NHR' is recommended.
+ * for other focuses other NHR centers are available [https://www.nhr-gs.de/ueber-uns/nhr-verein](https://www.nhr-gs.de/ueber-uns/nhr-verein)
+
+ Application Login:
+
+ * [https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=nhr](https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=nhr)
+
+??? abstract "Saxony Application:"
+
+ #### Saxony
+
+ This application is:
+
+ * only applicable for researchers from universities in Saxony.
+ * If you are from Saxony and your project matches the NHR
+ focus topics mentioned above, then either application kind
+ is feasible and there are no differences for the resulting
+ project between the two. We recommend to choose the application kind "NHR".
+ * to apply at the NHR Center of the TU-Dresden for further focus topics
+ which are not covered by an NHR application
+
+ Application Login:
+
+ * [https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=saxony](https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=saxony)
+
+??? abstract "TU Dresden (Tier 3) Application:"
+
+ #### TU Dresden
+
+ This application is:
+
+ * only for researchers at TU Dresden entitled
+ to special HPC contingents, either from TU Dresdens
+ own contribution to the funding of the NHR center or from own HPC funding.
+
+ Application Login:
+
+ * [https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=tier3](https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=tier3)
+
+!!! hint "ScaDS.AI Application:"
+
+ ### ScaDS.AI
+
+ This is a separate kind of application for ScaDS.AI Dresden/Leipzig
+ [https://scads.ai/research/resources-for-research/](https://scads.ai/research/resources-for-research/),
+ only applicable for members, assiciated members and partners of ScaDS.AI.
+ The following application steps are the same as for the others, though.
+
+### Login
+
+!!! info ZIH login
+ For the application of a project no ZIH Login is necessary.
+
+ You only need a ZIH login if you want to access
+ the resources you need for your project.
+
+ If you have a TU Dresden account already, then use the first option. Otherwise use the E-Mail callback option.
+
+#### With TU Dresden Account
+
+If you have a ZIH Login, you can use it in the form.
+
+![Login via TU Dresden Account][2]
+
+#### With E-Mail Callback
+
+If you do not have a ZIH login, you can have a login session emailed to you,
+just enter your e-mail address in the form.
+
+![Login via E-Mail Callback][3]
+
+Click on the link in the mail.
+
+![Callback Mail][4]
+
+### Jards Frontend
+
+After logging in, you will land on the overview page, which is divided into 3 parts.
+
+#### Overview
+
+In the first part you will get information about the site.
+Please pay attention to the title of the page and what project
+type of request you are making.
+
+![Overview][7]
+
+#### Active Applications
+
+In this section you can see all applications that have not yet been sent.
+You can edit these applications at any time.
+![Active Application][6]
+
+##### New Application
+
+To make a new request, press the button at the end of the listing.
+
+!!! hint "Create New Application"
+ Be aware of, when you press the 'New Project Application' button,
+ your project will be assigned a unique project ID.
+ If you are not sure about some details, you can save them and edit them later.
+
+If you decide to create a project proposal for the same project again,
+you will receive a new unique project ID.
+
+![New Application][8]
+
+!!! info New Application Kind
+ Please pay attention to the title of the page and what kind of request you are making.
+
+#### Finalized Applications
+
+Applications that have already been sent can be viewed in this section.
+These applications can no longer be updated and are under
+review and will be activated in case of a positive result.
+
+![Finalized Application][5]
+
+### Application
+
+- [Project Type](#project-type)
+- [Principal Investigator (PI) and Person to Contact (PC)](#principal-investigator-pi-and-person-to-contact-pc)
+- [Resources](#resources)
+- [Project Data](#project-data)
+- [Software](#software)
+- [Data Management](#data-management)
+- [Upload Full Project description](#upload-full-project-description)
+
+No matter which application you submit, the procedure is always identical.
+
+??? abstract "Project Type"
+
+ ### Project Type
+
+ After a new project application is created you can choose a
+
+ * **Trial project**: With a trial projects you can test
+ whether the HPC resources meet your requirements.
+ Trial projects are all applications with up to 3500 CPUh/month
+ or 250 GPUh/month. No detailed project description is required.
+ * **Regular project**: A regular project are for data intensive and
+ compute intensive HPC applications, e.g. FEM, CFD and MD simulations.
+ Regular projects have higher resource requirements than the trial projects.
+ A detailed project description is required in addition to the online application.
+ * **Courses**: Courses is a project type for teaching courses,
+ where you can enable up to 5000 CPUh/month, without additional
+ communication. If there is a higher resource requirement needed,
+ it can be enabled after consultation the HPC support.
+ No detailed project description is required.
+ Please be aware, that in exceptional cases, ZIH reserves the right
+ to request a more detailed abstract.
+
+ The project application differs depending on the type of
+ application - and thus which components of our HPC system - resources are applied for.
+
+ ![Project Type Selection][21]
+
+??? abstract "Principal Investigator (PI) and Person to Contact (PC)"
+
+ ### Principal Investigator (PI) and Person to Contact (PC)
+
+ Choose the principal investigator and the person to contact.
+ On the Button 'change my role ...' below, you can change your organisational part in the project.
+
+ Keep in mind that the principal investigator (PI) has to be:
+
+ * institute director
+ * Professors
+ * research group leader
+
+ ![Principal Investigator (PI)][22]
+
+ If you have not yet submitted an application to us, you will
+ be asked to provide your personal information.
+
+ ![Principal Investigator (PI)][23]
+ ![Principal Investigator (PI)][24]
+
+??? abstract "Resources"
+
+ ### Resources
+
+ Choose the needed resources. Typically, you can choose between GPU and CPU.
+ If you are unsure about some of the detail questions here and below,
+ please provide a rough estimate or your best guess instead of specifying 0 or no data.
+
+ !!! info
+ You can only choose after you have specified a project type.
+
+ For each choosen resource there are some questions after the project data.
+
+ ![Resource Selection][12]
+
+ Questions for CPU resources could be:
+
+ - How much computing time is required for your project in the upcoming
+ compute time period of one year (in core-hours)?
+ - What is your job size and how many cores do you need?
+ - Define your memory: How many GB per core do you need?
+
+ !!! hint "Hint"
+ If you have chosen only CPU resources, please be aware to specify
+ here only resources for pure CPU nodes. Resources needed on accelerators
+ (GPUs) must be specified in the corresponding section. If you like
+ to change your computing time requirements go one slide back.
+
+ ![CPU][13]
+
+ Questions for CPU resources could be:
+
+ - How much computing time is required on GPU nodes for your HPC project (in GPU-hours)?
+ - How many GPU do you use for a single job?
+ - How much GB of memory do you use for your typical job?
+ - Which GPU programming scheme (CUDA, OpenACC, etc.) do you use?
+ - Which software do you deploy on GPUs (own code, third party)?
+
+ !!! hint "Hint"
+ If you have chosen both CPU and GPU resources, but you do not need
+ compute time on GPUs type in 0 here to be able to continue with your
+ project application in Jards.
+
+ ![GPU][14]
+
+??? abstract "Project Data"
+
+ ### Project Data
+
+ In this step, the basic conditions of the project must be specified.
+
+ Depending on the selected project type, these can be different.
+
+ For example:
+
+ - How much time do you plan for your HPC project (add ending date)?
+ - What is your title of your HPC project (max. 250 char)?
+ - Define your keywords to explain your HPC project best.
+ - Please add a short project description (max. 6000 char).
+ - Explain your plans for this granting period (max. 500 char).
+ - Are you doing commissioned research (yes/no)?
+ - Who is sponsoring your HPC project?
+ - Classify your HPC project according to the following main and sub categories.
+ - Which methods (physical, mathematical, numerical, ...) are used?
+ - Which reasons make the use of this supercomputer necessary?
+
+ !!! hint "Commissioned Research"
+ Are you doing commissioned research?
+
+ Commissioned research means direct order by private third parties to the
+ TU Dresden as well as indirect assignments by private third parties on a
+ promoting institution (university , research institution, or similar institutions).
+ All research projects sponsored by public institutions such as state, country DFG,
+ EU etc. are excluded.
+
+ This specification is very important. In the end you must confirm this information
+ in writing. For this purpose, a PDF is generated, which you must send back to us.
+
+ ![Project Data][28]
+ ![Project Data][29]
+ ![Project Data][30]
+
+??? abstract "Software"
+
+ ### Software
+
+ Next you need to specify which software you want to use.
+
+ Here are the following categories, you should answer:
+
+ - Commercial Software Packages
+ - Compilers
+ - Programming Languages
+ - Other packages, not named here.
+ - Use own-developed packages, please name here and provide the links to
+ the open source software.
+ - Parallelization strategy
+
+ !!!hint "Information About Required Software"
+ This is important for us, because we need to see if the software is installed, there is a valid license and it is available under the appropriate architecture. The biggest problem is the imagination of the license writers. We have to abide by these conditions. Even if we try to provide the common HPC software including licenses, not every software vendor offers appropriate licenses.
+
+ ![Software][31]
+ ![Software][32]
+
+??? abstract "Data Management"
+
+ ### Data Management
+
+ The last thing to specify is the I/O behavior. All this information helps us
+ to check and, if necessary, to create the necessary conditions.
+
+ For example:
+
+ * How much memory do you need.
+ * How do your calculations behave (many small files or one big file)?
+ * Fetch data from external? How?
+
+ ![Data][33]
+ ![Data][34]
+
+??? abstract "Upload Full Project description"
+
+ ### Upload Full Project description
+
+ If you are choosing the project type 'Regular project' a
+ detailed project description is needed to complete the application.
+ You can save the application form and add the detailed description later,
+ before submitting and finalize the HPC project application.
+
+ You can find a template on this page:
+ [https://tu-dresden.de/zih/hochleistungsrechnen/zugang/projektantrag?set_language=en](https://tu-dresden.de/zih/hochleistungsrechnen/zugang/projektantrag?set_language=en).
+
+### Finalized Application
+
+The final step is to complete the application process.
+The application is submitted to us and approved for review. Editing is no longer possible.
+
+In the next step you will receive an email with the data of the application
+as a PDF. In it you will find a template for the confirmation of the commissioned research.
+
+![Finalize][18]
+
+!!! danger "Important"
+ Please send the confirmation of commissioned research signed back to us,
+ even if it is not commissioned research.
+
+[1]: misc/application_1.png "Select Application"
+[2]: misc/idm_login.png "Login via TU Dresden Account"
+[3]: misc/email_login.png "Login via E-Mail Callback"
+[4]: misc/email_link.png "Login via E-Mail Callback"
+[5]: misc/finalized_application.png "Finalize"
+[6]: misc/active_application.png
+[7]: misc/overview_application.png
+[8]: misc/new_application.png
+[10]: misc/app_project_type.png "Project Type Selection"
+[11]: misc/app_pi.png "PI Selection"
+[12]: misc/app_resources.png "Resource Selection"
+[13]: misc/app_resource_cpu.png "Resource CPU"
+[14]: misc/app_resource_gpu.png "Resource GPU"
+[15]: misc/app_project_data.png "Project Data"
+[16]: misc/app_software.png "Software"
+[17]: misc/app_data.png "Data"
+[18]: misc/app_finalize.png "Finalize"
+
+[19]: misc/nhr_1a_applicationlist.png
+[20]: misc/nhr_1b_applicationlist.png
+[21]: misc/nhr_2_projecttype.png
+[22]: misc/nhr_3_choose_pi_pc.png
+[23]: misc/nhr_4_data_pi.png
+[24]: misc/nhr_5_data_pc.png
+[25]: misc/nhr_6_resources.png
+[26]: misc/nhr_7a_CPUresources.png
+[27]: misc/nhr_7b_GPUresources.png
+[28]: misc/nhr_8a_project_data.png
+[29]: misc/nhr_8b_project_data.png
+[30]: misc/nhr_8c_project_data.png
+[31]: misc/nhr_9a_software.png
+[32]: misc/nhr_9b_software.png
+[33]: misc/nhr_10a_data_mgmt.png
+[34]: misc/nhr_10b_data_mgmt.png
+[35]: misc/nhr_11_upload_regular.png
+[36]: misc/nhr_11_upload_trial_project.png
+[37]: misc/project_application_small.png
+[38]: misc/project_application.png
diff --git a/doc.zih.tu-dresden.de/docs/application/project_request_form_jards2.md b/doc.zih.tu-dresden.de/docs/application/project_request_form_jards2.md
new file mode 100644
index 0000000000000000000000000000000000000000..a51d6a96d69e5ce9d9dbd1fbd5dd516778ae4b05
--- /dev/null
+++ b/doc.zih.tu-dresden.de/docs/application/project_request_form_jards2.md
@@ -0,0 +1,337 @@
+# Project Request Form Jards
+
+This page describes the steps to fill the form on
+[https://hpcprojekte.zih.tu-dresden.de/](https://hpcprojekte.zih.tu-dresden.de/application/).
+
+If you have not already reached the login form through a specialized page,
+here you have an overview of the possible project applications.
+
+Since 2021, HPC at universities has been restructured by the NHR network.
+The network consists of nine centers, which operate the systems and offer
+a coordinated consulting service on the methodological competence of scientific HPC.
+The aim is to provide scientists at German universities with computing capacity
+for their research and to strengthen their skills in the efficient use of this resource.
+
+Due to the structuring there are different ways to access [HPC resources](https://doc.zih.tu-dresden.de/jobs_and_resources/hardware_overview/).
+
+## Workflow
+
+ ``` mermaid
+ graph LR
+ A(NHR Type) --> |National| B(Login);
+ A --> |Saxony| B;
+ A --> |TU Dresden| B;
+ B --> |ZIH Login| H(Jards Frontend);
+ B --> |E-Mail Callback| H;
+ J --> |show| J;
+ J--> |copy| J;
+ H --> |create| J(Application);
+ J --> |edit| J;
+ J --> | submit | L(Finalized Application);
+
+ click A href "http://localhost:8000/application/project_request_form_jards/#application-type" _self;
+ click E href "http://localhost:8000/application/project_request_form_jards/#nhr" _self;
+ click F href "http://localhost:8000/application/project_request_form_jards/#saxony" _self;
+ click G href "http://localhost:8000/application/project_request_form_jards/#tu-dresden" _self;
+ click B href "http://localhost:8000/application/project_request_form_jards/#login" _self;
+ click C href "http://localhost:8000/application/project_request_form_jards/#with-tu-dresden-idm-account" _self;
+ click D href "http://localhost:8000/application/project_request_form_jards/#with-tu-dresden-idm-account" _self;
+ ```
+
+{: align="center"}
+
+=== "NHR Type"
+
+ ### NHR Type
+
+ Since January 2021 ZIH, TU Dresden is a NHR-center (Nationales Hochleistungsrechnen).
+ More details can be found in [https://tu-dresden.de/zih/hochleistungsrechnen/nhr-center](https://tu-dresden.de/zih/hochleistungsrechnen/nhr-center).
+
+ At ZIH, TU Dresden we have 3 different application categories for applying for HPC resources: NHR, Saxony and TUD/TIER3.
+
+ ![Picture 1: Select Application][1]
+ {: align="center"}
+
+ ??? abstract "National NHR Application:"
+
+ #### NHR
+
+ This application is:
+
+ * for researchers from all over Germany there is the possibility
+ to apply for HPC resources at the NHR Center of the TU Dresden
+ * for all research projects related to our focus topics
+ [https://tu-dresden.de/zih/hochleistungsrechnen/nhr-center](https://tu-dresden.de/zih/hochleistungsrechnen/nhr-center), application to our NHR center is recommended
+ * for other focuses other NHR centers are available [https://www.nhr-gs.de/ueber-uns/nhr-verein](https://www.nhr-gs.de/ueber-uns/nhr-verein)
+
+ Application Login:
+
+ * [https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=nhr](https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=nhr)
+
+ ??? abstract "Saxony Application:"
+
+ #### Saxony
+
+ This application is:
+
+ * for researchers from Saxon universities
+ * to apply at the NHR Center of the TU-Dresden for further focus topics
+ which are not covered by an NHR application
+
+ Application Login:
+
+ * [https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=saxony](https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=saxony)
+
+ ??? abstract "TU Dresden (Tier 3) Application:"
+
+ #### TU Dresden
+
+ This application is:
+
+ * for researchers of the TU Dresden with entitlement to special HPC contingents of the TU Dresden.
+ (This includes, for example, appointment commitments)
+
+ Application Login:
+
+ * [https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=tier3](https://hpcprojekte.zih.tu-dresden.de/application/login.php?appkind=tier3)
+
+ !!! hint "ScaDS.AI Application:"
+
+ ### ScaDS.AI
+
+ ScaDS.AI is not a NHR Type. If you need an application for ScaDS.AI, you know how.
+
+=== "Login"
+
+ ### Login
+
+ !!! info ZIH login
+ For the application of a project no ZIH Login is necessary. Only if you want to use the resources yourself, a login is required: [https://tu-dresden.de/zih/hochleistungsrechnen/hpc](https://tu-dresden.de/zih/hochleistungsrechnen/hpc).
+
+
+ #### With TU Dresden Account
+
+ If you have a ZIH Login, you can use it in the form.
+
+ ![Login via TU Dresden Account][2]
+
+ #### With E-Mail Callback
+
+ If you do not have a ZIH login, you can have a login session emailed to you, just enter your e-mail address in the form.
+
+ ![Login via E-Mail Callback][3]
+
+ Click on the link in the mail.
+
+ ![Calback Mail][4]
+
+=== "Jards Frontend"
+
+ ### Jards Frontend
+
+ After logging in, you will land on the overview page, which is divided into 3 parts.
+
+ #### Overview
+
+ In the first part you will get information about the site. Please pay attention to the title of the page and what type of request you are making.
+
+ ![Overview][7]
+
+ #### Active Applications
+
+ In this section you can see all applications that have not yet been sent. You can edit these applications at any time.
+ ![Active Application][6]
+
+ ##### New Application
+
+ To make a new request, press the button at the end of the listing.
+
+ !!! hint "Create New Application"
+ Be aware of, when you press the 'New Project Application' button, your project will be assigned a unique project ID.
+ If you are not sure about some details, you can save them and edit them later.
+
+ If you decide to create a project proposal for the same project again, you will receive a new unique project ID.
+
+ ![New Application][8]
+
+ !!! info New Application Type
+ Please pay attention to the title of the page and what type of request you are making
+
+ #### Finalized Applications
+
+ Applications that have already been sent can be viewed in this section. These applications can no longer be updated and are under review and will be activated in case of a positive result.
+
+ ![Finalized Application][5]
+
+=== "Application"
+
+ ### Application
+
+ No matter which application you submit, the procedure is always identical.
+
+ ??? abstract "Project Type"
+
+ Choose the project type. Please note the information about the project types on the page.
+
+ The project application differs depending on the type of application - and thus which components of our HPC system - resources are applied for.
+
+ ![Project Type Selection][10]
+
+ ??? abstract "Principal Investigator (PI) and Person to Contact (PC)"
+
+ Choose the principal investigator and the person to contact. On the Button 'change my role ...' below, you can change your organisational part in the project.
+
+ Keep in mind that the principal investigator (PI) has to be:
+
+ * institute director
+ * chair holder
+ * research group leader
+
+ ![Principal Investigator (PI)][11]
+
+ If you have not yet submitted an application to us, you will be asked to provide your information.
+
+ ??? abstract "Resources"
+ Choose the needed resources. Typically, you can choose between GPU and CPU.
+
+ !!! info
+ You can only choose after you have specified a project type.
+
+ For each choosen resource there are some questions after the project data.
+
+ ![Resource Selection][12]
+
+ Questions for CPU resources could be:
+
+ - How much computing time is required for your project in the upcoming compute time period of one year (in core-hours)?
+ - What is your job size and how many cores do you need?
+ - Define your memory: How many GB per core do you need?
+
+ !!! hint "Hint"
+ If you have chosen only CPU resources, please be aware to specify here only resources for pure CPU nodes. Resources needed on accelerators (GPUs) must be specified in the corresponding section. If you like to change your computing time requirements go one slide back.
+
+ ![CPU][13]
+
+ Questions for CPU resources could be:
+
+ - How much computing time is required on GPU nodes for your HPC project (in GPU-hours)?
+ - How many GPU do you use for a single job?
+ - How much GB of memory do you use for your typical job?
+ - Which GPU programming scheme (CUDA, OpenACC, etc.) do you use?
+ - Which software do you deploy on GPUs (own code, third party)?
+
+ !!! hint "Hint"
+ If you have chosen both CPU and GPU resources, but you do not need compute time on GPUs type in 0 here to be able to continue with your project application in Jards.
+
+ ![GPU][14]
+
+ ??? abstract "Project Data"
+ In this step, the basic conditions of the project must be specified.
+
+ Depending on the selected project type, these can be different.
+
+ For example:
+
+ - How much time do you plan for your HPC project (add ending date)?
+ - What is your title of your HPC project (max. 250 char)?
+ - Define your keywords to explain your HPC project best.
+ - Please add a short project description (max. 6000 char).
+ - Explain your plans for this granting period (max. 500 char).
+ - Are you doing commissioned research (yes/no)?
+ - Who is sponsoring your HPC project?
+ - Classify your HPC project according to the following main and sub categories.
+ - Which methods (physical, mathematical, numerical, ...) are used?
+ - Which reasons make the use of this supercomputer necessary?
+
+ !!! hint "Commissioned Research"
+ Are you doing commissioned research?
+
+ Commissioned research means direct order by private third parties to the TU Dresden as well as indirect assignments by private third parties on a promoting institution (university , research institution, or similar institutions). All research projects sponsored by public institutions such as state, country DFG , EU etc. are excluded.
+
+ This specification is very important. In the end you must confirm this information in writing. For this purpose, a PDF is generated, which you must send back to us.
+
+ ![Project Data][15]
+
+ ??? abstract "Software"
+ Next you need to specify which software you want to use.
+
+ Here are the following categories, you should answer:
+
+ - Commercial Software Packages
+ - Compilers
+ - Programming Languages
+ - Other packages, not named here.
+ - Use own-developed packages, please name here and provide the links to the open source software.
+ - Parallelization strategy
+
+ !!!hint "Information About Required Software"
+ This is important for us, because we need to see if the software is installed, there is a valid license and it is available under the appropriate architecture. The biggest problem is the imagination of the license writers. We have to abide by these conditions. Even if we try to provide the common HPC software including licenses, not every software vendor offers appropriate licenses.
+
+ ![Software][16]
+
+ ??? abstract "Data Management"
+ The last thing to specify is the I/O behavior. All this information helps us to check and, if necessary, to create the necessary conditions.
+
+ For example:
+
+ * How much memory do you need.
+ * How do your calculations behave (many small files or one big file)?
+ * Fetch data from external? How?
+
+ ![Data][17]
+
+ ??? abstract "Upload Full Projectdescription"
+ On some project types a detailed project description is needed to complete the application.
+
+ You can find a Template on this page:
+ [https://tu-dresden.de/zih/hochleistungsrechnen/zugang/projektantrag?set_language=en](https://tu-dresden.de/zih/hochleistungsrechnen/zugang/projektantrag?set_language=en).
+
+=== "Finalized Application"
+
+ ### Finalized Application
+
+ The final step is to complete the application process. The application is submitted to us and approved for review. Editing is no longer possible.
+
+ In the next step you will receive an email with the data of the application as a PDF. In it you will find a template for the confirmation of the commissioned research.
+
+ ![Finalize][18]
+
+ !!! danger "Important"
+ Please send the confirmation of commissioned research signed back to us, even if it is not commissioned research.
+
+[1]: misc/application_1.png "Select Application"
+[2]: misc/idm_login.png "Login via TU Dresden Account"
+[3]: misc/email_login.png "Login via E-Mail Callback"
+[4]: misc/email_link.png "Login via E-Mail Callback"
+[5]: misc/finalized_application.png "Finalize"
+[6]: misc/active_application.png
+[7]: misc/overview_application.png
+[8]: misc/new_application.png
+[10]: misc/app_project_type.png "Project Type Selection"
+[11]: misc/app_pi.png "PI Selection"
+[12]: misc/app_resources.png "Resource Selection"
+[13]: misc/app_resource_cpu.png "Resource CPU"
+[14]: misc/app_resource_gpu.png "Resource GPU"
+[15]: misc/app_project_data.png "Project Data"
+[16]: misc/app_software.png "Software"
+[17]: misc/app_data.png "Data"
+[18]: misc/app_finalize.png "Finalize"
+
+[19]: misc/nhr_1a_applicationlist.png
+[20]: misc/nhr_1b_applicationlist.png
+[21]: misc/nhr_2_projecttype.png
+[22]: misc/nhr_3_choose_pi_pc.png
+[23]: misc/nhr_4_data_pi.png
+[24]: misc/nhr_5_data_pc.png
+[25]: misc/nhr_6_resources.png
+[26]: misc/nhr_7a_CPUresources.png
+[27]: misc/nhr_7b_GPUresources.png
+[28]: misc/nhr_8a_project_data.png
+[29]: misc/nhr_8b_project_data.png
+[30]: misc/nhr_8c_project_data.png
+[31]: misc/nhr_9a_software.png
+[32]: misc/nhr_9b_software.png
+[33]: misc/nhr_10a_data_mgmt.png
+[34]: misc/nhr_10b_data_mgmt.png
+[35]: misc/nhr_11_upload_regular.png
+[36]: misc/nhr_11_upload_trial_project.png
diff --git a/doc.zih.tu-dresden.de/docs/archive/bioinformatics.md b/doc.zih.tu-dresden.de/docs/archive/bioinformatics.md
index 0a8a337417e5cfe7d5c78166d85254cc71229ef7..7d2335d93c4e095552b323cc1e09f42727d9db5e 100644
--- a/doc.zih.tu-dresden.de/docs/archive/bioinformatics.md
+++ b/doc.zih.tu-dresden.de/docs/archive/bioinformatics.md
@@ -6,10 +6,10 @@
| Software | Module |
|-----------------------------------|-------------------------------------------|
-| **[Infernal](#Infernal)** | infernal |
-| **[OpenProspect](#OpenProspect)** | openprospect, openprospect/885-mpi |
-| **[Phylip](#Phylip)** | phylip |
-| **[PhyML](#PhyML)** | phyml/2.4.4, phyml/2.4.5-mpi, phyml/3.0.0 |
+| **[Infernal](#infernal)** | infernal |
+| **[OpenProspect](#openprospect)** | openprospect, openprospect/885-mpi |
+| **[Phylip](#phylip)** | phylip |
+| **[PhyML](#phyml)** | phyml/2.4.4, phyml/2.4.5-mpi, phyml/3.0.0 |
## Infernal
diff --git a/doc.zih.tu-dresden.de/docs/archive/overview.md b/doc.zih.tu-dresden.de/docs/archive/overview.md
index 7600ef01e81d7f623f616d28d70abbf73cb07ed2..dfcb393a253c916a86ab21649aa75eb509ee2862 100644
--- a/doc.zih.tu-dresden.de/docs/archive/overview.md
+++ b/doc.zih.tu-dresden.de/docs/archive/overview.md
@@ -3,4 +3,4 @@
A warm welcome to the **archive**. You probably got here by following a link from within the compendium
or by purpose.
The archive holds outdated documentation for future reference.
-Hence, documentation in the archive, is not further updated.
+Hence, documentation in the archive is not further updated.
diff --git a/doc.zih.tu-dresden.de/docs/archive/systems_switched_off.md b/doc.zih.tu-dresden.de/docs/archive/systems_switched_off.md
index c4f9890ac3ad36580c617b6fb5292cb0b1ceffcb..0a9a50bb72c25b6920d41a66d2828ec57cd4c7b1 100644
--- a/doc.zih.tu-dresden.de/docs/archive/systems_switched_off.md
+++ b/doc.zih.tu-dresden.de/docs/archive/systems_switched_off.md
@@ -10,3 +10,29 @@ Documentation on former systems for future reference can be found on the followi
- [Windows-HPC-Server Titan](system_titan.md)
- [PC-Cluster Triton](system_triton.md)
- [Shared-Memory-System Venus](system_venus.md)
+
+## Historical Overview
+
+| Year | System |
+|------|--------|
+| 1968 | Zeiss-Rechenautomat Nr. 1 (ZRA1) Performance: 150 to 200 instructions/s, 4096 storage cells with 48 bit each (magnetic drum) |
+| 1970 | Commissioning of large stand-alone computers, coupled stand-alone computers and terminals (BESM, ESER) |
+| 1976 | Computer network DELTA and graphic workstations |
+| 1981 | Deployment of the first microcomputers; experimental testing of local area networks (LAN) |
+| 1986 | Workstation computers replace mechanical devices; the first PC pools for teaching and studying are set up |
+| 1991 | Short-term operation of used mainframe computers |
+| 1993 | VP200-EX (857 MFlop/s Peak) |
+| 1996 | Development of infrastructure on the TU campus |
+| 1997 | SGI Origin2000 (21,8 GFlop/s, 56 CPUs, 17 GB RAM, 350 GB disk capacity)|
+| 1998 | Cray T3E (38,4 GFlop/s, 64 CPUs, 8 GB RAM, 100 GB disk capacity)|
+| 2001/02 | SGI Origin3800 (51,2 + 102,4 GFlop/s, 64 + 128 CPUs, 64 + 64 GB RAM, 790 GB disk capacity)|
+| 2004 | Itanium-Cluster Castillo|
+| 2005/06 | Hochleistungsrechner/Speicherkomplex: <br/> SGI Altix 4700: 13 TFlop/s, 6,5 TB RAM <br/> PC-Farm: 13 TFlop/s, 5,5 TB RAM <br/> SAN capacity: 136 TB <br/> Tape archive: 1 PB, 2500 tapes |
+| 2007 | Setup PC-SAN <br/> NEC SX6: 72 GFlop/s |
+| 2008 | Microsoft HPC-System |
+| 2010 | IBM-Cluster iDataPlex |
+| 2012 | GPU-Cluster <br/> HPC-Cluster Atlas: 50 TFlop/s Peak, 13 TB RAM |
+| 2012/13| SGI UV 2000: 10,6 TFlop/s Peak, 8 TB RAM |
+| 2013 | HPC-Cluster Taurus (HRSK-II): 135 TFlop/s Peak, 18 TB RAM |
+| 2015 | HRSK-II Extension: 1,64 PFlop/s und 139 TB RAM |
+| 2017/18| HPC-DA (HRSK-II Extension) |
diff --git a/doc.zih.tu-dresden.de/docs/contrib/content_rules.md b/doc.zih.tu-dresden.de/docs/contrib/content_rules.md
index 358cd153282e3bdf4240f144bbafa618151f383d..9e4d1b46103def4b8333a4cb451a2f2695f1ef08 100644
--- a/doc.zih.tu-dresden.de/docs/contrib/content_rules.md
+++ b/doc.zih.tu-dresden.de/docs/contrib/content_rules.md
@@ -57,13 +57,24 @@ actively used, especially for longer code examples, warnings, tips, important in
should be highlighted, etc. Code examples, longer than half screen height should collapsed
(and indented):
-??? example
+??? "Collapsed example"
```Bash
[...]
# very long example here
[...]
```
+### Brief How-To on Markdown
+
+| Purpose | Markdown | Rendered HTML |
+|---|---|---|
+| Bold text | `**Bold Text**` | **Bold Text** |
+| Italic text | `*Italic Text*` | *Italic Text* |
+| Headings | `# Level 1`, `## Level 2`, `### Level 3`, ... | |
+| External link | `[website of TU Dresden](https://tu-dresden.de)` | [website of TU Dresden](https://tu-dresden.de) |
+| Internal link | `[Slurm page](../jobs_and_resources/slurm.md)` | [Slurm page](../jobs_and_resources/slurm.md)|
+| Internal link to section | `[section on batch jobs](../jobs_and_resources/slurm.md#batch-jobs)` | [section on batch jobs](../jobs_and_resources/slurm.md#batch-jobs) |
+
## Writing Style
* Avoid using tabs both in markdown files and in `mkdocs.yaml`. Type spaces instead.
@@ -130,7 +141,7 @@ We follow this rules regarding prompts:
* **Always use a prompt**, even there is no output provided for the shown command.
* All code blocks should use long parameter names (e.g. Slurm parameters), if available.
* All code blocks which specify some general command templates, e.g. containing `<` and `>`
- (see [Placeholders](#mark-placeholders)), should use `bash` for the code block. Additionally,
+ (see [Placeholders](#placeholders)), should use `bash` for the code block. Additionally,
an example invocation, perhaps with output, should be given with the normal `console` code block.
See also [Code Block description below](#code-blocks-and-syntax-highlighting).
* Using some magic, the prompt as well as the output is identified and will not be copied!
@@ -157,7 +168,7 @@ bar
Make sure that shell session and console code blocks are executable on the login nodes of HPC system.
-Command templates use [Placeholders](#mark-placeholders) to mark replaceable code parts. Command
+Command templates use [Placeholders](#placeholders) to mark replaceable code parts. Command
templates should give a general idea of invocation and thus, do not contain any output. Use a
`bash` code block followed by an invocation example (with `console`):
@@ -258,6 +269,10 @@ drwxr-xr-x 3 marie p_number_crunch 4096 Feb 12 2020 data
-rw-rw---- 1 marie p_number_crunch 4096 Jan 24 2020 readme.md
```
+### Placeholders
+
+TODO!
+
## Mark Omissions
If showing only a snippet of a long output, omissions are marked with `[...]`.
diff --git a/doc.zih.tu-dresden.de/docs/contrib/contribute_container.md b/doc.zih.tu-dresden.de/docs/contrib/contribute_container.md
index 6e6ac44cf53b56d3b7a96959314117642d3ed06b..f0d5fe56c8835867bda545948ad7ae0f6bbd09c5 100644
--- a/doc.zih.tu-dresden.de/docs/contrib/contribute_container.md
+++ b/doc.zih.tu-dresden.de/docs/contrib/contribute_container.md
@@ -200,9 +200,12 @@ wikiscript doc.zih.tu-dresden.de/util/check-no-floating.sh doc.zih.tu-dresden.de
#### Link Checker
-No one likes dead links. Therefore, we check the internal and external links within the markdown
-source files. To check a single file, e.g.
-`doc.zih.tu-dresden.de/docs/software/big_data_frameworks.md`, use:
+!!! quote "Unknown programmer"
+
+ No one likes dead links.
+
+Therefore, we check the internal and external links within the markdown source files. To check a
+single file, e.g. `doc.zih.tu-dresden.de/docs/software/big_data_frameworks.md`, use:
```bash
wikiscript doc.zih.tu-dresden.de/util/check-links.sh docs/software/big_data_frameworks.md
diff --git a/doc.zih.tu-dresden.de/docs/data_lifecycle/overview.md b/doc.zih.tu-dresden.de/docs/data_lifecycle/overview.md
index 1b5561db6c93052bd4ee68fc119ac796e0a3c4c9..6aca684354ab9beb0b0f338c86f0524bf9827e48 100644
--- a/doc.zih.tu-dresden.de/docs/data_lifecycle/overview.md
+++ b/doc.zih.tu-dresden.de/docs/data_lifecycle/overview.md
@@ -35,7 +35,7 @@ filesystems.
!!! hint "Recommendations to choose of storage system"
* For data that seldom changes but consumes a lot of space, the
- [warm_archive](file_systems.md#warm_archive) can be used.
+ [warm_archive](warm_archive.md) can be used.
(Note that this is mounted **read-only** on the compute nodes).
* For a series of calculations that works on the same data please use a `scratch` based
[workspace](workspaces.md).
diff --git a/doc.zih.tu-dresden.de/docs/data_lifecycle/workspaces.md b/doc.zih.tu-dresden.de/docs/data_lifecycle/workspaces.md
index 6180e5db831c8faf69a8752247ad5b8ee5ef6313..141ccef84a8ffe098e42ab9bea02afd560590901 100644
--- a/doc.zih.tu-dresden.de/docs/data_lifecycle/workspaces.md
+++ b/doc.zih.tu-dresden.de/docs/data_lifecycle/workspaces.md
@@ -99,13 +99,13 @@ days with an email reminder for 7 days before the expiration.
The lifetime of a workspace is finite. Different filesystems (storage systems) have different
maximum durations. A workspace can be extended multiple times, depending on the filesystem.
-| Filesystem (use with parameter `-F`) | Duration, days | Extensions | Remarks |
-|:------------------------------------:|:----------:|:-------:|:-----------------------------------:|
-| `ssd` | 30 | 2 | High-IOPS filesystem (`/lustre/ssd`, symbolic link: `/ssd`) on SSDs. |
-| `beegfs_global0` (deprecated) | 30 | 2 | High-IOPS filesystem (`/beegfs/global0`) on NVMes. |
-| `beegfs` | 30 | 2 | High-IOPS filesystem (`/beegfs`) on NVMes. |
-| `scratch` | 100 | 10 | Scratch filesystem (`/lustre/ssd`, symbolic link: `/scratch`) with high streaming bandwidth, based on spinning disks |
-| `warm_archive` | 365 | 2 | Capacity filesystem based on spinning disks |
+| Filesystem (use with parameter `-F`) | Duration, days | Extensions | [Filesystem Feature](../jobs_and_resources/slurm.md#filesystem-features) | Remarks |
+|:-------------------------------------|---------------:|-----------:|:-------------------------------------------------------------------------|:--------|
+| `ssd` | 30 | 2 | `fs_lustre_ssd` | High-IOPS filesystem (`/lustre/ssd`, symbolic link: `/ssd`) on SSDs. |
+| `beegfs_global0` (deprecated) | 30 | 2 | `fs_beegfs_global0` | High-IOPS filesystem (`/beegfs/global0`) on NVMes. |
+| `beegfs` | 30 | 2 | `fs_beegfs` | High-IOPS filesystem (`/beegfs`) on NVMes. |
+| `scratch` | 100 | 10 | `fs_lustre_scratch2` | Scratch filesystem (`/lustre/ssd`, symbolic link: `/scratch`) with high streaming bandwidth, based on spinning disks |
+| `warm_archive` | 365 | 2 | `fs_warm_archive_ws` | Capacity filesystem based on spinning disks |
To extent your workspace use the following command:
diff --git a/doc.zih.tu-dresden.de/docs/data_transfer/export_nodes.md b/doc.zih.tu-dresden.de/docs/data_transfer/export_nodes.md
index 5e4abf29b8b90f560fcd6dbbebbb2541bb76ae57..b4a22c95e3193bc9ff1a7c43b107fe5f7f74f953 100644
--- a/doc.zih.tu-dresden.de/docs/data_transfer/export_nodes.md
+++ b/doc.zih.tu-dresden.de/docs/data_transfer/export_nodes.md
@@ -137,7 +137,7 @@ the local machine.
Windows 10 (1809 and higher) comes with a
[built-in OpenSSH support](https://docs.microsoft.com/en-us/windows-server/administration/openssh/openssh_overview)
-including the above described [SCP](#SCP) and [SFTP](#SFTP).
+including the above described [SCP](#scp) and [SFTP](#sftp).
### GUI - Using WinSCP
diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/checkpoint_restart.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/checkpoint_restart.md
index 180ed1d62febd311fd5cddd739d4f086825bc5b7..f9aca1755f7f4db883d74b386791b88ffb0fdf28 100644
--- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/checkpoint_restart.md
+++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/checkpoint_restart.md
@@ -49,7 +49,7 @@ make it easier to utilize DMTCP together with Slurm.
## Using w.r.t. Chain Jobs
For long-running jobs that you wish to split into multiple shorter jobs
-([chain jobs](../jobs_and_resources/slurm.md#chain-jobs)), thereby enabling the job scheduler to
+([chain jobs](slurm_examples.md#chain-jobs)), thereby enabling the job scheduler to
fill the cluster much more efficiently and also providing some level of fault-tolerance, we have
written a script that automatically creates a number of jobs for your desired runtime and adds the
checkpoint/restart bits transparently to your batch script. You just have to specify the targeted
diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/overview.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/overview.md
index 1a96fc97145d5ee5587f2b9b216ffba004f4f9d8..d3e9674ced87e57dc6f45ccafccd71383c86d921 100644
--- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/overview.md
+++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/overview.md
@@ -6,9 +6,10 @@ research environment especially in the area of data analytics and machine learni
processing extremely large data sets. Moreover it is also a perfect platform for highly scalable,
data-intensive and compute-intensive applications.
-With shared [login nodes](#login-nodes) and [filesystems](../data_lifecycle/file_systems.md) our
-HPC system enables users to easily switch between [the components](hardware_overview.md), each
-specialized for different application scenarios.
+With shared [login nodes](hardware_overview.md#login-nodes) and
+[filesystems](../data_lifecycle/file_systems.md) our HPC system enables users to easily switch
+between [the components](hardware_overview.md), each specialized for different application
+scenarios.
When log in to ZIH systems, you are placed on a login node where you can
[manage data life cycle](../data_lifecycle/overview.md),
diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md
index f7456662f5ca54887b20b075e58dd25517aa3c96..2ba282a77bff4ff03a0c5ba92e4ef1e19494c669 100644
--- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md
+++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md
@@ -428,13 +428,13 @@ constraints, please refer to the [Slurm documentation](https://slurm.schedmd.com
A feature `fs_*` is active if a certain filesystem is mounted and available on a node. Access to
these filesystems are tested every few minutes on each node and the Slurm features set accordingly.
-| Feature | Description |
-|:-------------------|:---------------------------------------------------------------------|
-| `fs_lustre_scratch2` | `/scratch` mounted read-write (mount point is `/lustre/scratch2`) |
-| `fs_lustre_ssd` | `/ssd` mounted read-write (mount point is `/lustre/ssd`) |
-| `fs_warm_archive_ws` | `/warm_archive/ws` mounted read-only |
-| `fs_beegfs_global0` | `/beegfs/global0` mounted read-write |
-| `fs_beegfs` | `/beegfs` mounted read-write |
+| Feature | Description | [Workspace Name](../data_lifecycle/workspaces.md#extension-of-a-workspace) |
+|:---------------------|:-------------------------------------------------------------------|:---------------------------------------------------------------------------|
+| `fs_lustre_scratch2` | `/scratch` mounted read-write (mount point is `/lustre/scratch2`) | `scratch` |
+| `fs_lustre_ssd` | `/ssd` mounted read-write (mount point is `/lustre/ssd`) | `ssd` |
+| `fs_warm_archive_ws` | `/warm_archive/ws` mounted read-only | `warm_archive` |
+| `fs_beegfs_global0` | `/beegfs/global0` mounted read-write | `beegfs_global0` |
+| `fs_beegfs` | `/beegfs` mounted read-write | `beegfs` |
For certain projects, specific filesystems are provided. For those,
additional features are available, like `fs_beegfs_<projectname>`.
diff --git a/doc.zih.tu-dresden.de/docs/software/containers.md b/doc.zih.tu-dresden.de/docs/software/containers.md
index be74caec03c6ffcf098eade46f4c3adb313f8754..cca62479279afef568fbd69c3e0c6ecc56120e1a 100644
--- a/doc.zih.tu-dresden.de/docs/software/containers.md
+++ b/doc.zih.tu-dresden.de/docs/software/containers.md
@@ -33,7 +33,7 @@ environment.
However, new containers can be created on your local workstation and moved to ZIH systems for
execution. Follow the instructions for [locally installing Singularity](#local-installation) and
[container creation](#container-creation). Moreover, existing Docker container can easily be
-converted, see [Import a docker container](#importing-a-docker-container).
+converted, see [Import a docker container](#import-a-docker-container).
If you are already familiar with Singularity, you might be more interested in our [singularity
recipes and hints](singularity_recipe_hints.md).
diff --git a/doc.zih.tu-dresden.de/docs/software/data_analytics_with_r.md b/doc.zih.tu-dresden.de/docs/software/data_analytics_with_r.md
index 1f6be0614fc728f88212a5192fb1b11277ac8454..c7334d918cdba1ff5e97c2f4cd0ea3b788b2c26d 100644
--- a/doc.zih.tu-dresden.de/docs/software/data_analytics_with_r.md
+++ b/doc.zih.tu-dresden.de/docs/software/data_analytics_with_r.md
@@ -260,7 +260,7 @@ is limited to the number of cores on a single node. The maximum number of cores
be found in our [hardware documentation](../jobs_and_resources/hardware_overview.md).
Submitting a multicore R job to Slurm is very similar to submitting an
-[OpenMP Job](../jobs_and_resources/slurm.md#binding-and-distribution-of-tasks),
+[OpenMP Job](../jobs_and_resources/binding_and_distribution_of_tasks.md),
since both are running multicore jobs on a **single** node. Below is an example:
```Bash
@@ -292,7 +292,7 @@ This way of the R parallelism uses the
[Rmpi](http://cran.r-project.org/web/packages/Rmpi/index.html) package and the
[MPI](https://en.wikipedia.org/wiki/Message_Passing_Interface) (Message Passing Interface) as a
"back-end" for its parallel operations. The MPI-based job in R is very similar to submitting an
-[MPI Job](../jobs_and_resources/slurm.md#binding-and-distribution-of-tasks) since both are running
+[MPI Job](../jobs_and_resources/binding_and_distribution_of_tasks.md) since both are running
multicore jobs on multiple nodes. Below is an example of running R script with the Rmpi on the ZIH
system:
diff --git a/doc.zih.tu-dresden.de/docs/software/overview.md b/doc.zih.tu-dresden.de/docs/software/overview.md
index 9d2d86d7c06989acfcb9415f908fc1453538b6a8..2c560c30951ae3ec3419e01a19ce8716c8d441da 100644
--- a/doc.zih.tu-dresden.de/docs/software/overview.md
+++ b/doc.zih.tu-dresden.de/docs/software/overview.md
@@ -12,7 +12,7 @@ so called dotfiles in your home directory, e.g., `~/.bashrc` or `~/.bash_profile
## Software Environment
There are different options to work with software on ZIH systems: [modules](#modules),
-[Jupyter Notebook](#jupyternotebook) and [containers](#containers). Brief descriptions and related
+[Jupyter Notebook](#jupyter-notebook) and [containers](#containers). Brief descriptions and related
links on these options are provided below.
!!! note
diff --git a/doc.zih.tu-dresden.de/docs/software/python_virtual_environments.md b/doc.zih.tu-dresden.de/docs/software/python_virtual_environments.md
index 13b623174f21016084917fb2cd424b500727e5f3..a999c5596693a25c90bfd74c108551001c2294e8 100644
--- a/doc.zih.tu-dresden.de/docs/software/python_virtual_environments.md
+++ b/doc.zih.tu-dresden.de/docs/software/python_virtual_environments.md
@@ -66,6 +66,37 @@ the environment as follows:
(env) marie@compute$ deactivate #Leave the virtual environment
```
+??? example
+
+ This is an example on partition Alpha. The example creates a conda virtual environment, and
+ installs the package `torchvision` with conda.
+ ```console
+ marie@login$ srun --partition=alpha-interactive --nodes=1 --gres=gpu:1 --time=01:00:00 --pty bash
+ marie@alpha$ ws_allocate -F scratch my_python_virtualenv 100 # use a workspace for the environment
+ marie@alpha$ cd /scratch/ws/1/marie-my_python_virtualenv
+ marie@alpha$ module load modenv/hiera GCC/10.2.0 CUDA/11.1.1 OpenMPI/4.0.5 PyTorch/1.9.0
+ Module GCC/10.2.0, CUDA/11.1.1, OpenMPI/4.0.5, PyTorch/1.9.0 and 54 dependencies loaded.
+ marie@alpha$ which python
+ /sw/installed/Python/3.8.6-GCCcore-10.2.0/bin/python
+ marie@alpha$ pip list
+ [...]
+ marie@alpha$ virtualenv --system-site-packages my-torch-env
+ created virtual environment CPython3.8.6.final.0-64 in 42960ms
+ creator CPython3Posix(dest=[...]/my-torch-env, clear=False, global=True)
+ seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=~/.local/share/virtualenv)
+ added seed packages: pip==21.1.3, setuptools==57.2.0, wheel==0.36.2
+ activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator
+ marie@alpha$ source my-torch-env/bin/activate
+ (my-torch-env) marie@alpha$ pip install torchvision==0.10.0
+ [...]
+ Installing collected packages: torchvision==0.10.0
+ Successfully installed torchvision-0.10.0
+ [...]
+ (my-torch-env) marie@alpha$ python -c "import torchvision; print(torchvision.__version__)"
+ 0.10.0+cu102
+ (my-torch-env) marie@alpha$ deactivate
+ ```
+
### Persistence of Python Virtual Environment
To persist a virtualenv, you can store the names and versions of installed
@@ -134,34 +165,41 @@ can deactivate the conda environment as follows:
(conda-env) marie@compute$ conda deactivate #Leave the virtual environment
```
+!!! warning
+ When installing conda packages via `conda install`, ensure to have enough main memory requested
+ in your job allocation.
+
+!!! hint
+ We do not recommend to use conda environments together with EasyBuild modules due to
+ dependency conflicts. Nevertheless, if you need EasyBuild modules, consider installing conda
+ packages via `conda install --no-deps [...]` to prevent conda from installing dependencies.
+
??? example
- This is an example on partition Alpha. The example creates a virtual environment, and installs
- the package `torchvision` with pip.
+ This is an example on partition Alpha. The example creates a conda virtual environment, and
+ installs the package `torchvision` with conda.
```console
marie@login$ srun --partition=alpha-interactive --nodes=1 --gres=gpu:1 --time=01:00:00 --pty bash
- marie@alpha$ mkdir python-environments # please use workspaces
- marie@alpha$ module load modenv/hiera GCC/10.2.0 CUDA/11.1.1 OpenMPI/4.0.5 PyTorch
- Module GCC/10.2.0, CUDA/11.1.1, OpenMPI/4.0.5, PyTorch/1.9.0 and 54 dependencies loaded.
- marie@alpha$ which python
- /sw/installed/Python/3.8.6-GCCcore-10.2.0/bin/python
- marie@alpha$ pip list
+ marie@alpha$ ws_allocate -F scratch my_conda_virtualenv 100 # use a workspace for the environment
+ marie@alpha$ cd /scratch/ws/1/marie-my_conda_virtualenv
+ marie@alpha$ module load Anaconda3
+ Module Anaconda3/2021.11 loaded.
+ marie@alpha$ conda create --prefix my-torch-env python=3.8
+ Collecting package metadata (current_repodata.json): done
+ Solving environment: done
[...]
- marie@alpha$ virtualenv --system-site-packages python-environments/my-torch-env
- created virtual environment CPython3.8.6.final.0-64 in 42960ms
- creator CPython3Posix(dest=~/python-environments/my-torch-env, clear=False, global=True)
- seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=~/.local/share/virtualenv)
- added seed packages: pip==21.1.3, setuptools==57.2.0, wheel==0.36.2
- activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator
- marie@alpha$ source python-environments/my-torch-env/bin/activate
- (my-torch-env) marie@alpha$ pip install torchvision
+ Proceed ([y]/n)? y
[...]
- Installing collected packages: torchvision
- Successfully installed torchvision-0.10.0
+ marie@alpha$ conda activate my-torch-env
+ (my-torch-env) marie@alpha$ conda install -c pytorch torchvision
+ Collecting package metadata (current_repodata.json): done
[...]
+ Preparing transaction: done
+ Verifying transaction: done
+ (my-torch-env) marie@alpha$ which python # ensure to use the correct Python
(my-torch-env) marie@alpha$ python -c "import torchvision; print(torchvision.__version__)"
- 0.10.0+cu102
- (my-torch-env) marie@alpha$ deactivate
+ 0.12.0
+ (my-torch-env) marie@alpha$ conda deactivate
```
### Persistence of Conda Virtual Environment
diff --git a/doc.zih.tu-dresden.de/docs/software/tensorflow.md b/doc.zih.tu-dresden.de/docs/software/tensorflow.md
index db6b97596a153b852dabec4d5d9a1e73aa1aa19b..016d6aa25634a89fb7746dcb0117a8cb15a1116e 100644
--- a/doc.zih.tu-dresden.de/docs/software/tensorflow.md
+++ b/doc.zih.tu-dresden.de/docs/software/tensorflow.md
@@ -96,7 +96,7 @@ the notebook by pre-loading a specific TensorFlow module:
You can also define your own Jupyter kernel for more specific tasks. Please read about Jupyter
kernels and virtual environments in our
- [JupyterHub](../access/jupyterhub.md#creating-and-using-your-own-environment) documentation.
+ [JupyterHub](../access/jupyterhub.md#creating-and-using-a-custom-environment) documentation.
## TensorFlow in Containers
diff --git a/doc.zih.tu-dresden.de/docs/software/visualization.md b/doc.zih.tu-dresden.de/docs/software/visualization.md
index b1a103a0c1ab1c999a002c2584eefa1a1813916b..f9de3764e32ca78381c7e22a38d3bda5fe6bdd32 100644
--- a/doc.zih.tu-dresden.de/docs/software/visualization.md
+++ b/doc.zih.tu-dresden.de/docs/software/visualization.md
@@ -6,7 +6,7 @@
application. The ParaView package comprises different tools which are designed to meet interactive,
batch and in-situ workflows.
-ParaView is available on ZIH systems from the [modules system](modules.md#modules-environment). The
+ParaView is available on ZIH systems from the [modules system](modules.md#module-environments). The
following command lists the available versions
```console
diff --git a/doc.zih.tu-dresden.de/mkdocs.yml b/doc.zih.tu-dresden.de/mkdocs.yml
index f6957f1782fb1c1fc3f256f8b87e0cf3056ab7d9..c55bebb7bc677bc35815df1050c9a54b0db395a3 100644
--- a/doc.zih.tu-dresden.de/mkdocs.yml
+++ b/doc.zih.tu-dresden.de/mkdocs.yml
@@ -103,7 +103,7 @@ nav:
- Binding And Distribution Of Tasks: jobs_and_resources/binding_and_distribution_of_tasks.md
- Support:
- How to Ask for Support: support/support.md
- - Archive of the Old Wiki:
+ - Archive:
- Overview: archive/overview.md
- Bio Informatics: archive/bioinformatics.md
- CXFS End of Support: archive/cxfs_end_of_support.md
@@ -201,6 +201,27 @@ markdown_extensions:
# - mkdocs-video
+plugins:
+ - search
+ - markdown-caption
+ # https://github.com/manuzhang/mkdocs-htmlproofer-plugin
+ - htmlproofer:
+ # True by default
+ # Toggle via env. var. ENABLED_HTMLPROOFER=false
+ enabled: !ENV [ENABLED_HTMLPROOFER, True]
+ # Check URLs before serving. Build fails in case of bad URLs.
+ raise_error: True
+ # Ignore errors
+ #raise_error_excludes:
+ # 504: ['https://www.mkdocs.org/']
+ # Toggle validating external URLs
+ validate_external_urls: False
+ # Validate the entire rendered template, slow!
+ validate_rendered_template: True
+
+# Enable cross-page anchor validation
+use_directory_urls: False
+
extra:
tud_homepage: https://tu-dresden.de
tud_name: "TU Dresden"
@@ -220,7 +241,3 @@ extra:
name: "Data Protection Declaration / Datenschutzerklärung"
- link: https://tu-dresden.de/zertifikate
name: "Certificates"
-
-plugins:
- - search
- - markdown-caption
diff --git a/doc.zih.tu-dresden.de/tud_theme/stylesheets/extra.css b/doc.zih.tu-dresden.de/tud_theme/stylesheets/extra.css
index 98c54afa6b64cd8b38b576f52ff6f8117a75cf16..6b855870a148cc8a08d731561c5ee82d1d527695 100644
--- a/doc.zih.tu-dresden.de/tud_theme/stylesheets/extra.css
+++ b/doc.zih.tu-dresden.de/tud_theme/stylesheets/extra.css
@@ -36,6 +36,8 @@
/* interaction color */
--tud-red-90: rgb(221, 29, 29);
--fg-color--light: rgba(0, 0, 0, 0.6);
+
+ --icon-external-link: url('data:image/svg+xml, <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 20 20"> <g style="stroke:rgb(35,82,124);stroke-width:1"> <line x1="5" y1="5" x2="5" y2="14" /> <line x1="14" y1="9" x2="14" y2="14" /> <line x1="5" y1="14" x2="14" y2="14" /> <line x1="5" y1="5" x2="9" y2="5" /> <line x1="10" y1="2" x2="17" y2="2" /> <line x1="17" y1="2" x2="17" y2="9" /> <line x1="10" y1="9" x2="17" y2="2" style="stroke-width:1.5" /> </g> </svg>');
}
.md-typeset h1,
@@ -192,7 +194,26 @@ p {
margin: 0.2em;
}
/* main */
-
+/* style external links as found on https://stackoverflow.com/questions/5379752/css-style-external-links */
+.md-content a[href]:where([href*="\."]):not(:where(
+ /* exclude hash only links */
+ [href^="#"],
+ /* exclude relative but not double slash only links */
+ [href^="/"]:not([href^="//"]),
+ /* exclude page itself */
+ [href*="//doc.zih.tu-dresden.de"],
+ /* exclude relative links beginning with ../ */
+ [href^="\.\./"],
+ [href^="misc/"],
+ /* exclude buttons */
+ .md-content__button,
+ /* exclude icons */
+ .md-icon
+)):after {
+ content: '';
+ background: no-repeat var(--icon-external-link);
+ padding-right: 1em;
+}
/* footer */
.md-footer * {
justify-content: flex-start;
diff --git a/doc.zih.tu-dresden.de/wordlist.aspell b/doc.zih.tu-dresden.de/wordlist.aspell
index 758cae07744f907d37996a366e07f0ec01ec35a6..1dc7ca99f0490683a7eb630bf74089527cb7a818 100644
--- a/doc.zih.tu-dresden.de/wordlist.aspell
+++ b/doc.zih.tu-dresden.de/wordlist.aspell
@@ -6,8 +6,8 @@ ALLREDUCE
Altix
Amber
Amdahl's
-analytics
Analytics
+analytics
anonymized
Ansys
APIs
@@ -15,6 +15,7 @@ AVX
awk
BeeGFS
benchmarking
+BESM
BLAS
BMC
broadwell
@@ -33,23 +34,23 @@ CLI
CMake
COMSOL
conda
-config
CONFIG
-cpu
+config
CPU
+cpu
CPUID
-cpus
CPUs
+cpus
crossentropy
css
CSV
CUDA
cuDNN
CXFS
-dask
Dask
-dataframes
+dask
DataFrames
+dataframes
Dataheap
Datamover
DataParallel
@@ -83,6 +84,7 @@ engl
english
env
EPYC
+ESER
Espresso
ESSL
facto
@@ -91,18 +93,20 @@ FFT
FFTW
filesystem
filesystems
-flink
Flink
+flink
FlinkExample
FMA
foreach
Fortran
+Frontend
Galilei
Gauss
Gaussian
GBit
GDB
GDDR
+GFlop
GFLOPS
gfortran
GiB
@@ -113,8 +117,8 @@ GitLab's
glibc
Gloo
gnuplot
-gpu
GPU
+gpu
GPUs
gres
GROMACS
@@ -128,16 +132,19 @@ HDF
HDFS
HDFView
hiera
-horovod
+Hochleistungsrechnen
+Hochleistungsrechner
Horovod
+horovod
horovodrun
hostname
Hostnames
-hpc
HPC
+hpc
hpcsupport
HPE
HPL
+HRSK
html
hvd
hyperparameter
@@ -145,6 +152,7 @@ hyperparameters
hyperthreading
icc
icpc
+iDataPlex
ifort
ImageNet
img
@@ -159,11 +167,12 @@ ipython
IPython
ISA
Itanium
+Jards
jobqueue
jpg
jss
-jupyter
Jupyter
+jupyter
JupyterHub
JupyterLab
Jupytext
@@ -176,8 +185,8 @@ LAPACK
lapply
Leichtbau
LINPACK
-linter
Linter
+linter
lmod
LoadLeveler
localhost
@@ -193,6 +202,7 @@ Matplotlib
MEGWARE
mem
Memcheck
+MFlop
MiB
Microarchitecture
MIMD
@@ -208,6 +218,7 @@ Montecito
mortem
Mortem
mountpoint
+Mpi
mpi
mpicc
mpiCC
@@ -216,20 +227,23 @@ mpif
mpifort
mpirun
multicore
-multiphysics
Multiphysics
+multiphysics
multithreaded
Multithreading
NAMD
+Nationales
natively
nbgitpuller
nbsp
NCCL
+NEC
Neptun
NFS
NGC
-nodelist
+NHR
NODELIST
+nodelist
NRINGS
Nsight
ntasks
@@ -255,25 +269,26 @@ OpenBLAS
OpenCL
OpenGL
OpenMP
-openmpi
OpenMPI
+openmpi
OpenSSH
Opteron
OST
OTF
overfitting
-pandarallel
Pandarallel
+pandarallel
PAPI
parallelization
parallelize
parallelized
parfor
pdf
-perf
Perf
+perf
performant
PESSL
+PFlop
PGI
PiB
Pika
@@ -282,8 +297,8 @@ PMI
png
PowerAI
ppc
-pre
Pre
+pre
preload
Preload
preloaded
@@ -300,19 +315,20 @@ pty
PuTTY
pymdownx
PythonAnaconda
-pytorch
PyTorch
+pytorch
Quantum
queue
-quickstart
Quickstart
+quickstart
randint
reachability
README
+Rechenautomat
reproducibility
requeueing
-resnet
ResNet
+resnet
RHEL
Rmpi
rome
@@ -323,8 +339,8 @@ RStudio
rsync
Rsync
runnable
-runtime
Runtime
+runtime
sacct
salloc
Sandybridge
@@ -357,6 +373,7 @@ SMP
SMT
SparkExample
spawner
+Speicherkomplex
spython
squeue
srun
@@ -376,22 +393,25 @@ SXM
TBB
TCP
TensorBoard
-tensorflow
TensorFlow
+tensorflow
+TFlop
TFLOPS
Theano
tmp
-todo
ToDo
+todo
toolchain
toolchains
-torchvision
Torchvision
+torchvision
tracefile
tracefiles
tracepoints
transferability
Trition
+TUD
+und
undistinguishable
unencrypted
uplink
@@ -426,7 +446,8 @@ XLC
XLF
Xming
yaml
-zih
+Zeiss
ZIH
ZIH's
+ZRA
ZSH