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@@ -0,0 +1,342 @@
+# 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;
+```
+
+=== "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][21]
+
+ ??? 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)][22]
+
+ If you have not yet submitted an application to us, you will be asked to provide your information.
+
+ ![Principal Investigator (PI)][23]
+ ![Principal Investigator (PI)][24]
+
+ ??? 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][28]
+ ![Project Data][29]
+ ![Project Data][30]
+
+ ??? 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][31]
+ ![Software][32]
+
+ ??? 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][33]
+ ![Data][34]
+
+ ??? 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/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/install_jupyter.md b/doc.zih.tu-dresden.de/docs/archive/install_jupyter.md
index 02b78701bd8fa5b5eb3fbb7ed2de2cae9639042e..a1d2966509244d71d32c7bfa22d74c18b45be628 100644
--- a/doc.zih.tu-dresden.de/docs/archive/install_jupyter.md
+++ b/doc.zih.tu-dresden.de/docs/archive/install_jupyter.md
@@ -148,7 +148,7 @@ c.NotebookApp.allow_remote_access = True
#SBATCH --time=02:30:00
#SBATCH --mem=4000M
#SBATCH -J "jupyter-notebook" # job-name
-#SBATCH -A p_marie
+#SBATCH -A p_number_crunch
unset XDG_RUNTIME_DIR # might be required when interactive instead of sbatch to avoid 'Permission denied error'
srun jupyter notebook
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 17322f635a304c8b47a79923d84e1a3c900914ee..358cd153282e3bdf4240f144bbafa618151f383d 100644
--- a/doc.zih.tu-dresden.de/docs/contrib/content_rules.md
+++ b/doc.zih.tu-dresden.de/docs/contrib/content_rules.md
@@ -1,6 +1,22 @@
# Content Rules
-**Remark:** Avoid using tabs both in markdown files and in `mkdocs.yaml`. Type spaces instead.
+## Responsibility And License
+
+This documentation and the repository have two licenses (cf. [Legal Notice](../legal_notice.md)):
+
+* All documentation is licensed under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/).
+* All software components are licensed under [MIT license](../license_mit.txt).
+
+These licenses also apply to your contributions.
+
+!!! note
+
+ Each user is fully and solely responsible for the content he/she creates and has to ensure that
+ he/she has the right to create it under the laws which apply.
+
+If you are in doubt, please contact us either via
+[GitLab Issue](https://gitlab.hrz.tu-chemnitz.de/zih/hpcsupport/hpc-compendium/-/issues)
+or via [Email](mailto:hpcsupport@zih.tu-dresden.de).
## New Page and Pages Structure
@@ -50,6 +66,7 @@ should be highlighted, etc. Code examples, longer than half screen height should
## Writing Style
+* Avoid using tabs both in markdown files and in `mkdocs.yaml`. Type spaces instead.
* Capitalize headings, e.g. *Exclusive Reservation of Hardware*
* Give keywords in link texts, e.g. [Code Blocks](#code-blocks-and-syntax-highlighting) is more
descriptive than [this subsection](#code-blocks-and-syntax-highlighting)
@@ -117,7 +134,7 @@ We follow this rules regarding prompts:
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!
-* Stick to the [generic user name](#data-privacy-and-generic-user-name) `marie`.
+* Stick to the [generic user name](#data-privacy-and-generic-names) `marie`.
### Code Blocks and Syntax Highlighting
@@ -228,16 +245,17 @@ _Result_:
-### Data Privacy and Generic User Name
+### Data Privacy and Generic Names
-Where possible, replace login, project name and other private data with clearly arbitrary placeholders.
-E.g., use the generic login `marie` and the corresponding project name `p_marie`.
+Where possible, replace login, project name and other private data with clearly arbitrary
+placeholders. In particular, use the generic login `marie` and the project title `p_number_crunch`
+as placeholders.
```console
marie@login$ ls -l
-drwxr-xr-x 3 marie p_marie 4096 Jan 24 2020 code
-drwxr-xr-x 3 marie p_marie 4096 Feb 12 2020 data
--rw-rw---- 1 marie p_marie 4096 Jan 24 2020 readme.md
+drwxr-xr-x 3 marie p_number_crunch 4096 Jan 24 2020 code
+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
```
## Mark Omissions
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 15382289e3b0b7abcfb9621fcbb33cde302dc1fc..6e6ac44cf53b56d3b7a96959314117642d3ed06b 100644
--- a/doc.zih.tu-dresden.de/docs/contrib/contribute_container.md
+++ b/doc.zih.tu-dresden.de/docs/contrib/contribute_container.md
@@ -42,11 +42,37 @@ description of your changes. If you work on an issue, please also add "Closes 17
`git push origin 174-check-contribution-documentation`.
1. As an output you get a link to create a merge request against the preview branch.
1. When the merge request is created, a continuous integration (CI) pipeline automatically checks
-your contributions.
-
-When you contribute, please follow our [content rules](content_rules.md) to make incorporating your
-changes easy. We also check these rules via continuous integration checks and/or reviews.
-You can find the details and commands to preview your changes and apply checks in the next sections.
+your contributions. If you forked the repository, these automatic checks are not available, but you
+can [run checks locally](#run-the-proposed-checks-inside-container).
+
+!!! tip
+
+ When you contribute, please follow our [content rules](content_rules.md) to make incorporating
+ your changes easy. We also check these rules via continuous integration checks and/or reviews.
+ You can find the details and commands to [preview your changes](#start-the-local-web-server) and
+ [apply checks](#run-the-proposed-checks-inside-container).
+
+## Merging of Forked Repositories
+
+When you have forked the repository as mentioned above, the process for merging is a bit different
+from internal merge requests. Because branches of forks are not automatically checked by CI,
+someone with at least developer access needs to do some more steps to incorporate the changes of
+your MR:
+
+1. The developer informs you about the start of merging process.
+1. The developer needs to review your changes to make sure that your changes are specific and don't introduce
+problems, such as changes in the Dockerfile or any script could.
+1. The developer needs to create a branch in our repository. Let's call this "internal MR branch".
+1. The developer needs to change the target branch of your MR from "preview" to "internal MR branch".
+1. The developer needs to merge it.
+1. The developer needs to open another MR from "internal MR branch" to "preview" to check whether
+ the changes pass the CI checks.
+1. The developer needs to fix things that were found by CI.
+1. The developer informs you about the MR or asks for your support while fixing the CI.
+
+When you follow our [content rules](content_rules.md) and
+[run checks locally](#run-the-proposed-checks-inside-container), you are making this process
+faster.
## Tools to Ensure Quality
diff --git a/doc.zih.tu-dresden.de/docs/contrib/howto_contribute.md b/doc.zih.tu-dresden.de/docs/contrib/howto_contribute.md
index 693229344e0eeee1d263899e906996b54cba207f..4a14f2d245a481e9a1a3cdfd2abccdd5a63efa4a 100644
--- a/doc.zih.tu-dresden.de/docs/contrib/howto_contribute.md
+++ b/doc.zih.tu-dresden.de/docs/contrib/howto_contribute.md
@@ -4,7 +4,21 @@
Ink is better than the best memory.
-In principle, there are three possible ways how to contribute to this documentation.
+Even though we try to cover all aspects of working with the ZIH systems and keep the documentation
+up to date, you might miss something. In principle, there are three possible ways how you can
+contribute to this documentation as outlined below.
+
+## Content Rules
+
+To ensure a high-quality and consistent documentation and to make it easier for readers to
+understand all content, we set some [content rules](content_rules.md). Please follow these rules
+when contributing! Furthermore, reviewing your changes take less time and your improvements appear
+faster on the official documentation.
+
+!!! note
+
+ Each user is fully and solely responsible for the content he/she creates and has to ensure that
+ he/she has the right to create it under the laws which apply.
## Contribute via Issue
@@ -38,9 +52,3 @@ used in the back-end. Using them should ensure that merge requests will not be b
due to automatic checking.
The page on [Contributing via local clone](contribute_container.md) provides you with the details
about how to setup and use your local clone.
-
-## Content rules
-
-To ensure quality and to make it easier for readers to understand all content, we follow some
-[content rules](content_rules.md). If you follow these rules, you can be sure, that reviews of
-your changes take less time and your improvements appear faster on the official web site.
diff --git a/doc.zih.tu-dresden.de/docs/data_lifecycle/intermediate_archive.md b/doc.zih.tu-dresden.de/docs/data_lifecycle/intermediate_archive.md
index 73322cf3031a2550ddec1223546b3b393579b8b5..894626208947186e48ba7d08b439cf6aace48655 100644
--- a/doc.zih.tu-dresden.de/docs/data_lifecycle/intermediate_archive.md
+++ b/doc.zih.tu-dresden.de/docs/data_lifecycle/intermediate_archive.md
@@ -20,13 +20,16 @@ Some more information:
## Access the Intermediate Archive
For storing and restoring your data in/from the "Intermediate Archive" you can use the tool
-[Datamover](../data_transfer/datamover.md). To use the DataMover you have to login to ZIH systems.
+[Datamover](../data_transfer/datamover.md). To use the Datamover you have to login to ZIH systems.
### Store Data
```console
marie@login$ dtcp -r /<directory> /archiv/<project or user>/<directory> # or
marie@login$ dtrsync -av /<directory> /archiv/<project or user>/<directory>
+# example:
+marie@login$ dtcp -r /scratch/marie/results /archiv/marie/ # or
+marie@login$ dtrsync -av /scratch/marie/results /archiv/marie/results
```
### Restore Data
@@ -34,11 +37,16 @@ marie@login$ dtrsync -av /<directory> /archiv/<project or user>/<directory>
```console
marie@login$ dtcp -r /archiv/<project or user>/<directory> /<directory> # or
marie@login$ dtrsync -av /archiv/<project or user>/<directory> /<directory>
+# example:
+marie@login$ dtcp -r /archiv/marie/results /scratch/marie/ # or
+marie@login$ dtrsync -av /archiv/marie/results /scratch/marie/results
```
-### Examples
+!!! note "Listing files in archive"
-```console
-marie@login$ dtcp -r /scratch/rotscher/results /archiv/rotscher/ # or
-marie@login$ dtrsync -av /scratch/rotscher/results /archiv/rotscher/results
-```
+ The intermediate archive is not mounted on the login nodes, but only on the [export nodes](../data_transfer/export_nodes.md).
+
+ In order to list the user's files in the archive use the `dtls` command
+ ```console
+ marie@login$ dtls /archiv/$USER/
+ ```
diff --git a/doc.zih.tu-dresden.de/docs/data_lifecycle/longterm_preservation.md b/doc.zih.tu-dresden.de/docs/data_lifecycle/longterm_preservation.md
index 9a4c7e760282269792fbcb844935d37fd88f4bb3..3b1ad0c9c595fa4d09c0e113b65c82a71b274a35 100644
--- a/doc.zih.tu-dresden.de/docs/data_lifecycle/longterm_preservation.md
+++ b/doc.zih.tu-dresden.de/docs/data_lifecycle/longterm_preservation.md
@@ -74,13 +74,65 @@ Below are some examples:
## Where can I get more information about management of research data?
-Go to [http://www.forschungsdaten.org/en/](http://www.forschungsdaten.org/en/) to find more
-information about managing research data.
-
-## I want to store my research data at ZIH. How can I do that?
-
-You can use the following services for long-term preservation of research data:
-
- - [Long-term archive](https://tu-dresden.de/zih/dienste/service-katalog/arbeitsumgebung/backup_archiv/archivierung_am_zih)
- - [Long-term Archiving and Publication with OpARA (Open Access Repository and Archive)](https://tu-dresden.de/zih/dienste/service-katalog/arbeitsumgebung/backup_archiv/archivierung_am_zih#section-2-2)
- - [intermediate archive](https://tu-dresden.de/zih/dienste/service-katalog/arbeitsumgebung/backup_archiv/archivierung_am_zih#section-2-1)
+Please visit the wiki [forschungsdaten.org](https://www.forschungsdaten.org/en/) to learn more about
+all of the different aspects of research data management.
+
+For questions or individual consultations regarding research data management in general or any of
+its certain aspects, you can contact the
+[Service Center Research Data](https://tu-dresden.de/forschung-transfer/services-fuer-forschende/kontaktstelle-forschungsdaten?set_language=en)
+(Kontaktstelle Forschungsdaten) of TU Dresden.
+
+## I want to archive my research data at ZIH safely. How can I do that?
+
+For TU Dresden there exist two different services at ZIH for archiving research data. Both of
+them ensure high data safety by duplicating data internally at two separate locations and
+require some data preparation (e.g. packaging), but serve different use cases:
+
+### Storing very infrequently used data during the course of the project
+
+The intermediate archive is a tape storage easily accessible as a directory
+(`/archiv/<HRSK-project>/` or `/archiv/<login>/`) using the
+[export nodes](../data_transfer/export_nodes.md)
+and
+[Datamover tools](https://doc.zih.tu-dresden.de/data_transfer/datamover/) to move your data to.
+For detailed information please visit the
+[ZIH intermediate archive documentation](https://tu-dresden.de/zih/dienste/service-katalog/arbeitsumgebung/backup_archiv/archivierung_am_zih#section-2-1).
+
+!!! note
+
+ The usage of the HRSK-project-related archive is preferable to the login-related archive, as
+ this enables assigning access rights and responsibility across multiple researchers, due to the
+ common staff turnover in research.
+
+The use of the intermediate archive usually is limited by the end of the corresponding
+research project. Afterwards data is required to be removed, tidied up and submitted to a
+long-term repository (see next section).
+
+The intermediate archive is the preferred service when you keep large, mostly unused data volumes
+during the course of your research project; if you want or need to free storage capacities, but
+you are still not able to define certain or relevant datasets for long-term archival.
+
+If you are able to identify complete and final datasets, which you probably won't use actively
+anymore, then repositories as described in the next section may be the more appropriate selection.
+
+### Archiving data beyond the project lifetime, for 10 years and above
+
+According to good scientific practice (cf.
+[DFG guidelines, #17](https://www.dfg.de/download/pdf/foerderung/rechtliche_rahmenbedingungen/gute_wissenschaftliche_praxis/kodex_gwp.pdf))
+and
+[TU Dresden research data guidelines](https://tu-dresden.de/tu-dresden/qualitaetsmanagement/ressourcen/dateien/wisprax/Leitlinien-fuer-den-Umgang-mit-Forschungsdaten-an-der-TU-Dresden.pdf),
+relevant research data needs to be archived at least for 10 years. The
+[OpARA service](https://opara.zih.tu-dresden.de/xmlui/) (Open Access Repository and Archive) is the
+joint research data repository service for Saxon universities to address this requirement.
+
+Data can be uploaded and, to comply to the demands of long-term understanding of data, additional
+metadata and description must be added. Large datasets may be optionally imported beforehand. In
+this case, please contact the
+[TU Dresden Service Desk](mailto:servicedesk@tu-dresden.de?subject=OpARA:%20Data%20Import).
+Optionally, data can also be **published** by OpARA. To ensure data quality, data submissions
+undergo a review process.
+
+Beyond OpARA, it is also recommended to use discipline-specific data repositories for data
+publications. Usually those are well known in a scientific community, and offer better fitting
+options of data description and classification. Please visit [re3data.org](https://re3data.org)
+to look up a suitable one for your discipline.
diff --git a/doc.zih.tu-dresden.de/docs/data_transfer/datamover.md b/doc.zih.tu-dresden.de/docs/data_transfer/datamover.md
index 0bd3fbe88e6a7957232a04a98c2c5eeb33a245ad..28aba7bbfdcec8411f6510061d509c949d128f34 100644
--- a/doc.zih.tu-dresden.de/docs/data_transfer/datamover.md
+++ b/doc.zih.tu-dresden.de/docs/data_transfer/datamover.md
@@ -1,7 +1,7 @@
# Datamover - Data Transfer Inside ZIH Systems
-With the **datamover**, we provide a special data transfer machine for transferring data with best
-transfer speed between the filesystems of ZIH systems. The datamover machine is not accessible
+With the **Datamover**, we provide a special data transfer machine for transferring data with best
+transfer speed between the filesystems of ZIH systems. The Datamover machine is not accessible
through SSH as it is dedicated to data transfers. To move or copy files from one filesystem to
another filesystem, you have to use the following commands:
@@ -37,7 +37,7 @@ To identify the mount points of the different filesystems on the data transfer m
| | `/warm_archive/ws` | `/warm_archive/ws` |
| | `/home` | `/home` |
| | `/projects` | `/projects` |
-| **Archive** | | `/archive` |
+| **Archive** | | `/archiv` |
| **Group storage** | | `/grp/<group storage>` |
## Usage of Datamover
@@ -45,7 +45,7 @@ To identify the mount points of the different filesystems on the data transfer m
!!! example "Copying data from `/beegfs/global0` to `/projects` filesystem."
``` console
- marie@login$ dtcp -r /beegfs/global0/ws/marie-workdata/results /projects/p_marie/.
+ marie@login$ dtcp -r /beegfs/global0/ws/marie-workdata/results /projects/p_number_crunch/.
```
!!! example "Moving data from `/beegfs/global0` to `/warm_archive` filesystem."
@@ -57,7 +57,7 @@ To identify the mount points of the different filesystems on the data transfer m
!!! example "Archive data from `/beegfs/global0` to `/archiv` filesystem."
``` console
- marie@login$ dttar -czf /archiv/p_marie/results.tgz /beegfs/global0/ws/marie-workdata/results
+ marie@login$ dttar -czf /archiv/p_number_crunch/results.tgz /beegfs/global0/ws/marie-workdata/results
```
!!! warning
@@ -66,7 +66,7 @@ To identify the mount points of the different filesystems on the data transfer m
!!! note
The [warm archive](../data_lifecycle/warm_archive.md) and the `projects` filesystem are not
writable from within batch jobs.
- However, you can store the data in the `warm_archive` using the datamover.
+ However, you can store the data in the `warm_archive` using the Datamover.
## Transferring Files Between ZIH Systems and Group Drive
diff --git a/doc.zih.tu-dresden.de/docs/data_transfer/overview.md b/doc.zih.tu-dresden.de/docs/data_transfer/overview.md
index a8af87cc55814ca0afe5b30193589cf1905ce356..6e8a1bf1cc12e36e4aa15bd46b9eaf84e24171bc 100644
--- a/doc.zih.tu-dresden.de/docs/data_transfer/overview.md
+++ b/doc.zih.tu-dresden.de/docs/data_transfer/overview.md
@@ -14,9 +14,9 @@ copy data to/from ZIH systems. Please follow the link to the documentation on
## Data Transfer Inside ZIH Systems: Datamover
-The recommended way for data transfer inside ZIH Systems is the **datamover**. It is a special
+The recommended way for data transfer inside ZIH Systems is the **Datamover**. It is a special
data transfer machine that provides the best transfer speed. To load, move, copy etc. files from one
filesystem to another filesystem, you have to use commands prefixed with `dt`: `dtcp`, `dtwget`,
`dtmv`, `dtrm`, `dtrsync`, `dttar`, `dtls`. These commands submit a job to the data transfer
machines that execute the selected command. Please refer to the detailed documentation regarding the
-[datamover](datamover.md).
+[Datamover](datamover.md).
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 38d6686d7a655c1c5d7161d6607be9d6f55d8b5c..180ed1d62febd311fd5cddd739d4f086825bc5b7 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
@@ -63,9 +63,13 @@ To use it, first add a `dmtcp_launch` before your application call in your batch
of MPI applications, you have to add the parameters `--ib --rm` and put it between `srun` and your
application call, e.g.:
-```bash
-srun dmtcp_launch --ib --rm ./my-mpi-application
-```
+???+ my_script.sbatch
+
+ ```bash
+ [...]
+
+ srun dmtcp_launch --ib --rm ./my-mpi-application
+ ```
!!! note
@@ -79,7 +83,7 @@ Then just substitute your usual `sbatch` call with `dmtcp_sbatch` and be sure to
and `-i` parameters (don't forget you need to have loaded the `dmtcp` module).
```console
-marie@login$ dmtcp_sbatch --time 2-00:00:00 --interval 28000,800 my_batchfile.sh
+marie@login$ dmtcp_sbatch --time 2-00:00:00 --interval 28000,800 my_script.sbatch
```
With `-t, --time` you set the total runtime of your calculations. This will be replaced in the batch
diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm_examples.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm_examples.md
index b6ec206cf1950f416e81318daab0c9e0e88ba45a..ebfd52972ac785b851a0c02758904a68dd09af8f 100644
--- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm_examples.md
+++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm_examples.md
@@ -109,7 +109,7 @@ for `sbatch/srun` in this case is `--gres=gpu:[NUM_PER_NODE]` (where `NUM_PER_NO
#SBATCH --cpus-per-task=6 # use 6 threads per task
#SBATCH --gres=gpu:1 # use 1 GPU per node (i.e. use one GPU per task)
#SBATCH --time=01:00:00 # run for 1 hour
- #SBATCH --account=p_marie # account CPU time to project p_marie
+ #SBATCH --account=p_number_crunch # account CPU time to project p_number_crunch
srun ./your/cuda/application # start you application (probably requires MPI to use both nodes)
```
diff --git a/doc.zih.tu-dresden.de/docs/legal_notice.md b/doc.zih.tu-dresden.de/docs/legal_notice.md
index 3c9432ecb16eaa0a2fae1a40da4217f92da8a454..e5029584f538f8d909d4bd6f0cf786b73e9872df 100644
--- a/doc.zih.tu-dresden.de/docs/legal_notice.md
+++ b/doc.zih.tu-dresden.de/docs/legal_notice.md
@@ -30,4 +30,4 @@ E-Mail: zih@tu-dresden.de
This documentation and the repository have two licenses:
* All documentation is licensed under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/).
-* All software components are licensed under [MIT license](https://opensource.org/licenses/MIT).
+* All software components are licensed under [MIT license](license_mit.txt).
diff --git a/doc.zih.tu-dresden.de/docs/license_mit.txt b/doc.zih.tu-dresden.de/docs/license_mit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02c33cdf3c7a4f4ce54a670efc885018868f3f26
--- /dev/null
+++ b/doc.zih.tu-dresden.de/docs/license_mit.txt
@@ -0,0 +1,16 @@
+Copyright 2021, 2022 TU Dresden / ZIH
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and
+associated documentation files (the "Software"), to deal in the Software without restriction,
+including without limitation the rights to use, copy, modify, merge, publish, distribute,
+sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial
+portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT
+NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES
+OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/doc.zih.tu-dresden.de/docs/software/building_software.md b/doc.zih.tu-dresden.de/docs/software/building_software.md
index c83932a16c1c0227cb160d4853cd1815626fc404..73952b06efde809b7e91e936be0fbf9b240f88a8 100644
--- a/doc.zih.tu-dresden.de/docs/software/building_software.md
+++ b/doc.zih.tu-dresden.de/docs/software/building_software.md
@@ -17,16 +17,16 @@ For instance, when using CMake and keeping your source in `/projects`, you could
```console
# save path to your source directory:
-marie@login$ export SRCDIR=/projects/p_marie/mysource
+marie@login$ export SRCDIR=/projects/p_number_crunch/mysource
# create a build directory in /scratch:
-marie@login$ mkdir /scratch/p_marie/mysoftware_build
+marie@login$ mkdir /scratch/p_number_crunch/mysoftware_build
# change to build directory within /scratch:
-marie@login$ cd /scratch/p_marie/mysoftware_build
+marie@login$ cd /scratch/p_number_crunch/mysoftware_build
# create Makefiles:
-marie@login$ cmake -DCMAKE_INSTALL_PREFIX=/projects/p_marie/mysoftware $SRCDIR
+marie@login$ cmake -DCMAKE_INSTALL_PREFIX=/projects/p_number_crunch/mysoftware $SRCDIR
# build in a job:
marie@login$ srun --mem-per-cpu=1500 --cpus-per-task=12 --pty make -j 12
diff --git a/doc.zih.tu-dresden.de/docs/software/containers.md b/doc.zih.tu-dresden.de/docs/software/containers.md
index 0d96479e335b61d8e004710cec12e32d366091ab..be74caec03c6ffcf098eade46f4c3adb313f8754 100644
--- a/doc.zih.tu-dresden.de/docs/software/containers.md
+++ b/doc.zih.tu-dresden.de/docs/software/containers.md
@@ -46,7 +46,7 @@ instructions from the official documentation to install Singularity.
1. Check if `go` is installed by executing `go version`. If it is **not**:
```console
- marie@local$ wget <https://storage.googleapis.com/golang/getgo/installer_linux> && chmod +x
+ marie@local$ wget 'https://storage.googleapis.com/golang/getgo/installer_linux' && chmod +x
installer_linux && ./installer_linux && source $HOME/.bash_profile
```
@@ -88,7 +88,9 @@ instructions from the official documentation to install Singularity.
There are two possibilities:
1. Create a new container on your local workstation (where you have the necessary privileges), and
- then copy the container file to ZIH systems for execution.
+ then copy the container file to ZIH systems for execution. Therefore you also have to install
+ [Singularity](https://sylabs.io/guides/3.0/user-guide/quick_start.html#quick-installation-steps)
+ on your local workstation.
1. You can, however, import an existing container from, e.g., Docker.
Both methods are outlined in the following.
@@ -103,10 +105,11 @@ You can create a new custom container on your workstation, if you have root righ
which is different to the x86 architecture in common computers/laptops. For that you can use
the [VM Tools](singularity_power9.md).
-Creating a container is done by writing a **definition file** and passing it to
+Creating a container is done by writing a definition file, such as `myDefinition.def`, and passing
+it to `singularity` via
```console
-marie@local$ singularity build myContainer.sif <myDefinition.def>
+marie@local$ singularity build myContainer.sif myDefinition.def
```
A definition file contains a bootstrap
@@ -167,7 +170,7 @@ https://github.com/singularityware/singularity/tree/master/examples.
You can import an image directly from the Docker repository (Docker Hub):
```console
-marie@local$ singularity build my-container.sif docker://ubuntu:latest
+marie@login$ singularity build my-container.sif docker://ubuntu:latest
```
Creating a singularity container directly from a local docker image is possible but not
@@ -175,20 +178,20 @@ recommended. The steps are:
```console
# Start a docker registry
-$ docker run -d -p 5000:5000 --restart=always --name registry registry:2
+marie@local$ docker run -d -p 5000:5000 --restart=always --name registry registry:2
# Push local docker container to it
-$ docker tag alpine localhost:5000/alpine
-$ docker push localhost:5000/alpine
+marie@local$ docker tag alpine localhost:5000/alpine
+marie@local$ docker push localhost:5000/alpine
# Create def file for singularity like this...
-$ cat example.def
+marie@local$ cat example.def
Bootstrap: docker
Registry: <a href="http://localhost:5000" rel="nofollow" target="_blank">http://localhost:5000</a>
From: alpine
# Build singularity container
-$ singularity build --nohttps alpine.sif example.def
+marie@local$ singularity build --nohttps alpine.sif example.def
```
#### Start from a Dockerfile
@@ -284,7 +287,7 @@ While the `shell` command can be useful for tests and setup, you can also launch
inside the container directly using "exec":
```console
-marie@login$ singularity exec my-container.img /opt/myapplication/bin/run_myapp
+marie@login$ singularity exec my-container.sif /opt/myapplication/bin/run_myapp
```
This can be useful if you wish to create a wrapper script that transparently calls a containerized
@@ -299,7 +302,7 @@ if [ "z$X" = "z" ] ; then
exit 1
fi
-singularity exec /scratch/p_myproject/my-container.sif /opt/myapplication/run_myapp "$@"
+singularity exec /projects/p_number_crunch/my-container.sif /opt/myapplication/run_myapp "$@"
```
The better approach is to use `singularity run`, which executes whatever was set in the `%runscript`
@@ -325,20 +328,20 @@ singularity build my-container.sif example.def
Then you can run your application via
```console
-singularity run my-container.sif first_arg 2nd_arg
+marie@login$ singularity run my-container.sif first_arg 2nd_arg
```
Alternatively you can execute the container directly which is equivalent:
```console
-./my-container.sif first_arg 2nd_arg
+marie@login$ ./my-container.sif first_arg 2nd_arg
```
With this you can even masquerade an application with a singularity container as if it was an actual
program by naming the container just like the binary:
```console
-mv my-container.sif myCoolAp
+marie@login$ mv my-container.sif myCoolAp
```
### Use-Cases
diff --git a/doc.zih.tu-dresden.de/docs/software/data_analytics.md b/doc.zih.tu-dresden.de/docs/software/data_analytics.md
index 036a1c7a454faf84b8352f5fb79dbfc09343cb89..c3cb4afe1be3d613a915e42f1db1020919ecfa3c 100644
--- a/doc.zih.tu-dresden.de/docs/software/data_analytics.md
+++ b/doc.zih.tu-dresden.de/docs/software/data_analytics.md
@@ -29,7 +29,7 @@ can be installed individually by each user. If possible, the use of
recommended (e.g. for Python). Likewise, software can be used within [containers](containers.md).
For the transfer of larger amounts of data into and within the system, the
-[export nodes and datamover](../data_transfer/overview.md) should be used.
+[export nodes and Datamover](../data_transfer/overview.md) should be used.
Data is stored in the [workspaces](../data_lifecycle/workspaces.md).
Software modules or virtual environments can also be installed in workspaces to enable
collaborative work even within larger groups.
diff --git a/doc.zih.tu-dresden.de/docs/software/data_analytics_with_python.md b/doc.zih.tu-dresden.de/docs/software/data_analytics_with_python.md
index a7d2781669fc909e0628c6518825542cf8f7ced8..cf8c1b559f4f496a729388a1e1f4353cdcd14733 100644
--- a/doc.zih.tu-dresden.de/docs/software/data_analytics_with_python.md
+++ b/doc.zih.tu-dresden.de/docs/software/data_analytics_with_python.md
@@ -219,7 +219,7 @@ from dask_jobqueue import SLURMCluster
cluster = SLURMCluster(queue='alpha',
cores=8,
processes=2,
- project='p_marie',
+ project='p_number_crunch',
memory="8GB",
walltime="00:30:00")
@@ -242,7 +242,7 @@ from dask import delayed
cluster = SLURMCluster(queue='alpha',
cores=8,
processes=2,
- project='p_marie',
+ project='p_number_crunch',
memory="80GB",
walltime="00:30:00",
extra=['--resources gpu=1'])
@@ -294,7 +294,7 @@ for the Monte-Carlo estimation of Pi.
#create a Slurm cluster, please specify your project
- cluster = SLURMCluster(queue='alpha', cores=2, project='p_marie', memory="8GB", walltime="00:30:00", extra=['--resources gpu=1'], scheduler_options={"dashboard_address": f":{portdash}"})
+ cluster = SLURMCluster(queue='alpha', cores=2, project='p_number_crunch', memory="8GB", walltime="00:30:00", extra=['--resources gpu=1'], scheduler_options={"dashboard_address": f":{portdash}"})
#submit the job to the scheduler with the number of nodes (here 2) requested:
diff --git a/doc.zih.tu-dresden.de/docs/software/energy_measurement.md b/doc.zih.tu-dresden.de/docs/software/energy_measurement.md
index 36c0abc661d10a828384c35155fe6a5c6074a301..3c0e5b2f61634f086c485a0c0defff5cbc0cd43e 100644
--- a/doc.zih.tu-dresden.de/docs/software/energy_measurement.md
+++ b/doc.zih.tu-dresden.de/docs/software/energy_measurement.md
@@ -8,11 +8,11 @@ available through several different interfaces, which are described below.
| Interface | Sensors | Rate |
|:-------------------------------------------|:----------------|:--------------------------------|
-| Dataheap (C, Python, VampirTrace, Score-P) | Blade, (CPU) | 1 Sa/s |
-| HDEEM\* (C, Score-P) | Blade, CPU, DDR | 1 kSa/s (Blade), 100 Sa/s (VRs) |
-| HDEEM Command Line Interface | Blade, CPU, DDR | 1 kSa/s (Blade), 100 Sa/s (VR) |
-| Slurm Accounting (`sacct`) | Blade | Per Job Energy |
-| Slurm Profiling (HDF5) | Blade | Up to 1 Sa/s |
+| Dataheap (C, Python, VampirTrace, Score-P) | Blade, (CPU) | 1 sample/s |
+| HDEEM\* (C, Score-P) | Blade, CPU, DDR | 1000 samples/s (Blade), 100 samples/s (VRs) |
+| HDEEM Command Line Interface | Blade, CPU, DDR | 1000 samples/s (Blade), 100 samples/s (VR) |
+| Slurm Accounting (`sacct`) | Blade | Per Job Energy |
+| Slurm Profiling (HDF5) | Blade | Up to 1 sample/s |
!!! note
@@ -24,15 +24,15 @@ available through several different interfaces, which are described below.
In addition to the above mentioned interfaces, you can access the measurements through a
[C API](#using-the-hdeem-c-api) to get the full temporal and spatial resolution:
-- ** Blade:**1 kSa/s for the whole node, includes both sockets, DRAM,
+- ** Blade:** 1000 samples/s for the whole node, includes both sockets, DRAM,
SSD, and other on-board consumers. Since the system is directly
water cooled, no cooling components are included in the blade
consumption.
-- **Voltage regulators (VR):** 100 Sa/s for each of the six VR
+- **Voltage regulators (VR):** 100 samples/s for each of the six VR
measurement points, one for each socket and four for eight DRAM
lanes (two lanes bundled).
-The GPU blades also have 1 Sa/s power instrumentation but have a lower accuracy.
+The GPU blades also have 1 sample/s power instrumentation but have a lower accuracy.
HDEEM measurements have an accuracy of 2 % for Blade (node) measurements, and 5 % for voltage
regulator (CPU, DDR) measurements.
@@ -44,7 +44,7 @@ loading the `hdeem` module. They are commonly used on the node under test to sta
query the measurement device.
- `startHdeem`: Start a measurement. After the command succeeds, the
- measurement data with the 1000 / 100 Sa/s described above will be
+ measurement data with the 1000 / 100 samples/s described above will be
recorded on the Board Management Controller (BMC), which is capable
of storing up to 8h of measurement data.
- `stopHdeem`: Stop a measurement. No further data is recorded and
@@ -64,13 +64,13 @@ provided metric plugins for Score-P (and VampirTrace). The plugins are provided
all necessary environment variables that are required to record data for all nodes that are part of
the current job.
-For 1 Sa/s Blade values (Dataheap):
+For 1 sample/s Blade values (Dataheap):
- [Score-P](scorep.md): use the module `scorep-dataheap`
- [VampirTrace](../archive/vampirtrace.md): use the module `vampirtrace-plugins/power-1.1`
(**Remark:** VampirTrace is outdated!)
-For 1000 Sa/s (Blade) and 100 Sa/s (CPU{0,1}, DDR{AB,CD,EF,GH}):
+For 1000 samples/s (Blade) and 100 samples/s (CPU{0,1}, DDR{AB,CD,EF,GH}):
- [Score-P](scorep.md): use the module `scorep-hdeem`. This
module requires a recent version of `scorep/sync-...`. Please use
diff --git a/doc.zih.tu-dresden.de/docs/software/fem_software.md b/doc.zih.tu-dresden.de/docs/software/fem_software.md
index 3f9bf79d54d36711560054101536c82dfbbfe000..af6b9fb80986e2bc727ae88e97b2cca614ffd629 100644
--- a/doc.zih.tu-dresden.de/docs/software/fem_software.md
+++ b/doc.zih.tu-dresden.de/docs/software/fem_software.md
@@ -8,7 +8,9 @@
```console
marie@login$ module avail ANSYS
[...]
- marie@login$ module load ANSYS/<version>
+ marie@login$ # module load ANSYS/<version>
+ marie@login$ # e.g.
+ marie@login$ module load ANSYS/2020R2
```
The section [runtime environment](modules.md) provides a comprehensive overview
@@ -59,7 +61,7 @@ Slurm or [writing job files](../jobs_and_resources/slurm.md#job-files).
#SBATCH --job-name=yyyy # give a name, what ever you want
#SBATCH --mail-type=END,FAIL # send email when the job finished or failed
#SBATCH --mail-user=<name>@mailbox.tu-dresden.de # set your email
- #SBATCH --account=p_marie # charge compute time to project p_marie
+ #SBATCH --account=p_number_crunch # charge compute time to project p_number_crunch
# Abaqus has its own MPI
@@ -105,7 +107,9 @@ all data via `-C`.
```console
# SSH connection established using -CX
-marie@login$ module load ANSYS/<version>
+marie@login$ # module load ANSYS/<version>
+marie@login$ # e.g.
+marie@login$ module load ANSYS/2020R2
marie@login$ runwb2
```
@@ -113,7 +117,9 @@ If more time is needed, a CPU has to be allocated like this (see
[batch systems Slurm](../jobs_and_resources/slurm.md) for further information):
```console
-marie@login$ module load ANSYS/<version>
+marie@login$ # module load ANSYS/<version>
+marie@login$ # e.g.
+marie@login$ module load ANSYS/2020R2
marie@login$ srun --time=00:30:00 --x11=first [SLURM_OPTIONS] --pty bash
[...]
marie@login$ runwb2
@@ -153,7 +159,9 @@ parameter (for batch mode), `-F` for your project file, and can then either add
unset SLURM_GTIDS # Odd, but necessary!
- module load ANSYS/<version>
+ # module load ANSYS/<version>
+ # e.g.
+ module load ANSYS ANSYS/2020R2
runwb2 -B -F Workbench_Taurus.wbpj -E 'Project.Update' -E 'Save(Overwrite=True)'
#or, if you wish to use a workbench replay file, replace the -E parameters with: -R mysteps.wbjn
@@ -208,7 +216,7 @@ firewall of ZIH. For further information, please refer to the COMSOL manual.
```console
marie@login$ module load COMSOL
- marie@login$ srun --ntasks=1 --cpus-per-task=4 --mem-per-cpu=2500 --time=8:00 comsol -np 4 server
+ marie@login$ srun --ntasks=1 --cpus-per-task=4 --mem-per-cpu=2500 --time=08:00:00 comsol -np 4 server
```
??? example "Interactive Job"
@@ -218,7 +226,7 @@ firewall of ZIH. For further information, please refer to the COMSOL manual.
```console
marie@login$ module load COMSOL
- marie@login$ srun --ntasks=1 --cpus-per-task=4 --mem-per-cpu=2500 --time=8:00 --pty --x11=first comsol -np 4
+ marie@login$ srun --ntasks=1 --cpus-per-task=4 --mem-per-cpu=2500 --time=08:00:00 --pty --x11=first comsol -np 4
```
Please make sure, that the option *Preferences* --> Graphics --> *Renedering* is set to *software
@@ -264,10 +272,10 @@ You need a job file (aka. batch script) to run the MPI version.
srun mpp-dyna i=neon_refined01_30ms.k memory=120000000
```
- Submit the job file to the batch system via
+ Submit the job file named `job.sh` to the batch system via
```console
- marie@login$ sbatch <filename>
+ marie@login$ sbatch job.sh
```
Please refer to the section [Slurm](../jobs_and_resources/slurm.md) for further details and
diff --git a/doc.zih.tu-dresden.de/docs/software/machine_learning.md b/doc.zih.tu-dresden.de/docs/software/machine_learning.md
index 1f40e6199e88f6aa4fd68037a0f4b32113001913..e293b007a9c07fbaf41ba3ec7ce25f29024f44d7 100644
--- a/doc.zih.tu-dresden.de/docs/software/machine_learning.md
+++ b/doc.zih.tu-dresden.de/docs/software/machine_learning.md
@@ -155,7 +155,7 @@ The following HPC related software is installed on all nodes:
There are many different datasets designed for research purposes. If you would like to download some
of them, keep in mind that many machine learning libraries have direct access to public datasets
without downloading it, e.g. [TensorFlow Datasets](https://www.tensorflow.org/datasets). If you
-still need to download some datasets use [datamover](../data_transfer/datamover.md) machine.
+still need to download some datasets use [Datamover](../data_transfer/datamover.md) machine.
### The ImageNet Dataset
diff --git a/doc.zih.tu-dresden.de/docs/software/mathematics.md b/doc.zih.tu-dresden.de/docs/software/mathematics.md
index 909970debf879b3b3c227fd80dbd26e06463309e..66fdc7050b050b77b899c83133d73758ac2dced6 100644
--- a/doc.zih.tu-dresden.de/docs/software/mathematics.md
+++ b/doc.zih.tu-dresden.de/docs/software/mathematics.md
@@ -105,7 +105,7 @@ marie@compute$ matlab
```
With following command you can see a list of installed software - also
-the different versions of matlab.
+the different versions of MATLAB.
```console
marie@login$ module avail
@@ -123,7 +123,7 @@ Or use:
marie@login$ module load MATLAB
```
-(then you will get the most recent Matlab version.
+(then you will get the most recent MATLAB version.
[Refer to the modules section for details.](../software/modules.md#modules))
### Interactive
@@ -135,7 +135,7 @@ with command
marie@login$ srun --pty --x11=first bash
```
-- now you can call "matlab" (you have 8h time to work with the matlab-GUI)
+- now you can call "matlab" (you have 8h time to work with the MATLAB-GUI)
### Non-interactive
@@ -218,9 +218,347 @@ marie@login$ srun ./run_compiled_executable.sh $EBROOTMATLAB
Please refer to the documentation `help parfor` for further information.
-## Octave
+### MATLAB Parallel Computing Toolbox
-GNU [Octave](https://www.gnu.org/software/octave/index) is a high-level language, primarily intended
-for numerical computations. It provides a convenient command line interface for solving linear and
-nonlinear problems numerically, and for performing other numerical experiments using a language that
-is mostly compatible with Matlab. It may also be used as a batch-oriented language.
+In the following, the steps to configure MATLAB to submit jobs to a cluster, retrieve results, and
+debug errors are outlined.
+
+#### Configuration – MATLAB client on the cluster
+
+After logging into the HPC system, you configure MATLAB to run parallel jobs on the HPC system by
+calling the shell script `configCluster.sh`. This only needs to be called once per version of
+MATLAB.
+
+```console
+marie@login$ module load MATLAB
+marie@login$ configCluster.sh
+```
+
+Jobs will now default to the HPC system rather than submit to the local machine.
+
+#### Installation and Configuration – MATLAB client off the cluster
+
+The MATLAB support package for ZIH Systems can be found as follows:
+
+* Windows:
+ * [tud.nonshared.R2021b.zip](misc/tud.nonshared.R2021b.zip)
+ * [tud.nonshared.R2022a.zip](misc/tud.nonshared.R2022a.zip)
+* Linux/macOS:
+ * [tud.nonshared.R2021b.tar.gz](misc/tud.nonshared.R2021b.tar.gz)
+ * [tud.nonshared.R2022a.tar.gz](misc/tud.nonshared.R2022a.tar.gz)
+
+Download the appropriate archive file and start MATLAB. The archive file should be extracted
+in the location returned by calling
+
+```matlabsession
+>> userpath
+```
+
+Configure MATLAB to run parallel jobs on ZIH Systems by calling `configCluster`. `configCluster`
+only needs to be called once per version of MATLAB.
+
+```matlabsession
+>> configCluster
+```
+
+Submission to the remote cluster requires SSH credentials. You will be prompted for your SSH
+username and password or identity file (private key). The username and location of the private key
+will be stored in MATLAB for future sessions. Jobs will now default to the cluster rather than
+submit to the local machine.
+
+!!! note
+
+ If you would like to submit to the local machine then run the following command:
+
+ ```matlab
+ >> % Get a handle to the local resources
+ >> c = parcluster('local');
+ ```
+
+#### Configuring Jobs
+
+Prior to submitting the job, you can specify various parameters to pass to your jobs, such as queue,
+e-mail, walltime, etc. *Only `MemPerCpu` and `QueueName` are required*.
+
+```matlabsession
+>> % Get a handle to the cluster
+>> c = parcluster;
+
+[REQUIRED]
+
+>> % Specify memory to use, per core (default: 2gb)
+>> c.AdditionalProperties.MemPerCpu = '4gb';
+
+>> % Specify the walltime (e.g., 5 hours)
+>> c.AdditionalProperties.WallTime = '05:00:00';
+
+[OPTIONAL]
+
+>> % Specify the account to use
+>> c.AdditionalProperties.Account = 'account-name';
+
+>> % Request constraint
+>> c.AdditionalProperties.Constraint = 'a-constraint';
+
+>> % Request job to run on exclusive node(s) (default: false)
+>> c.AdditionalProperties.EnableExclusive = true;
+
+>> % Request email notification of job status
+>> c.AdditionalProperties.EmailAddress = 'user-id@tu-dresden.de';
+
+>> % Specify number of GPUs to use (GpuType is optional)
+>> c.AdditionalProperties.GpusPerNode = 1;
+>> c.AdditionalProperties.GpuType = 'gpu-card';
+
+>> % Specify the queue to use
+>> c.AdditionalProperties.Partition = 'queue-name';
+
+>> % Specify a reservation to use
+>> c.AdditionalProperties.Reservation = 'a-reservation';
+```
+
+Save changes after modifying `AdditionalProperties` for the above changes to persist between MATLAB
+sessions.
+
+```matlabsession
+>> c.saveProfile
+```
+
+To see the values of the current configuration options, display `AdditionalProperties`.
+
+```matlabsession
+>> % To view current properties
+>> c.AdditionalProperties
+```
+
+You can unset a value when no longer needed.
+
+```matlabsession
+>> % Turn off email notifications
+>> c.AdditionalProperties.EmailAddress = '';
+>> c.saveProfile
+```
+
+#### Interactive Jobs - MATLAB Client on the Cluster
+
+To run an interactive pool job on the ZIH systems, continue to use `parpool` as you’ve done before.
+
+```matlabsession
+>> % Get a handle to the cluster
+>> c = parcluster;
+
+>> % Open a pool of 64 workers on the cluster
+>> pool = c.parpool(64);
+```
+
+Rather than running local on your machine, the pool can now run across multiple nodes on the
+cluster.
+
+```matlabsession
+>> % Run a parfor over 1000 iterations
+>> parfor idx = 1:1000
+ a(idx) = …
+ end
+```
+
+Once you are done with the pool, delete it.
+
+```matlabsession
+>> % Delete the pool
+>> pool.delete
+```
+
+#### Independent Batch Job
+
+Use the batch command to submit asynchronous jobs to the HPC system. The `batch` command will return
+a job object which is used to access the output of the submitted job. See the MATLAB documentation
+for more help on `batch`.
+
+```matlabsession
+>> % Get a handle to the cluster
+>> c = parcluster;
+
+>> % Submit job to query where MATLAB is running on the cluster
+>> job = c.batch(@pwd, 1, {}, ...
+ 'CurrentFolder','.', 'AutoAddClientPath',false);
+
+>> % Query job for state
+>> job.State
+
+>> % If state is finished, fetch the results
+>> job.fetchOutputs{:}
+
+>> % Delete the job after results are no longer needed
+>> job.delete
+```
+
+To retrieve a list of currently running or completed jobs, call `parcluster` to retrieve the cluster
+object. The cluster object stores an array of jobs that were run, are running, or are queued to
+run. This allows us to fetch the results of completed jobs. Retrieve and view the list of jobs as
+shown below.
+
+```matlabsession
+>> c = parcluster;
+>> jobs = c.Jobs;
+```
+
+Once you have identified the job you want, you can retrieve the results as done previously.
+
+`fetchOutputs` is used to retrieve function output arguments; if calling `batch` with a script, use
+`load` instead. Data that has been written to files on the cluster needs be retrieved directly
+from the filesystem (e.g. via ftp). To view results of a previously completed job:
+
+```matlabsession
+>> % Get a handle to the job with ID 2
+>> job2 = c.Jobs(2);
+```
+
+!!! note
+
+ You can view a list of your jobs, as well as their IDs, using the above `c.Jobs` command.
+
+ ```matlabsession
+ >> % Fetch results for job with ID 2
+ >> job2.fetchOutputs{:}
+ ```
+
+#### Parallel Batch Job
+
+You can also submit parallel workflows with the `batch` command. Let’s use the following example
+for a parallel job, which is saved as `parallel_example.m`.
+
+```matlab
+function [t, A] = parallel_example(iter)
+
+if nargin==0
+ iter = 8;
+end
+
+disp('Start sim')
+
+t0 = tic;
+parfor idx = 1:iter
+ A(idx) = idx;
+ pause(2)
+ idx
+end
+t = toc(t0);
+
+disp('Sim completed')
+
+save RESULTS A
+
+end
+```
+
+This time when you use the `batch` command, to run a parallel job, you will also specify a MATLAB
+Pool.
+
+```matlabsession
+>> % Get a handle to the cluster
+>> c = parcluster;
+
+>> % Submit a batch pool job using 4 workers for 16 simulations
+>> job = c.batch(@parallel_example, 1, {16}, 'Pool',4, ...
+ 'CurrentFolder','.', 'AutoAddClientPath',false);
+
+>> % View current job status
+>> job.State
+
+>> % Fetch the results after a finished state is retrieved
+>> job.fetchOutputs{:}
+ans =
+ 8.8872
+```
+
+The job ran in 8.89 seconds using four workers. Note that these jobs will always request N+1 CPU
+cores, since one worker is required to manage the batch job and pool of workers. For example, a
+job that needs eight workers will consume nine CPU cores.
+
+You might run the same simulation but increase the Pool size. This time, to retrieve the results later,
+you will keep track of the job ID.
+
+!!! note
+
+ For some applications, there will be a diminishing return when allocating too many workers, as
+ the overhead may exceed computation time.
+
+ ```matlabsession
+ >> % Get a handle to the cluster
+ >> c = parcluster;
+
+ >> % Submit a batch pool job using 8 workers for 16 simulations
+ >> job = c.batch(@parallel_example, 1, {16}, 'Pool', 8, ...
+ 'CurrentFolder','.', 'AutoAddClientPath',false);
+
+ >> % Get the job ID
+ >> id = job.ID
+ id =
+ 4
+ >> % Clear job from workspace (as though you quit MATLAB)
+ >> clear job
+ ```
+
+Once you have a handle to the cluster, you can call the `findJob` method to search for the job with
+the specified job ID.
+
+```matlabsession
+>> % Get a handle to the cluster
+>> c = parcluster;
+
+>> % Find the old job
+>> job = c.findJob('ID', 4);
+
+>> % Retrieve the state of the job
+>> job.State
+ans =
+ finished
+>> % Fetch the results
+>> job.fetchOutputs{:};
+ans =
+ 4.7270
+```
+
+The job now runs in 4.73 seconds using eight workers. Run code with different number of workers to
+determine the ideal number to use. Alternatively, to retrieve job results via a graphical user
+interface, use the Job Monitor (Parallel > Monitor Jobs).
+
+
+{: summary="Retrieve job results via GUI using the Job Monitor." align="center"}
+
+#### Debugging
+
+If a serial job produces an error, call the `getDebugLog` method to view the error log file. When
+submitting independent jobs, with multiple tasks, specify the task number.
+
+```matlabsession
+>> c.getDebugLog(job.Tasks(3))
+```
+
+For Pool jobs, only specify the job object.
+
+```matlabsession
+>> c.getDebugLog(job)
+```
+
+When troubleshooting a job, the cluster admin may request the scheduler ID of the job. This can be
+derived by calling `schedID`.
+
+```matlabsession
+>> schedID(job)
+ans =
+ 25539
+```
+
+#### Further Reading
+
+To learn more about the MATLAB Parallel Computing Toolbox, check out these resources:
+
+* [Parallel Computing Coding
+ Examples](https://www.mathworks.com/help/parallel-computing/examples.html)
+* [Parallel Computing Documentation](http://www.mathworks.com/help/distcomp/index.html)
+* [Parallel Computing Overview](http://www.mathworks.com/products/parallel-computing/index.html)
+* [Parallel Computing
+ Tutorials](http://www.mathworks.com/products/parallel-computing/tutorials.html)
+* [Parallel Computing Videos](http://www.mathworks.com/products/parallel-computing/videos.html)
+* [Parallel Computing Webinars](http://www.mathworks.com/products/parallel-computing/webinars.html)
diff --git a/doc.zih.tu-dresden.de/docs/software/misc/matlab_monitor_jobs.png b/doc.zih.tu-dresden.de/docs/software/misc/matlab_monitor_jobs.png
new file mode 100644
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new file mode 100644
index 0000000000000000000000000000000000000000..481ab9a1d1a18515abcda82fbdb7d1ab3b580a5e
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diff --git a/doc.zih.tu-dresden.de/docs/software/papi.md b/doc.zih.tu-dresden.de/docs/software/papi.md
index 7460e3deef48bdf991e1b6fda36332cf0fc149b0..d8108bba3048da33661e0dd320a2807a0dd001aa 100644
--- a/doc.zih.tu-dresden.de/docs/software/papi.md
+++ b/doc.zih.tu-dresden.de/docs/software/papi.md
@@ -105,11 +105,11 @@ multiple events, please check which events can be measured concurrently using th
The PAPI tools must be run on the compute node, using an interactive shell or job.
!!! example "Example: Determine the events on the partition `romeo` from a login node"
- Let us assume, that you are in project `p_marie`. Then, use the following commands:
+ Let us assume, that you are in project `p_number_crunch`. Then, use the following commands:
```console
marie@login$ module load PAPI
- marie@login$ salloc --account=p_marie --partition=romeo
+ marie@login$ salloc --account=p_number_crunch --partition=romeo
[...]
marie@compute$ srun papi_avail
marie@compute$ srun papi_native_avail
@@ -121,12 +121,12 @@ Instrument your application with either the high-level or low-level API. Load th
compile your application against the PAPI library.
!!! example
- Assuming that you are in project `p_marie`, use the following commands:
+ Assuming that you are in project `p_number_crunch`, use the following commands:
```console
marie@login$ module load PAPI
marie@login$ gcc app.c -o app -lpapi
- marie@login$ salloc --account=p_marie --partition=romeo
+ marie@login$ salloc --account=p_number_crunch --partition=romeo
marie@compute$ srun ./app
[...]
# Exit with Ctrl+D
diff --git a/doc.zih.tu-dresden.de/docs/software/private_modules.md b/doc.zih.tu-dresden.de/docs/software/private_modules.md
index 6dd2d3d0498d78ca188c9af1af272fa3e6e6537d..00982700ec5bc35fe757660897cc1631453a820f 100644
--- a/doc.zih.tu-dresden.de/docs/software/private_modules.md
+++ b/doc.zih.tu-dresden.de/docs/software/private_modules.md
@@ -27,12 +27,12 @@ marie@compute$ cd privatemodules/<sw_name>
```
Project private module files for software that can be used by all members of your group should be
-located in your global projects directory, e.g., `/projects/p_marie/privatemodules`. Thus, create
+located in your global projects directory, e.g., `/projects/p_number_crunch/privatemodules`. Thus, create
this directory:
```console
-marie@compute$ mkdir --verbose --parents /projects/p_marie/privatemodules/<sw_name>
-marie@compute$ cd /projects/p_marie/privatemodules/<sw_name>
+marie@compute$ mkdir --verbose --parents /projects/p_number_crunch/privatemodules/<sw_name>
+marie@compute$ cd /projects/p_number_crunch/privatemodules/<sw_name>
```
!!! note
@@ -110,7 +110,7 @@ marie@login$ module use $HOME/privatemodules
for your private module files and
```console
-marie@login$ module use /projects/p_marie/privatemodules
+marie@login$ module use /projects/p_number_crunch/privatemodules
```
for group private module files, respectively.
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/scs5_software.md b/doc.zih.tu-dresden.de/docs/software/scs5_software.md
index 2907bb9f35937ce7ca5573b0c1752989c7fa3d95..73311c7fcc78001ad2dc201c19c0eb657397b33a 100644
--- a/doc.zih.tu-dresden.de/docs/software/scs5_software.md
+++ b/doc.zih.tu-dresden.de/docs/software/scs5_software.md
@@ -49,7 +49,7 @@ still work under SCS5. That's why those modenv versions are hidden.
Example:
```Bash
-$ ml modenv/classic ansys/19.0
+marie@compute$ ml modenv/classic ansys/19.0
The following have been reloaded with a version change:
1) modenv/scs5 => modenv/classic
diff --git a/doc.zih.tu-dresden.de/mkdocs.yml b/doc.zih.tu-dresden.de/mkdocs.yml
index 08d2926a0976e0391b12bcec6e647e825483bb60..cdd4294bcd44bb599e4698a9efc02a7e657a566e 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
@@ -223,4 +223,4 @@ extra:
plugins:
- search
- - markdown-caption
\ No newline at end of file
+ - markdown-caption
diff --git a/doc.zih.tu-dresden.de/tud_theme/partials/toc.html b/doc.zih.tu-dresden.de/tud_theme/partials/toc.html
index aa0d25faf7db6bf0cd1478daf6106edaf8b5dd8f..341dccc3bbfb70ee83b89c7606ae1dcf3e19a8a6 100644
--- a/doc.zih.tu-dresden.de/tud_theme/partials/toc.html
+++ b/doc.zih.tu-dresden.de/tud_theme/partials/toc.html
@@ -40,7 +40,7 @@
HPC Support
</label>
<p>
- <img class="operation-status-logo" alt="operation status" src="https://bs.zih.tu-dresden.de/bs.php?action=status_icon&dienst=6">
+ <img class="operation-status-logo" alt="operation status" src="https://doc.zih.tu-dresden.de/misc/status/bs.php?action=status_icon&dienst=6">
<a href="http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/aktuelles/betriebsstatus/index_html?action=dienstinfo&dienst=6">
Operation Status
</a>
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/util/check-spelling.sh b/doc.zih.tu-dresden.de/util/check-spelling.sh
index f6b3fca83d71283a6430f260f5a75bdbca3a7e2a..d97f93e20df73b9ea47e501e7196f605f0cacd48 100755
--- a/doc.zih.tu-dresden.de/util/check-spelling.sh
+++ b/doc.zih.tu-dresden.de/util/check-spelling.sh
@@ -7,7 +7,7 @@ basedir=`dirname "$scriptpath"`
basedir=`dirname "$basedir"`
wordlistfile=$(realpath $basedir/wordlist.aspell)
branch="origin/${CI_MERGE_REQUEST_TARGET_BRANCH_NAME:-preview}"
-files_to_skip=(doc.zih.tu-dresden.de/docs/accessibility.md doc.zih.tu-dresden.de/docs/data_protection_declaration.md doc.zih.tu-dresden.de/docs/legal_notice.md)
+files_to_skip=(doc.zih.tu-dresden.de/docs/accessibility.md doc.zih.tu-dresden.de/docs/data_protection_declaration.md doc.zih.tu-dresden.de/docs/legal_notice.md doc.zih.tu-dresden.de/docs/access/key_fingerprints.md)
aspellmode=
if aspell dump modes | grep -q markdown; then
aspellmode="--mode=markdown"
diff --git a/doc.zih.tu-dresden.de/util/grep-forbidden-patterns.sh b/doc.zih.tu-dresden.de/util/grep-forbidden-patterns.sh
index b2f8b3478d7d8aaa2247b392c97dc09d09348743..cacde0d9ee84f903a55d3109dcd330d3e43184ad 100755
--- a/doc.zih.tu-dresden.de/util/grep-forbidden-patterns.sh
+++ b/doc.zih.tu-dresden.de/util/grep-forbidden-patterns.sh
@@ -46,9 +46,9 @@ i ^[ |]*|$
Avoid spaces at end of lines.
doc.zih.tu-dresden.de/docs/accessibility.md
i [[:space:]]$
-When referencing projects, please use p_marie for consistency.
+When referencing projects, please use p_number_crunch for consistency.
-i \<p_ p_marie
+i \<p_ p_number_crunch
Avoid \`home\`. Use home without backticks instead.
i \`home\`
diff --git a/doc.zih.tu-dresden.de/wordlist.aspell b/doc.zih.tu-dresden.de/wordlist.aspell
index c23a24974f141644fa58e309cd304c300c94b4db..8bfd5ba596e6858e6d8f7a4f468a0b68330e751b 100644
--- a/doc.zih.tu-dresden.de/wordlist.aspell
+++ b/doc.zih.tu-dresden.de/wordlist.aspell
@@ -1,4 +1,4 @@
-personal_ws-1.1 en 427
+personal_ws-1.1 en 429
Abaqus
Addon
Addons
@@ -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
@@ -33,25 +34,25 @@ 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
+Datamover
DataParallel
dataset
Dataset
@@ -85,6 +86,7 @@ engl
english
env
EPYC
+ESER
Espresso
ESSL
facto
@@ -93,18 +95,20 @@ FFT
FFTW
filesystem
filesystems
-flink
Flink
+flink
FlinkExample
FMA
foreach
Fortran
+Frontend
Galilei
Gauss
Gaussian
GBit
GDB
GDDR
+GFlop
GFLOPS
gfortran
GiB
@@ -115,12 +119,13 @@ GitLab's
glibc
Gloo
gnuplot
-gpu
GPU
+gpu
GPUs
gres
GROMACS
GUIs
+Hackenberg
hadoop
haswell
HBM
@@ -129,16 +134,18 @@ HDF
HDFS
HDFView
hiera
-horovod
+Hochleistungsrechner
Horovod
+horovod
horovodrun
hostname
Hostnames
-hpc
HPC
+hpc
hpcsupport
HPE
HPL
+HRSK
html
hvd
hyperparameter
@@ -146,6 +153,7 @@ hyperparameters
hyperthreading
icc
icpc
+iDataPlex
ifort
ImageNet
img
@@ -160,11 +168,12 @@ ipython
IPython
ISA
Itanium
+Jards
jobqueue
jpg
jss
-jupyter
Jupyter
+jupyter
JupyterHub
JupyterLab
Jupytext
@@ -177,23 +186,24 @@ LAPACK
lapply
Leichtbau
LINPACK
-linter
Linter
+linter
lmod
LoadLeveler
localhost
lsf
lustre
+macOS
markdownlint
Mathematica
MathKernel
MathWorks
-matlab
-MatLab
+MATLAB
Matplotlib
MEGWARE
mem
Memcheck
+MFlop
MiB
Microarchitecture
MIMD
@@ -209,6 +219,7 @@ Montecito
mortem
Mortem
mountpoint
+Mpi
mpi
mpicc
mpiCC
@@ -217,8 +228,8 @@ mpif
mpifort
mpirun
multicore
-multiphysics
Multiphysics
+multiphysics
multithreaded
Multithreading
NAMD
@@ -226,11 +237,13 @@ natively
nbgitpuller
nbsp
NCCL
+NEC
Neptun
NFS
NGC
-nodelist
+NHR
NODELIST
+nodelist
NRINGS
Nsight
ntasks
@@ -256,25 +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
@@ -283,8 +297,8 @@ PMI
png
PowerAI
ppc
-pre
Pre
+pre
preload
Preload
preloaded
@@ -301,19 +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
@@ -324,8 +339,8 @@ RStudio
rsync
Rsync
runnable
-runtime
Runtime
+runtime
sacct
salloc
Sandybridge
@@ -358,6 +373,7 @@ SMP
SMT
SparkExample
spawner
+Speicherkomplex
spython
squeue
srun
@@ -377,22 +393,24 @@ SXM
TBB
TCP
TensorBoard
-tensorflow
TensorFlow
+tensorflow
+TFlop
TFLOPS
Theano
tmp
-todo
ToDo
+todo
toolchain
toolchains
-torchvision
Torchvision
+torchvision
tracefile
tracefiles
tracepoints
transferability
Trition
+und
undistinguishable
unencrypted
uplink
@@ -412,6 +430,8 @@ VMs
VMSize
VNC
VPN
+VRs
+walltime
WebVNC
WinSCP
WML
@@ -425,7 +445,8 @@ XLC
XLF
Xming
yaml
-zih
+Zeiss
ZIH
ZIH's
+ZRA
ZSH