From b9e4bbc95a9c31de50929bb44778c2a332d287d9 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Thu, 29 Aug 2024 10:21:49 +0200 Subject: [PATCH] add scratch to projects form; LF change --- bih-cluster/docs/admin/getting-access.md | 255 ++++++++++++----------- 1 file changed, 128 insertions(+), 127 deletions(-) diff --git a/bih-cluster/docs/admin/getting-access.md b/bih-cluster/docs/admin/getting-access.md index 85be8d0a5..fab1eecae 100644 --- a/bih-cluster/docs/admin/getting-access.md +++ b/bih-cluster/docs/admin/getting-access.md @@ -1,127 +1,128 @@ -# Getting Access -Access to the BIH HPC cluster is conceptually based on **user groups** (also known as labs or units) and **projects**. -Users have a relatively limited storage quota within their private home folder and store big data primarily within their group's work space or in project folders. -**Projects** are collaborative efforts involving multiple PIs/groups and are allocated separate storage space on the cluster. - -Independent group leaders at BIH/Charité/MDC can request a **group** on the cluster and name group **members**. -The work group **leader** (the group PI) bears the responsibility for the group's **members** and ensures that [cluster policies and etiquette](./policies.md) are followed. -In brief: Fair usage rules apply and the cluster ist not to be abused for unethical or illegal purposes. -Major and/or continued violations may lead to exclusion of the entire group. - -The group leader may also name one **delegate** (typically an IT-savvy Post-Doc) who is thereby allowed to take decision about cluster usage and work group management on behalf of the group leader. -The above mentioned responsibilities stay with the group leader. - -!!! note - - - A Charité or MDC user account is required for accessing HPC 4 Research. - - Please only use email addresses from the institutions Charite, BIH, or MDC in the forms below. - -## Work Groups and Users -All cluster users are member of exactly one primary work group. -This affiliation is usually defined by real life organisational structures within Charité/BIH/MDC. -Leaders of independent research groups (PIs) can apply for a new cluster work group as follows: - -1. The group leader sends an email to hpc-helpdesk@bih-charite.de and includes the filled-out form below. - Please read the notes box before sending. -2. The HPC helpdesk decides on the request and creates corresponding objects on the cluster (users, groups, directories). -3. New users are notified and sent further instructions via email. - -!!! warning "Important" - Changes to an existing group (adding new users, changes in resources, etc.) can only be requested by group leaders and delegates. - -### Form: New Group -Example values are given in curly braces. - -``` -# Group "ag-{doe}" -Group leader/PI: {John Doe} -Delegate [optional]: {Max Mustermann} -Purpose of cluster usage [short]: {RNA-seq analysis in colorectal cancer} - -Required resources: -- Tier 1 storage: {1 TB} -- Tier 1 scratch: {10 TB} -- Tier 2 storage: {10 TB} - -# Users -## User 1 -- first name: {John} -- last name: {Doe} -- affiliation: {Charité, Department of Oncology} -- institute email: {john.doe@charite.de} -- user has account with - - [ ] BIH - - [x] Charite - - [ ] MDC -- BIH/Charité/MDC user name: {doej} - -## User 2 -[etc.] -``` - -### Form: Add User to Group -Example values are given in curly braces. - -``` -# New user of AG {Doe} -- first name: {Mia} -- last name: {Smith} -- affiliation: {Charité, Department of Oncology} -- institute email: {mia.smith@charite.de} -- user has account with - - [ ] BIH - - [x] Charite - - [ ] MDC -- BIH/Charité/MDC user name: {smithm} -``` - -!!! note "Notes" - - All cluster groups must have an owner and may have one delegate. - - Group ownership implies control but also accountability for their group files and members. - - Users can only be members of one primary work group. - - We **strongly** dis-encourage on-boarding non-lab members into your group. - This cause biases in usage accounting, may raise concerns in IT security and data privacy audits and also puts unfair responsibilities on the group leader. - -## Projects - -Projects are secondary user groups to enable: - -- collaboration and data sharing across different work groups, -- fine-grained allocation of additional storage resources, -- organising data in a fine-grained manner for better data lifecycle management. - -Project creation can be initiated by group leaders and group delegates as follows: - -1. Send an email to hpc-helpdesk@bih-charite.de and includes the filled-out form below. - Please read the notes box before sending. -2. The HPC helpdesk decides on the request and creates corresponding objects on the cluster (groups, directories). - -!!! warning "Important" - Changes to an existing project (adding new users, changes in resources, etc.) can only be requested by project owners and delegates. - Please send us cluster user names for adding new project members. - -### Form - -Example values are given in curly braces. - -``` -# Project "{doe-dbgap-rna}" -Project owner: {John Doe}, {doej_c} -Delegate [optional]: {Max Mustermann}, {musterm_c} -Purpose of cluster usage [short]: {RNA-seq data from dbGAP} - -Required resources: -- Tier 1 storage: {0 TB} -- Tier 2 storage: {1 TB} - -Additional members (cluster user names): -- {sorgls_c} -- ... -``` - -!!! note "Notes" - - All projects must have one owner and may have one delegate. - - Please note that we will enforce [kebab case]([url](https://en.wikipedia.org/wiki/Letter_case#Kebab_case)) for all project names and folders. - - Tier 1 project storage will be supplemented with 10 TB of T1 scratch by default. - - Users can be associated with multiple projects. - - Project membership does not grant cluster access. A primary group affiliation is still required. +# Getting Access +Access to the BIH HPC cluster is conceptually based on **user groups** (also known as labs or units) and **projects**. +Users have a relatively limited storage quota within their private home folder and store big data primarily within their group's work space or in project folders. +**Projects** are collaborative efforts involving multiple PIs/groups and are allocated separate storage space on the cluster. + +Independent group leaders at BIH/Charité/MDC can request a **group** on the cluster and name group **members**. +The work group **leader** (the group PI) bears the responsibility for the group's **members** and ensures that [cluster policies and etiquette](./policies.md) are followed. +In brief: Fair usage rules apply and the cluster ist not to be abused for unethical or illegal purposes. +Major and/or continued violations may lead to exclusion of the entire group. + +The group leader may also name one **delegate** (typically an IT-savvy Post-Doc) who is thereby allowed to take decision about cluster usage and work group management on behalf of the group leader. +The above mentioned responsibilities stay with the group leader. + +!!! note + + - A Charité or MDC user account is required for accessing HPC 4 Research. + - Please only use email addresses from the institutions Charite, BIH, or MDC in the forms below. + +## Work Groups and Users +All cluster users are member of exactly one primary work group. +This affiliation is usually defined by real life organisational structures within Charité/BIH/MDC. +Leaders of independent research groups (PIs) can apply for a new cluster work group as follows: + +1. The group leader sends an email to hpc-helpdesk@bih-charite.de and includes the filled-out form below. + Please read the notes box before sending. +2. The HPC helpdesk decides on the request and creates corresponding objects on the cluster (users, groups, directories). +3. New users are notified and sent further instructions via email. + +!!! warning "Important" + Changes to an existing group (adding new users, changes in resources, etc.) can only be requested by group leaders and delegates. + +### Form: New Group +Example values are given in curly braces. + +``` +# Group "ag-{doe}" +Group leader/PI: {John Doe} +Delegate [optional]: {Max Mustermann} +Purpose of cluster usage [short]: {RNA-seq analysis in colorectal cancer} + +Required resources: +- Tier 1 storage: {1 TB} +- Tier 1 scratch: {10 TB} +- Tier 2 storage: {10 TB} + +# Users +## User 1 +- first name: {John} +- last name: {Doe} +- affiliation: {Charité, Department of Oncology} +- institute email: {john.doe@charite.de} +- user has account with + - [ ] BIH + - [x] Charite + - [ ] MDC +- BIH/Charité/MDC user name: {doej} + +## User 2 +[etc.] +``` + +### Form: Add User to Group +Example values are given in curly braces. + +``` +# New user of AG {Doe} +- first name: {Mia} +- last name: {Smith} +- affiliation: {Charité, Department of Oncology} +- institute email: {mia.smith@charite.de} +- user has account with + - [ ] BIH + - [x] Charite + - [ ] MDC +- BIH/Charité/MDC user name: {smithm} +``` + +!!! note "Notes" + - All cluster groups must have an owner and may have one delegate. + - Group ownership implies control but also accountability for their group files and members. + - Users can only be members of one primary work group. + - We **strongly** dis-encourage on-boarding non-lab members into your group. + This cause biases in usage accounting, may raise concerns in IT security and data privacy audits and also puts unfair responsibilities on the group leader. + +## Projects + +Projects are secondary user groups to enable: + +- collaboration and data sharing across different work groups, +- fine-grained allocation of additional storage resources, +- organising data in a fine-grained manner for better data lifecycle management. + +Project creation can be initiated by group leaders and group delegates as follows: + +1. Send an email to hpc-helpdesk@bih-charite.de and includes the filled-out form below. + Please read the notes box before sending. +2. The HPC helpdesk decides on the request and creates corresponding objects on the cluster (groups, directories). + +!!! warning "Important" + Changes to an existing project (adding new users, changes in resources, etc.) can only be requested by project owners and delegates. + Please send us cluster user names for adding new project members. + +### Form + +Example values are given in curly braces. + +``` +# Project "{doe-dbgap-rna}" +Project owner: {John Doe}, {doej_c} +Delegate [optional]: {Max Mustermann}, {musterm_c} +Purpose of cluster usage [short]: {RNA-seq data from dbGAP} + +Required resources: +- Tier 1 work: {0 TB} +- Tier 1 scratch: {0 TB} +- Tier 2 storage: {1 TB} + +Additional members (cluster user names): +- {sorgls_c} +- ... +``` + +!!! note "Notes" + - All projects must have one owner and may have one delegate. + - Please note that we will enforce [kebab case]([url](https://en.wikipedia.org/wiki/Letter_case#Kebab_case)) for all project names and folders. + - Tier 1 project storage will be supplemented with 10 TB of T1 scratch by default. + - Users can be associated with multiple projects. + - Project membership does not grant cluster access. A primary group affiliation is still required.