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| # 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 [email protected] 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: {[email protected]} | ||
| - 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: {[email protected]} | ||
| - 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 [email protected] 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 [email protected] 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: {[email protected]} | ||
| - 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: {[email protected]} | ||
| - 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 [email protected] 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. |