The information on this page only applies to Marvin. Bender does not have a concept of group shares, and Bonna is covered in the Bonna wiki.
¶ Marvin Research Groups and Fair Shares
On Marvin, contingents of compute time are allocated to different research groups. When you register for Marvin, you need to specify who is your research group leader. This is typically, but not necessarily, a professor. Your group leader will then be asked to confirm that you are part of their group before you can run jobs.
You can log in to Marvin once you receive your access data, but you cannot run any compute jobs until your group leader has added you to their group. Every user needs to belong to at least one group to be able to run jobs.
When your group leader has added you, you will get an e-mail notification. It may take up to two hours after your group leader has added you until you get notified.
Your user and your group membership are separate things. When you are removed from all groups, you will still be able to log in to Marvin, but you will no longer be able to compute on it.
You can belong to more than one group. If you cooperate with multiple groups on different projects, or if you change groups, you can fill out the registration form again with your new group leader. Of course, your new group leader needs to do the same if they are not already registered.
¶ Running jobs
When you run a compute job, you always need to specify which contingent you want to use for the job.
SLURM calls these contingents accounts, but they are not to be confused with user accounts. Rather, you can think of them like bank accounts that all group members can access.
To list which account(s) you belong to, you can use the following command on Marvin:
sacctmgr list user <Your HPC user ID>
To run a job with a certain account, you need to use the --account option in your sbatch call or job script options, click here for more information about job scripts. Remember that you do not need to do this on Bender.
sbatch --account=<Your group name> ...
To see which account(s) you belong to, you can use the command sshare.
You can belong to multiple accounts. It is in the power of each research group leader to add you to their account.
Tip: if you do not want to use the --account option every time, you can set your default account with the following command:
$ sacctmgr modify user set defaultaccount=<NAME OF YOUR ACCOUNT> where name=<YOUR USER NAME>
¶ Sharing files and directories with your group
You might want to share your data with others from your research group. You can do this on Marvin both with data in your home directory and in your workspaces. In both cases, basic Linux mechanisms like POSIX groups and file permissions are used, so if you are familiar with the Linux console, you can use file permissions to the extent that every (non-root) user can, otherwise, see our Linux tutorial, particularly the section on users and permissions.
By default, your primary group on Marvin is hpcuser. Your membership in your research group(s) is also implemented via POSIX groups, and you can use the normal Linux commands (e.g. id) to list all your groups. In Linux, all files and directories also have an owning user and an owning group, which is hpcuser by default.
In other words, if you want to share data with your research group, all you need is already there. For example, if you want to share a folder in your home directory, you can change the owning group of that directory. Here is an example command to change the owning group:
chown :<group> <directory
E.g.:
chown :ag_demo /home/demo_user/shared_folder
Note the colon before the group name, ensuring that only the group gets changed, not the owning user - you cannot change the owning user without root permissions.
You might want to use the -R option to chown to do this recursively, i.e. for all subdirectories as well.
Also, all directories above your shared directory need to have the x permission for others to actually get to it, and you might need to use chmod here. Your home directory has that permission for everyone by default. You can also control whether your group can read and/or write in this directory with chmod and its various options.
You can also do any of the above for your home directory as a whole. However, we advise caution in sharing everything in your home directory with others.
¶ Setting group for all new files
If you want to ensure that all new files in a certain directory belong to your research group, take a look at the following Linux features:
- The
newgrpcommand, see documentation, to switch your current primary group - The
setgidbit, see Wikipedia umask, see Wikipedia
¶ Marvin: Workspaces
When creating workspaces on Marvin, you can control whether your group has access with the -g and -G options to the ws_allocate command, see the Workspaces user guide. If you want to change the permissions after creating the workspace, you can modify the directory permissions directly as described in the previous sections.
¶ Research group leaders' role
First: As group leader, you have the control over your group's contingent of compute time. This is due to a decision by Uni Bonn leadership that all research groups should be able to use Marvin equally.
You control who uses your contingent by adding and removing users from your group.
Using up a contingent does not stop your group members from running jobs. It only reduces their priority so others get their turn using Marvin. The contingent also regenerates constantly, so your group will only reach the limit if they run many jobs in a short time.
Second: when somebody from your group does not renew their Marvin access, or leaves the university altogether, you assume ownership of their data that is still on Marvin. This is necessary to avoid data protection and other legal problems.
As the group leader, you are also a regular member of your own group and can run compute jobs on Marvin.
You will not need to log in to Marvin to manage your group (but you may if you want to). Additionally, you may delegate group management.
¶ Creating a group share on Marvin
To create a new group share, please fill out the standard Marvin registration form here, and put yourself in as group leader.
From that point, whenever a user applies for Marvin use and specifies you as their group leader, you will get a notification from us. You can then add and remove group members in our web portal, see the instructions below. Your login data for the web portal are the same as for Marvin, and will be in the initial welcome e-mail when you register.
Note that you will not be notified about group members that registered before you. So when you register, there might be somebody from your group already waiting. You will have to coordinate with your group members in this case.
Your group members can log in to Marvin, but they cannot run compute jobs until you have added them to your group. Every user needs to belong to at least one group to be able to run jobs.
Group leadership is initially for five years and can be extended in five-year intervals. When the group's lifetime is about to expire, you will get a notification asking you whether you still want to manage the group.
You do not need to hold a professorship or any other official title to qualify as group leader for our purposes.
¶ Can I delegate group management?
We realize that some group leaders might want to delegate adding and removing users to e.g. their sysadmin or an experienced group member.
For legal and administrative reasons, the group leader needs to exist on our system, and therefore also needs to fill out the registration form. However, it is possible to delegate group management after registering.
For that purpose, the group leader needs to send an e-mail to marvin-support@hpc.uni-bonn.de, from an e-mail address that is recognizably that of the group leader, containing the following:
- The HPC user ID of the group member in question
- The name of the group
- An acknowledgment that the group leader gives consent to delegate group management
¶ Managing your group members
To manage your group's membership, log in to our user management web portal.
You will be asked to change your password the first time you log in.
The link to your group's management page will also be in your e-mail. On your group's page, you can see all users who are members of your group. If you do not see this list, make sure you are in the "Users" tab under the "User Group: <your group name>" heading.
Tip: If you ever need to find your group again, you can go to the group overview page and type your group's name in the search bar.
To remove a user from the group, click the checkbox to the left of their name, then click the Delete button.
To add group members, click the + Add button. A dialog will pop up where you can pick out your group members. Their HPC user IDs will have been e-mailed to you when they requested to join. Click the box next to everyone you want to add on the left, then click the > button to add them. If you do not see their HPC user ID, type it in the "Filter available users" bar and click Filter.
