Uppsala Multidisciplinary Center for Advanced Computational Science

UPPNEX concepts and terms

This list is incomplete. Please write to support@uppmax.uu.se, if you notice errors or omissions.

Deputy

This title is invented at UPPMAX for someone that the principal investigator of a project has delegated the rights and duties for the project. In SUPR, the deputy is called the proxy.

The deputy may handle all aspects of the project, except creation, termination and extension.

P.I.

Means principal investigator. Att UPPMAX it is the person that applies for the project. She or he has the right to handle all aspects of the project.

According to the rules for SNIC and NGI, this person must be a senior scientist, defined as a person that is at least at the level of assistant professor (forskarassistent).

Project directory

This is a file directory that is associated with the project and that all project members may use.

If the project name is b2XXXYYY, the project directory will be given the name /proj/b2XXXYYY.

The project's usage and quota are measured. You can produce a report of those values for your projects with the command "uquota".

If the usage goes above the quota, there are two ways to go:

  1. Remove files or compress files, so the usage goes below the quota.
  2. Apply for a higher quota. If the application is for some reason denied, you still need to go below the quota.

Normally there is an automatic warning sent by e-mail to the Technical, Deputy and P.I. when the quota is overdrafted.

Within the project directory, normally at least the following subdirectories will be found:

  • INBOX - where NextGen Sequencing Platforms can deliver files. (Please note that the INBOX directory is not backed up. Deliveries should not be kept there, but moved elsewhere.)
  • nobackup - where jobs can be run and where other files that do not need a backup may reside
  • private - where the project members only can read files (contains also a subdirectory, also named nobackup, where jobs can be run and where other files that do not need a backup may reside).

The two directories named "nobackup", that are mentioned above can physically be located in other storage systems. In that case, there is a separate file quota for the project's usage within that storage system.

Project_nobackup directory

This is a file directory, that is associated with the project and that all project members may use.

Here is a good place to run project jobs. If you have other files that do not need a backup, this is a good place also for them.

As the name indicates, no automatic backups will be made. If these files by accident are removed, you have to rerun your jobs or once again copy your data to this place. This is a possible inconvenience, but gives UPPMAX the opportunity to buy much more storage for the projects, because backup storage is much more expensive compared to non-backuped storage.

If the project name is b2XXXYYY, the project_nobackup directory will be given the name /proj/b2XXXYYY/nobackup.

The project's usage and quota are measured. You can produce a report of those values for your projects with the command "uquota".

If the usage goes above the quota, there are two ways to go:

  1. Remove files or compress files, so the usage goes below the quota.
  2. Apply for a higher quota. If the application is for some reason denied, you still need to go below the quota.

Normally there is an automatic warning sent by e-mail to the Technical, Deputy or P.I., when the quota is overdrafted, and some e-mail nagging about the overdraft if you do not quickly go below the quota [not yet implemented at the end of January].

Within the project directory, normally at least the following subdirectory will be found:

  • private - where the project members only can read files

Technical

This title is invented at UPPMAX for someone that handles technical aspects of the project. Those aspects are primarily the administration of the project directories.

The P.I. (and Deputy) decides on whom to give this title. That person must have a user account, so an appointment also indirectly means a membership within the project.

The Technical may decide on the permissions and ownerships of all files within the project directories, by contacting UPPMAX support. This person normally gets e-mail warnings when there is a file quota overdraft.

The Technical may not decide on other aspects of the project, like end date and member list.