Confluence Retirement

Due to the feedback from stakeholders and our commitment to not adversely impact USGS science activities that Confluence supports, we are extending the migration deadline to January 2023.

In an effort to consolidate USGS hosted Wikis, myUSGS’ Confluence service is targeted for retirement. The official USGS Wiki and collaboration space is now SharePoint. Please migrate existing spaces and content to the SharePoint platform and remove it from Confluence at your earliest convenience. If you need any additional information or have any concerns about this change, please contact myusgs@usgs.gov. Thank you for your prompt attention to this matter.
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Recording and Presentation:

The Webex recording and slides and are available to CDI Members. Log in to view the recording and slides. If you would like to become a member of CDI, email cdi@usgs.gov.


Topic 1: Yeti info

  • Janice Gordon gave Powerpoint presentation about Yeti (will share on site)
  • Denise: Yeti help group is fantastic at providing help with this. There is a lot of support, so don’t feel intimidated or afraid to ask for help.

 

Q & A

What is UV system and when is it more advantageous?

            UV partition is 3 different nodes on a single machine (512 cpu cores)

            When you need more than one node or larger scratch space

 

Are data transfer nodes in full operation and should we use them yet?

One data transfer node is up and running. Depending on your dataset, supported methods to move data include SFTP, BBCP, GlobusConnect Client. What is not working is hosting our own FTP server connected to Globus. Most encrypted protocols will be supported (i.e., not FTP for uploading).

If you have transfers that take multiple days/weeks, using data transfer node keeps this from impacting other users on login node. Way of separating out resources. Credentials are the same for both login node and data transfer node.

 

More information on wiki for setting permissions?

            Permissions basics document can be produced.

 

Are there plans in the future to create long term archives?

            Yes, as long term as they can keep it. In the hopper to get done is to create storage that can be copied via single command to multiple places. Working with data management to make it easier to publish/release data produced on Yeti via ScienceBase (directly from tape storage).

            They do no blindly backup everything (would take too long). So they put control in users hands to request backup/storage.

  

When sitting in queue, what does “node list resources” mean?

            Scheduler cannot currently find enough resources to satisfy your request (e.g., not enough CPUs free). Priority means someone has higher priority job than you. They also do backfill scheduling policy, if jobs can be fit in front of yours because of free resource need match, that will happen.

            If something set up on Yeti server and seem to be running out of time, you can email and request an extension. Judgement call to be fair and allow everyone to get their work done. Sometimes cannot extend time because someone else is waiting, but will do everything they can to help you get things done. Working on checkpoint restart so you can begin from last checkpoint rather than having to start at beginning. A few hours is easier to accommodate than a few days.

 

 

Topic 2: CDI Communication (Leslie Hu)

 

CDI working groups -> Bioinformatics -> email list, notes, etc.

 

New since last call; can share any page directly from wiki without using email list.

Share button, type cdi-bioinfo and then can share link to page instead of using email list.

 

Leslie would like to put everyone on list; easy to opt out

 

 

Topic for next call?

            Laboratory Management Resources

 

 

 

 

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