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o_guest's profile
Olivia Guest | Ολίβια Γκεστ
Olivia Guest | Ολίβια Γκεστ
Olivia Guest | Ολίβια Γκεστ
@o_guest

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Olivia Guest | Ολίβια Γκεστ

@o_guest

• goth gremlin • computational cognitive/neuroscience modeling • geek & techish Cypriot • plant aficionada • came up with #bropenscience • http://neuroplausible.com  •

Τότεναμ, Λονδίνο & Cyprus
olivia.science
Joined October 2015

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    1. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 14 Jul 2018
      • Report Tweet

      This is so cool. Automatically create a @Docker from your @github repo and create a @ProjectJupyter notebook too! Great idea to help with code lifespan!pic.twitter.com/sK8Z1GtJdm

      13 replies 312 retweets 835 likes
      Show this thread
    2. Dr Lucy Forrest‏ @LucyRForrest 15 Jul 2018
      • Report Tweet
      Replying to @o_guest @Docker and

      Our main issue is that @Docker requires permissions that academic compute systems won’t allow. We have to use #Singularity instead. Great idea though!

      3 replies 1 retweet 4 likes
      Olivia Guest | Ολίβια Γκεστ‏ @o_guest 15 Jul 2018
      • Report Tweet
      Replying to @LucyRForrest @Docker and

      I wish I could say more, I'm tagging @mybinderteam.

      4:48 AM - 15 Jul 2018
      • 2 Likes
      • pacoramon Dr Lucy Forrest
      1 reply 0 retweets 2 likes
        1. New conversation
        2. Niema Moshiri‏ @niemasd 15 Jul 2018
          • Report Tweet
          Replying to @o_guest @LucyRForrest and

          Singularity is compatible with Docker images (albeit somewhat painfully at times). I have a tool whose image can be run using Docker (https://github.com/niemasd/FAVITES/blob/master/run_favites_docker.py …) and Singularity (https://github.com/niemasd/FAVITES/blob/master/run_favites_singularity.py …) (same image). Hopefully that helps!

          1 reply 0 retweets 2 likes
        3. Dr Lucy Forrest‏ @LucyRForrest 15 Jul 2018
          • Report Tweet
          Replying to @niemasd @o_guest and

          I believe the problem is the docker images themselves raise a security hazard, but I will double check - thanks for following up!

          1 reply 0 retweets 1 like
        4. Singularity‏ @SingularityApp 15 Jul 2018
          • Report Tweet
          Replying to @LucyRForrest @niemasd and

          We’d love to hear more about why it is painful too! BTW: full OCI image (and runtime) support for Singularity coming in just a few months which will solve any conversion painpoints! The countdown to the release is on!

          1 reply 0 retweets 2 likes
        5. Niema Moshiri‏ @niemasd 15 Jul 2018
          • Report Tweet
          Replying to @SingularityApp @LucyRForrest and

          I think the difficulties arose from the strict security of our HPC cluster. I was getting "Configuration disallows users from running directory based containers" when doing "singularity shell" directly on the docker:// string

          2 replies 0 retweets 2 likes
        6. Singularity‏ @SingularityApp 15 Jul 2018
          • Report Tweet
          Replying to @niemasd @LucyRForrest and

          Ahh, the best practice for both Singularity v2 and v3 is to build (or pull) the container from Docker and then use the built container. With that said I wonder why the admins choose to disable sandbox/directory based containers.

          1 reply 0 retweets 2 likes
        7. Dr Lucy Forrest‏ @LucyRForrest 16 Jul 2018
          • Report Tweet
          Replying to @SingularityApp @niemasd and

          I think because sysadmin permissions are required to create the container and therefore could modify directories within the cluster? @GiacomoFiorin @antoniyaaleks @EdoSarti

          1 reply 0 retweets 2 likes
        8. Niema Moshiri‏ @niemasd 16 Jul 2018
          • Report Tweet
          Replying to @LucyRForrest @SingularityApp and

          This was on the @SDSC_UCSD (I believe on Comet and TSCC), so perhaps they can provide more information regarding why they chose the security settings they did, but I agree that it was likely a "prevent modifying cluster directories" security issue

          0 replies 0 retweets 1 like
        9. End of conversation

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