Cluster 2 account

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Get started on Cluster 2.

  • 1. Your account. Get it from your system administrator Benjamin Wong (or John Irwin).
  • 2. Your home is on /nfs/home/<your_id>/. This area is backed up and is for important persistent files.
  • 3. You should run docking jobs and other intense calculations in /nfs/work/<your_id>/ which is symlinked to ~/work by default.
  • 4. You should keep static data (e.g. crystallography data, results of published papers) in /nfs/store/<your_id>/, which is symlinked to ~/store by default.
  • 5. Lab guests get 100GB in each of these areas, and lab members get 500GB. You may request more, just ask!
  • 6. If you go over your limit, you get email warnings for 2 weeks. If the problem remains unresolved after two weeks, the sysadmin will have a chat with you.
  • 7. You may choose bash or tcsh to be your default shell. We don't care. Everything should work equally well with both.
  • 8. There is a special kind of static data, databases, for which you may request space. They will go in /nfs/db/<your_id>/ or perhaps /nfs/db/<dbname>/ e.g. /nfs/db/zinc/ and /nfs/db/dude/ and /nfs/db/pdb and so on.
  • 9. Please run large docking jobs on /nfs/work and not on /nfs/store or /nfs/home. Find a way to archive key input files and possibly output files to your home or store directories. To be clear, these disk are all top quality with two levels of redundancy, so we are really not expecting you to experience a disk failure. But we cannot say it won't happen, so please take precautions. When you publish a paper, please delete what you can, compress the rest, and move it to /store/. Do not leave it on /work/ if you are no longer using it actively.
  • 10. Set up your account so that you can log in all across the cluster without a password. ssh-keygen; cd .ssh; cp id_rsa.pub authorized_keys; chmod 600 authorized_keys;
  • 11. Software lives in /nfs/soft/. All our machines are 64 bit Centos 6.5 unless otherwise indicated.
  • 12. Python 2.7 and 3.0 are installed. We currently recommend 2.7 because of library availability, but that may change soon. (April 2014)
  • 13. If you use tcsh, begin by copying .cshrc from /nfs/soft/labenv/cshrc. If you use bash, start with .bashrc from /nfs/soft/labenv/bashrc.

Back to Cluster 2.