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General Tips/Requests

The cluster is a shared resource

Generally expected knowledge + Take care not to use too many resources on the login nodes. Anything CPU, RAM, or input/output intensive should be done on compute nodes rather than one of the login nodes. + Anything more than a quick ls including: copying large files, recursively changing permissions, creating or extracting tar or zip archives, running a find should be done in a session on a compute node. + Data transfers of files larger about 1GB should be done through jhpce-transfer01.jhsph.edu rather than a login node. + Try to avoid having directories with more than 100 files in them. + Try to avoid storing programs and scripts in data directories like DCL*. + Most storage on the cluster is raided but not backed up. + We do back up home directories and a few other select directories on the DCS and DCL systems for groups that have requested backups. We do have additional backup storage capacity available for a small fee. + Make use of your 1 TB of fastscratch storage for IO intensive job + Please remember that DCS and DCL stand for “Dirt Cheap Storage” and “Dirt Cheap Lustre”, and were designed with cost-effectiveness as a primary driving factor over performance. + Sharing data can be done in several ways on the cluster: i.) traditional Unix file permissions and groups and ii.) Access Control Lists (ACLs). + Sharing files with external collaborators can be done via Globus.

Best practices: passwords and authentication

  • Do not share your password with ANYONE. You are responsible for the use of your account.
  • Choose a "strong" password.
  • Use the "kpasswd" command to choose a new password. It requires your new password to have three of the following four sets of characters: upper-case, lower-case, numerical digits, and special characters.
  • It would be best if your password was unique and not the same password you use on other systems.
  • If you believe your password or your computer have been compromised please alert us via email to bitsupport@lists.jh.edu. Then reset your password using a different device. Visit https://jhpce-app02.jhsph.edu/  to reset your password.  This web site is only available on campus, so if you are outside of the school network, you will need login to the JHU VPN first. You will log into that page with your JHED ID and password.
  • Hopkins staff will *NEVER* send you an email message asking for your password or login credentials
  • NEVER give out your password and login ID to anyone in an email message or on a web page.

If you have never used a Linux or Unix system before, we strongly recommend going through the Unix Command Line tutorial. The cluster is entirely Linux based. Our Orientation is about using the cluster, not using Linux. This tutorial should only take 30 minutes or so to go through.

New C-SUB user orientation

What to do BEFORE the C-SUB JHPCE Orientation Session

There is a lot of material for us to cover and you to absorb. It is vital for your success that you complete a number of steps PRIOR to attending the Orientation Session for the CMS Subcluster of the JHPCE (pronounced by its letters J-H-P-C-E) cluster.

  • Download a copy of the slides from the Orientation from:JHPCE-Overview-CMS.pdf.

  • In order to access the JHPCE cluster and make use of the applications on the cluster, you may need to install additional software on your smart phone and laptop.

  • Install the 2 Factor Authentication program.  The JHPCE cluster makes use of "Google Authenticator" to provide enhanced security.  You can choose to either install an app on your smartphone or, if you do not have an Apple or Android based smart phone, you can install an extension to the Google Chrome browser.  Prior to the Orientation Session, you will only need to download the GoogleAuthenticator app on your smart phone, or install the Authy Chrome extension. We will be configuring Google Authenticator during the Orientation Session. Please see http://jhpce-old.jhu.edu/knowledge-base/authentication/2-factor-authentication/#otp for instructions.

  • Install required client software.  You may need to install a couple of programs on your laptop or desktop in order to access the JHPCE Cluster.  You will need 1) an SSH client for logging in, 2) an SFTP client for transferring files to and from the cluster, and 3) an X11 client for displaying graphics back from the JHPCE cluster.  The SSH client is a requirement -- the SFTP and X11 clients are preferable but optional.
    • Microsoft Windows We have found that the easiest program to use for accessing the JHPCE cluster is MobaXterm as it combines the functionality of all 3 software packages (SSH, SFTP, and X11) in 1 program.  Install MobaXterm by following the first few steps of https://jhpce.jhu.edu/access/mobaxterm.md .  Alternatively, if you already use an SSH client, (such as putty or Cygwin) and an SCP client  (such as WinSCP), you can continue using that software.
    • Apple Macintosh There are built in command line tools for ssh and scp that can be run from a Terminal window. The Terminal program can be found in "Applications -> Utilities". From a Terminal window, you would type:\ ssh <username>@jhpcecms01.jhsph.eduand then login with the login id and the password we provided to you.- In order to run graphical programs on the cluster and have them displayed on your Mac, you will need to install XQuartz from http://xquartz.macosforge.org/landing/.- Optionally, you can also install a GUI based SFTP program such as "Filezilla". One note about Filezilla -- if you download the package from the default link on SourceForge, you may be be blocked by your MalWare/Virus Scanner, or prompted to install Potentially Unwanted Programs (PUPs) during installation.  We recommend you follow the alternative download link here to download a clean copy of the program.