Apply for cluster

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To obtain a account on cluster do the following:

STEP 1: Online Registration

  1. Go to
  2. Follow links to guest registration(under "bnl site access" toolbar)
  3. Fill out the Brookhaven National Laboratory Guest Registration Form

Instruction on the Form:

  1. Purpose of visit Research
  2. BNL Department Associated with Computational Science Center
  3. Facility being requested to Conduct Research NONE
  4. Beam line/experiment being requested NONE
  5. Type of Research Open Research
  6. Type of Access Requested Physical On-Site Access
  7. Expected Start Date = One month or less from today
  8. Expected End Date = Two years after start date
  9. Number of days you estimate to be onsite over a two-year 180 Days intermittently
  10. Subject Code for this Visit/Assignment Biomedical Sciences, Applied Studies
  11. Justification of visit/assignment "Member of Robert C. Rizzo Lab, Stony Brook Univ."
  12. Conducting Thesis Research During Visit/Assignment "No"
  13. Host Michael McGuigan
  14. Name of Current Affiliation SUNY @ Stony Brook United States New York
  15. Type of Affiliation University
  16. Job Title PhD Student
  17. Field of Work or Research Structural Biology
  18. Michael McGuigan's BNL extention is 2695

STEP 2: Training

  1. After approval, you should receive via e-mail a BNL "Life Number"
  2. Use life number, take 2 online web courses at, and be sure to print out conformations that you have taken the online courses
 Cyber Security
 Guest Site Orientation 

STEP 3: Logging In

  1. You have to wait for one day after cyber security to apply for accounts
    1. For Cluster, apply for SSH Gateway access account and a BNL domain account
    2. By Yulin: For Cluster, apply for SSH Gateway access account and Unix System.
    3. As of 6/23/09: Request SSH Gateway, BNL domain and Unix System.
    4. Request a username to be your lastname
  1. Uses Putty to generate a public and private key; never share the private key with any one.

  1. e-mail public key to BNL help desk at
  2. They will e-mail you back confirming that you have a gateway account.
  3. Next, test your account by doing the following:

Open putty and save a session 'bnl_cluster' having hostname: and port 22.

Also enter private key for authorization.


After logging in to gateway, it will ask you for the passphrase for key (if you assigned one during key generation). Log on to cluster (ssh cluster) using the password that they emailed you for the BNL domain account and change password. The password should comply with their security requirements.

In order to use SSH client do the following:

  1. setup a tunnel under ssh-gateway session

Tunnel BNL.png

  1. open Secure Shell Client software.
  2. create a profile.
  3. edit profile.

Ssh client tunnel.png

  1. insert your username instead of "username" most likely your last name.
  2. one can also now view cluster details at


Mailing list

you can subscribe to this list here: [1] (internal web site).


After logging on to cluster, check that your shell is tcsh.

echo $SHELL

If not, mail the help desk to change it to tcsh.