Stony Brook Seawulf Cluster: FAQ

How to log on to Seawulf?
Only secured connections with key authentication to the Seawulf Cluster is supported. From any computer, issuing the command
 % ssh seawulf.stonybrook.edu 
or as a specific user
 % ssh username@seawulf.stonybrook.edu 
Both commands will prompt the user of his/her passphrase and get connected to the Seawulf Cluster.
All insecure methods of connection (rlogin, rsh, telnet) are disabled. If your local computer system does not support SSH, please install the software before connecting to Seawulf. SSH software can be found at the websites of Open SSH (http://www.openssh.com) or SSH (http://www.openssh.com). You may also consult the system administrator(s) of your local computer system for help. More information can be found here.

If you are connecting from a Windows machine, Putty is a free lightweight ssh client.
How to move data between Seawulf and another computer system?
There are several secured methods to use. Examples are scp, sftp, and passive ftp.
Using "scp", you can use be very flexible in moving data from one computer system to another. For example, if you want to copy files from the system where you issue the command to a remote destination system, you may use the command
     % scp filename user@remotehost:/dest/dir/for/file/ 
An example of this would be when you copy your files from Seawulf to an AMS computer, such as poincare. In that case, you can issue the command on starzero:
     % scp filename user@poincare:/dest/dir/for/file/
You may also copy a directory recursively, using the option "-r", for example,
     % scp -r a_directory user@poincare:/dest/dir/

Of course, using "scp" you can also copy files from a remote system to the computer you are logged in. The command would be

     % scp user@remotehost:/dir/remotefile /dest/dir/file


Another powerful tool for file transfer is "sftp". Not only "sftp" is secure, it is also much more convenient due to its recursive transfer of directories. On the machine where you are logged in (such as Seawulf), just issuing the command
     % sftp remote_host 
will establish the connection. Then, if you use the sftp command
  sftp> get a_directory 
you will get all the files under the directory recursively. The sftp commands are very similar to the conventional "ftp". The only thing one should pay particular attention to is that "sftp" must be connected to a machine which is running ssh2 service.


What should I read for new changes?
Read the login message of the day (motd). This is one forum where important changes are announced. We also send out announcement to all users by e-mail about important modifications (such as software upgrade) of the system. We also announced planned system downtimes beforehand so that users can get prepared. For new users, we also recommend everybody to browse the web page, including this FAQ, to familiarize themselves with the system.
How do I get in touch with anyone?
Seawulf admin: seawulf_admin@lists.sunysb.edu

Where is Seawulf located?
The Seawulf Lab and the staff can be found in room 154 in Stony Brook's Heavy Engineering Building. All of the nodes are located in this room.
How do I get a Seawulf account?
Apply online at Seawulf Official Website
Are data stored on Seawulf secure?
Relatively. All data is stored on raids with builtin redundancy and error checking. The raids are also backed up everyday.
Are data stored on Seawulf automatically backed up?
System wide backups are performed on everyday basis onto IDE drives. Nevertheless, we should emphasize the different levels of importance of computer data. Most of the data on Galaxy are generated by programs, and could be regenerated, in case of necessity. The source code, on the other hand, are very precious to the developers, and could not easily be regenerated. The users are highly recommended to do everything possible for ensuring those critical material (programs etc.) never be lost. For example, the users should keep multiple copies of these important files on different computer systems, including users' local system. Use scp or sftp to move your data off Seawulf.
Where can I run X-windows applications from?
Normally, only from seawulf, the Seawulf front-end. This includes: emacs, vim, etc. Please realize that these applications soak up considerable bandwidth. Having to share bandwidth is one of the reasons such applications do not always run smoothly. Too many users running many jobs on it at the same time can make the load impossible to be handled by seawulf.

It is now possible to run X programs directly off a computer node using ssh. If you are running an X server on your workstation and you use it to connect to seawulf via ssh, ssh will create a virtual display on seawulf which all your X-programs will connect to, and ssh will then forward the X connections to your real X server. You may use the following procedure to use a node for many interactive work (assuming you are already on seawulf at the beginning):

Step 1: Before logging on to a node, use the command
 % echo $DISPLAY 
This will give you the display channel you are using on seawulf, for example, it could be
 seawulf:20.0 
Here the number "20.0" is just an example, it usually a different number, let use "seawulf:??.?" in the next steps to indicate the number you get from here. Step 2: Using qsub to connect to a node: If you would like to use any node assigned by PBS, just issue the command:
% qsub -I
If you want to specify a node, use the command
% qsub -I -l nodes=NODENAME:ppn=1
where NODENAME is the name of the desired node. For example, if you want to use wulfie006, just use
% qsub -I -l nodes=wulfie006:ppn=1
Step 3: Set the display: Using the command in csh or tcsh:
% setenv DISPLAY seawulf:??.?
Please note that in "seawulf:??.?", the "??.?" should be replaced by whatever channel you get in Step 1.

What can I do to reduce my use of storage?
Remove what you don't need, habitually zip (bzip2, gzip, or zip), learn about CVS. Suggestion: follow any fclose in your programs with a system call to a zip program. Another suggestion: many people use the same binaries... check to see if your program is already installed before putting loads of source code in your home directory.
Installing Software on Seawulf?
Please minimize the installation of downloaded software for personal use. If it is reasonable software to have, it should be installed in /usr/ or /usr/local. Please send e-mail to seawulf_staff@lists.sunysb.edu to request software that you need to use.
I hate the shell I got, how to change it?
Use the command:
% chsh 

How to find something on Seawulf?
Linux has a utility called locate, which creates periodically a database of all the system files (/usr/, /etc/,..) and their path on the system. locate searches that database, which is updated nightly.
scp
SSH has been installed on Seawulf. "scp" is the secure and recommended way to move data between the Seawulf system and other computers.
How is Seawulf Sponsored?
Seawulf is sponsored through funds from the Vice President for Research, Provost, Dean of CEAS, Dept. of AMS and David Green (start up funds). In addition a number of companies (Dell Inc., and Force 10) have been very helpful in our obtaining some of their equipment.