Research Computing At Haas

Haas research computing for PhD students currently consists of bear and phd-pgsql. This page details these resources.

Bear

Bear is a 12 node research computing cluster. The official blurb says that bear has two sets of 5 compute nodes, one set with 64Gb of RAM per node, and one with 16Gb of RAM per node. Nodes have dual core 3Ghz Xenon processors.

There are three ways of using bear:

Storing Data on Bear

Your "R" drive lives on bear. We tested access times to the R drive and found that they are much faster than to HCS-Data or other shares that you have access to (other than your C drive, though the speeds are actually comparable with those to C). You should use R:\bulk as your primary data storage area.

If your R drive isn't mapped already then map a network drive to:

\\bear\username$

SSH'ing into Bear

You can use a copy of PuTTY to SSH onto bear. PuTTY is a free SSH client that you can download from its author. You don not need to 'install' it - it is a standalone executable file. Details for the configuration are available from the howdoi section of the haas website, but none is really needed.

The address to connect to bear is:

bear.haas.berkeley.edu

And the connection is on the standard port (22). You can set your username under:

Connection -> Data -> Auto-login Username

And save the connection settings if you want.

If you are running scripts then you should use the bsub to have them execute on the compute nodes, rather than the login node, as otherwise a runaway script can bring the entire of bear to a stand still. An example syntax for running a perl script is:

bsub -Is "perl Script.pl"

Available scripting languages include:

• Perl
• Python
• R

There are also (apparently - I haven't tested them) compilers for:

• C++ (GNU Cpp)
• Fortran 77

To see your files you might want the following simple commands:

• ls -alt - list the files in the current directory in all their glory
• cd bulk - change into the bulk directory
• cd .. - change up a directory

Using Xwindow Applications on Bear

There are copies of the following Xwindow applications ready for use on bear:

• Matlab (matlab)
• Stata (xstata)
• Stata-SE (xstata-se)
• SAS (sas)

To use these applications you need an Xwindows client. The eXceed client is available from available from software.berkeley.edu for download. Download it and install it. You can accept a typical installation for just one user. There is a very old set-up guide from HCS that may be useful, but the details below should suffice. Note that there is a security notice warning of risks when you use eXceed. We are partly protected from these risks by the design of the Haas network, but you might want to consider following the advanced configuration instructions.

Now save a bear configuration in PuTTy by entering the following parameters and hitting "Save":

Session -> Host Name (or IP address)  bear.haas.berkeley.edu
Connection -> Data -> Auto-login Username   Your_Username
Connection -> Data -> SSH -> Encryption Cipher  Move Blowfish to the top 
Connection -> Data -> SSH -> X11 -> Enable X11 Fowarding   Tick the box
Session -> Saved Sessions   Bear + Click Save

Now start eXceed running (and leave it running in the background) and SSH onto bear using Putty. At the command line type the name of the program, for example "xstata-se", and the program will launch in an eXceed window on your desktop. Voila!

For example my terminal looked like this to launch STATA-SE:

[ed_egan@bear-b ~]$ xstata-se

There is a Best Practises blurb from HCS regarding these apps that specifically asks us not to background our processes using "&". That is do not type: xstata-se &

If no licenses are available then you should be able to see who is running other copies (so you know who to complain about) by using the command:

bjobs -u all

Remember - Bear is your R drive, so the root of bear, when you login, is the root of your R drive!

PhD-PGSQL

phd-pgsql is a new and experimental database server for PhD students and faculty. It hosts a copy of PostgreSQL with support for R, Perl and C++ scripting inside of the RDMS. At present the server is being deployed. More news will be available here shortly!

In the meantime, those with permission can see the Haas PhD Server Configuration page.