Klauda Lab Simulation Wiki

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Listed below are instructions for setting up an account on Zaratan (ZT1) located at UMD.  

//Instructions//:

Dr. Klauda will submit a request to add you as a user to our account on ZT1. Once this is done, you should get a generic email from IT regarding the resource. 

Details of ZT1 can be found:

https://hpcc.umd.edu/

Now for the cluster setup:

If you are not familiar with the use of LINUX, I would first go through some on-line tutorials for commands to use in LINUX and here ([[Linux Guide]]). To login to ZT1 (login.zaratan.umd.edu) with Windows you will need to have PuTTY ([[Extra Software]]) to connect to Zaratan:

http://www.chiark.greenend.org.uk/%7Esgtatham/putty/

And the following program will be useful to transfer files between deepthought and your computer

http://winscp.net/eng/index.php

Built-in commands for MAC users can be used to connect via the command line (scp) and apps for file transfer (eg, cyberduck).

Then, take a general look at the website of the HPCC OIT to get a general idea on how to login and submit jobs.  Your jobs should not run in your home directory.  They should instead be in the /scratch directory.  A subdirectory is already made for you on scratch (/scratch/zt1/project/energybio/user). Running simulations should be in organized directories.  So think of some naming scheme for simulations. Before starting a simulation, you will need to make a slight change to you .cshrc file in your home directory.  Using the program nano or vim type the following when you are in your home directory:

<code commend> nano .cshrc.mine </code>

At the end of the file add the following line:

<code commend> unset noclobber </code>

This is needed for the simulations to allow for files to write over existing files.  

One more recent change is that you will need to allow users to look into your /scratch and /shell files.  You will need to allow access to the files by typing and replacing username with yours below. Please copy and paste these commands after the first, as if you omit a '.' this will now work properly.

<code commend>cd /scratch/zt1/project/energybio/user/username 
chmod a+r . 
chmod -R a+r * 
find . -type d -exec chmod a+x {} \; 
mkdir /afs/shell.umd.edu/project/energybio/shared/username
cd /afs/shell.umd.edu/project/energybio/user/username 
chmod a+r . 
chmod -R a+r * 
find . -type d -exec chmod a+x {} \; 
</code>

The scratch filesystem is **ONLY** for current jobs running and analysis. We have a smaller quota on this resource which you can see how much with the command scratch_quota. Most data that is for a current project but not yet published should be placed in the SHELL shared directory. You will need to make your own directory in /afs/shell.umd.edu/project/energybio/shared with your username (this is the last line in the code above).