Banana Slug Genomics

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====== campusrocks ======

===== Address =====

''
Name:	 campusrocks.cse.ucsc.edu\\
Address: 128.114.48.114
''

===== Hardware =====

[[Hardware|Machine-specific capabilities]]

^Machine ^GB RAM ^CPUs ^Cores ^MHz ^Model ^
|campusrocks.local(head node?)|30 |1 |1 |1000 |Dual-Core AMD Opteron(tm) Processor 2218 HE|
|campusrocks-0-2(through 30).local |15 |4 |2 |1800 |Dual-Core AMD Opteron(tm) Processor 2218 HE|
|campusrocks-1-0(through 31).local |15 |2 |1 |2592 |Dual-Core AMD Opteron(tm) Processor 2218 HE|

campusrocks-0-6.local exceptionally has 30 GB RAM

===== Account/Documentation =====

   * [[Creating an account|Create a new account]]
   * [[http://campusrocks.soe.ucsc.edu/roll-documentation/sge/5.2/|Documentation]] (works only on campus or when connected via [[http://vpn.soe.ucsc.edu |VPN]].)
   * [[http://campusrocks.soe.ucsc.edu/ganglia/|Status page]]
   * [[Installed Software|Software]]



===== Stats =====


  * All user accounts are created under ''/campusdata''
  * 3.4TB available
  * OS: GNU/Linux 2.6.18-128.1.14.el5xen

===== Setting Environmental Variables =====
If you would like to set your startup shell to bash, make a file called .profile in your home directory and add this to the //end// of the file.

  if [ "$SHELL" = "/bin/sh" ]
  then
        SHELL=/bin/bash
        export SHELL
        bash
  fi

I also copied the contents of the file .bashrc (already in my home directory) into my .profile file, and then deleted my .bashrc file. This may not be necessary, but if your settings aren't working this is something to try.

If you would like to add our classes bin directory (or any other directory for that matter) then add this to your .profile:

  PATH=/campusdata/BME235/bin:$PATH
  export PATH

To use the gcc-4.5 family of compilers stored in our bin directory then you can specify the LD_LIBRARY_PATH environmental variable:
  LD_LIBRARY_PATH=/campusdata/BME235/lib:/campusdata/BME235/lib64:$LD_LIBRARY_PATH
  export LD_LIBRARY_PATH

To make your default folder creation settings group readable and writable then add this line to your .profile:
  umask 007



===== Sungrid Job scheduler =====

Campusrocks uses sungrid for scheduling jobs.  The techstaff request that jobs only be run
on the compute nodes, not the head node, as jobs run there slow down the entire cluster.
They threaten to kill jobs found running on the head node.

There is [[http://campusrocks.soe.ucsc.edu/roll-documentation/sge/5.2/|Online documentation]] of how to use sungrid to submit jobs on the cluster.  The main commands are
  * qsub: Submits a job (create a shell script, then run "qsub -cwd shellscript")
  * qdel: Delete a job
  * qlogin: Interactive login 
  * qstat: See the status of jobs in the queue
  * qmon: Graphical User Interface (GUI)

The web site is locked so that it can only be accessed oncampus.

[[http://web.njit.edu/topics/HPC/basement/sge/SGE.html|SunGrid Quick Start]]

Useful submit-script settings for SGE:

#$ -N some_name_here\\
Apparently, you must have a single word after -N\\
This gives a nicer name to your script when you run qstat.\\

#$ -V\\
Your jobs use **your** environment variables.
Banana Slug Genomics

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