GettingStartedAtIRKMLab

* Setting up your computer

  1. get your SOE account http://www.soe.ucsc.edu/sites/default/files/TermsOfAgr.pdf
  2. get access to wireless network http://support.soe.ucsc.edu/soe-wpa
  3. familiar yourself with SOE computing http://support.soe.ucsc.edu/home

 

Get access to our servers:

Make sure you are a group member of irkm on linux, so that you can login into our servers and access our directories. Change your default linux group: add "newgrp irkm" into .cshrc file in your home directory (optional)

 Computing cluster shared by all IRKM students and faculty: irkm1.soe, irkm2.soe, irkm0.soe

For GPU computing, SOE computing server CITRISDANCE.soe.ucsc.edu has two nVidia Tesla K20c GPUs and you can use /projects/tecwave2/irkm or your home directory for files there. We need to pay for space in  /projects/tecwave2/. It's ok if you keep a few hundred G there. For several Terabyes of data, please discuss with Yi. 

You can also use general SOE computing resources http://www.soe.ucsc.edu/administration/computing-support/servers

You can also request virtual machine http://support.soe.ucsc.edu/vm if you need root access. However the space and CPU on SOE virtual machine is limited. 

Get an account at github.com and use it to manage your research projects source code, documentation and papers. Please set the project access right to "private" for each new project. You can either get an education account for free "private" access or ask Yi to create a private one for you. 

Set up your homepage at www.soe.ucsc.edu/~your_soe_id or some place you prefer.

For computing issue, submit a request to https://ucsc.service-now.com/ess/ (cc to yiz@soe if it needs her approval)

 

Storage space 

On SOE *nix:  /notbackedup/irkm1 and /projects/tecwave2/irkm/ (To save space for your peers, please delete (backup elsewhere) big files if you are unlikely to use it in near future)

If you need to handle a dataset > 100G, please use your local hard drive to hold the data.

Please create a new directory using your login name (such as /notbackedup/irkm1/yiz  /projects/tecwave2/irkm/yiz) and only working under that directory. Other directories you created on the same level might be deleted.

Known ways to access our storage server irkm-buffalo from a computer on campus:

unix- sudo mount -t cifs -o user=its,password=derek //128.114.52.11/share destination_folder/

windows-

1. Open Windows Explorer and go to 'tools' -> 'map network drive'
2. Select drive letter and under folder put \\
128.114.52.11\share
3. Select the option to 'connect using a different user name' and input:
Username: {its}
Password: {derek}

Writing source code

Please follow the copyright rule of UCSC

Please paste the following lines at the top of your source code file

-----------------------------------

Copyright © 2009 The Regents of the University of CaliforniaAll Rights ReservedInformation Retrieval and Knowledge Management LabUniversity of California Santa Cruz
Created by *** (your name), Department of ***, your_email@*** (permanent email)-----------------------------------------------

Please clearly document your source code if it will be shared with others (use doxygen)

For each paper you published, please freeze the data and program that are used to generate the experimental results, so that you can reproduce the results in the future

For any lab project, please discuss with Yi before sharing the code with people outside our lab

 

Rooms

As a member of IRKM, you should be able to access E2-477 and E2-486.