This document provides the details you'll need to know in order to work in the CSG or on the FUSION project. Most of this document is general information. If you are computer literate enough to understand this and do it your own way - feel free. If you are less comfortable, we suggest you do it our way, and change your environment as you'd like when you are ready.
While most of us have a Windows machine, a large amount of our work is done on Unix. You will need to become proficient in both environments.
The FUSION group has a private web site. Access to FUSION data is restricted to the FUSION group. The URL for the web site is https://fusion.sph.umich.edu/private/ (FUSIONeers should bookmark this page). There is a great deal of information on this page (please feel free to suggest additions to Peggy).
The CSG group has a completely public web site. The URL is http://csg.sph.umich.edu/ (bookmark this now). Please feel free to suggest additions to Peggy.
Helpful documentation for CSG members (general CSG, information on the clusters, instructions for installing printers, information for R users, helpful travel links, Unix documents, and password management can be found using the "Documentation" link in the "Main" box on the CSG web page.
Helpful documentation for FUSIONeers can be found using the "Documentation" link in the "General" box on the right side of the page. Your FUSION web page password can be changed by using the "FUSION Pwd Mgr" link in the "Tools" box on the left side of the page.
All University of Michigan students receive a uniqname - unique on all systems within the University. uniqnames are used with accessing Windows, Macintosh, or Unix machines on campus. Each system has its own password system. Information on changing your passwords can be found at http://www.sph.umich.edu/computing/account/change_passwd.html. There are links to this page under "Documentation" on the CSG web page and under "Tools" on the FUSION web page.
Everyone in the CSG is required to change passwords twice a year. We have had several bad experiences when our machines have been attacked. Careful password management is the first level of protection for us all.
As another layer of security for our systems, we do not allow TELNET or FTP access to our Unix machines. We use SSH (in place of telnet) and SCP or SFTP (in place of FTP). Documentation on how to install and use these can be found under the "Documentation/Unix Docs" link on the CSG web page and under the "Documentation" link on the FUSION web page.
We have a black and white printer and a color printer available for CSG members. There are links to instructions on installing and using the printers under "Documentation" on the CSG web page and under "Tools" on the FUSION web page.
We have several Linux servers for CSG members - compute19 (AFS), mars, snowwhite, and fantasia. A few individuals have Unix machines instead of PCs. In general, you should use the public servers. You may also duse other machines, but please ask the "owners" first. The machines are generally fast enough to handle general analysis as well as "personal" work.
Our Unix systems make use of a network file system called 'AFS'. Data is not kept on the physical machines but is on a central server backed up on a regular basis. Unix on AFS is the same as Unix on the Linux machines.
AFS allows us to control very precisely who has access to our Unix data. All CSG members have full read access to any data/documents they use. SPH Computing Servicesw (our support group for the School of Public Health) has documented AFS Tips.
A convenient feature of AFS is that we always have a copy of all data. These data are one day old and are found in a directory called 'OldFiles' which you will occasionally see in our directories. OldFiles are updated each evening, so if you accidentally delete a file and notice it right away, you can get yesterday's copy from OldFiles. If you wait too long, though, getting files restored is much more tedious.
People who have never used Unix might find Learn UNIX in 10 minuteshelpful.
FUSION-related data are in AFS starting at the directory /group/boehnke/fusion. We use this so often that the sample shell mentioned above provides an alias 'fusion' which will cd to this directory. Many times people will simply refer to this path as 'fusion'. The directory /group/boehnke/fusion/Share is used by FUSIONeers to share data with others in the FUSION group.
Temporary files should be written tp /tmp. This is a local disk on all Unix machines; it is not backed up. All temporary files are removed after a few weeks or at a reboot (the time period can vary). The tmp directory is a good place to put true temporary files. Be very careful naming files in this directory. File names should unique (perhaps include your userid and the processid ($$) (e.g. /tmp/$USER.$$.sas.crap). Please have your scripts remove temporary files when final files have been created. The tmp space is not very large, so please don't put 100GB files here. The system can misbehave if the tmp space fills up.
Extra space is available on compute19/fdata. You can create a subdirectory here (e.g. mkdir /fdata/uniqname). fdata is not on AFS and is not backed up. Please remove unused and old files as fdata is a shared space.
Your Windows machine should be set up correctly. You should SSH to a compute server to run analyses and write scripts.
Two programs for SSH are available. PuTTY is a simple, but very clean SSH client. You only need a copy of the program to use it. A second (fancier) program is a SSH graphical client for SSH (telnet).
There are two programs for SCP (SFTP) available. PuTTY has an 'scp' command that you invoke from a DOS terminal (cmd.exe) window, and behaves exactly as scp on Unix. SFTP is part of the SSH graphical client. This allows you to use a Windows file broswer through your and download Unix files to your PC.
Many of our tools on Unix have graphical interfaces (e.g. nedit); these will not work unless you have an X server running on your Windows machine. We use 'Exceed' for this. Generally, once you start Exceed, all Unix-based applications can be run in open windows on your WPC.
Please see Peggy if you need help with any computing issues. She won't hesitate to ask Terry if she needs him!
