This document provides the details you'll need to know in order to work on the FUSION project or in the CSG. Most of what follows are just our conventions on names and how we do business. 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 when you are ready, change your environment as you'd like.
While most people have a Windows machine at their desk, a very large amount of our work is done on Unix in addition to Windows. You will need to become proficient in both environments.
The FUSION group runs it's own private web site and databases. Access to these data is restricted to the FUSION group and to students working in our area. The web site is our repository for most information you will need. The URL is https://fusion.sph.umich.edu/private/ - you should bookmark this now.
The CSG group runs a completely public web site ad http://csg.sph.umich.edu/ - you should bookmark this now.
Our FUSION web site is password protected, requiring a userid (your uniqname) and a separate password (not the same password as your uniqname). This will be set up for you shortly after you arrive. Using this resource, you can find much of the information you will need to work in the group.
The first and most important link for you is where all our documentation is saved. You can find a link to 'Documentation' in the block labeled 'General' on the right hand side of the FUSION homepage. Look there first for "how to" questions. If your topic is not covered there, this will tell us we need to write something for the next person.
You may change your FUSION web site password from the link found in the block labeled 'Tools' on the left hand side of the FUSION homepage.
Upon arriving at the University of Michigan you will receive a uniqname - unique on all systems within the University. This name will be used when accessing both Windows, Macintosh or Unix machines on campus. Each system has its own password system, so setting your password is not as simple as we might want.
Information on how to change your UMICH passwords can be found on a link in the block labeled 'Tools' on the left hand side o the FUSION homepage. Changing your passwords twice a year is a requirement of our group. 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. Rather, we use programs called SSH (in place of telnet) and SCP or SFTP (in place of FTP). Documentation on how to install and use these is available from the FUSION documentation link.
We have two general purpose printers available to the group. Details on how to setup your machine and how to use the printers from Windows or Unix is available from the FUSION documentation link.
There are several servers available for use by group members: compute11, compute12, compute14, and compute15 running Solaris and mars, snowwhite and fantasia running Linux. Additionally a few individuals have Unix machines at their desk. In general you should do your work on the public servers. You may also do work on the other machines, but we ask that you simply ask the "owners" first. Generally the machines are fast enough to handle general analysis work as well as "personal" work.
We also have access to a cluster of Intel machines (running Linux). In the 2003-2004 school year we will begin using the cluster for a wider range of work. Ask if you think you need to use the cluster.
Our Unix systems make use of a network file system called 'AFS'. We keep no data on the physical machines themselves, rather everything is on a central server so it can be backed up. While AFS is a little different, you should find that Unix here behaves just like Unix you've seen elsewhere.
AFS allows us to control very precisely who has access to our Unix data. You will have full read access to all our data. We also have people in Bethesda and Los Angeles who have access to our systems. You will have your own space (called a volume) which will be writable by you and the administrators (Peggy and Terry), but generally not available to others. Computing Services (our support group for the School of Public Health) has documented AFS.
One convenient feature of AFS is that we always have a copy of all data. These data are one day old and is found in a directory called 'OldFiles' which you will occaisionally see in our directories. These get updated each evening. So if you accidentally delete a file and notice it right away, we can get yesterday's copy from OldFiles. If you wait too long, though, getting files restored is much more tedious.
Just because you have a uniqname and can login to a Unix machine does not mean you are "all set". There are a few customizations you will want to do as soon as you get onto Unix. These are covered in a document named 'FUSION Computing Hints' and are available from the FUSION documentation link. Don't ignore this, because someday you will not have our environment available and this will cause problems later. Do it now.
People who have never seen Unix might find Learn UNIX in 10 minutes of interest.
All of our 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 place. Many times people will simply refer to this path as 'fusion'. Your personal volume will be available starting at this directory.
When we want to share data, many people put the data in /group/boehnke/fusion/Share. Many times people simply refer to this path as 'share'. Generally people put data they wish to share in a subdirectory off this. These data disappear after a few weeks. Never leave something here that you wish to keep.
Temporary files should best be written tp /tmp. This is a local disk on all Unix machines and is not backed up. All files here are removed after a few weeks or at a reboot (period can vary). Nonetheless, it's a great place for your truly temporary files. Please be careful choosing names for files here. File names should unique (perhaps including your userid and the processid ($$) (e.g. /tmp/$USER.$$.sas.crap). Be nice and make sure your scripts remove these in your scripts. This space is not enormously large - so don't go creating 100GB files here. If this space fills, the system can begin to misbehave.
Extra space is available on AFS machines in /fdata. You should create a subdirectory here (e.g. mkdir /fdata/uniqname). These data do not disappear like Share. This space is not in AFS. It is not backed up. Since you share this with others, please clean it up - once this space is filled, others cannot get their work done.
Generally your Windows machine will be set up correctly. Printers and SSH/SCP have been mentioned above. The normal mode of operation is for you to SSH to a computeXX server and run your analysis from there.
Two programs for SSH are available. PuTTY is a simple, but very clean SSH client. You only need a copy of the program (perhaps on your Desktop) to use it. A second program is a fancy SSH graphical client for SSH (telnet). It is fancier, but more complex to use.
Similarly, there are two programs for SCP (SFTP) available. PuTTY has an 'scp' command that you invoke from a DOS terminal (cmd.exe) window. It behaves exactly as scp on Unix does. An alternative is SFTP which is part of the fancy SSH graphical client. With this you can navigate with a Windows file broswer through your Windows) and remove (Unix) files.
Many of our tools on Unix have graphical interfaces (e.g. nedit) and these will not work unless you have an X server running on your Windows machine. We use 'Exceed' for this. Normally, all you need do is start Exceed and then Unix-based applications can open windows on your Windows machine.
This is intended as a quick high level introduction to your new environment. It is definitely not everything you will need to know. Please take the time now to set up your accounts. It will make you more productive and avoid unecessary problems later when you work with others in the group.
