NSR Linux User Information.

This page contains information for internal (on site) use only.

Basic information to get you started:

NSR supports LINUX only. We provide tools to connect to computers running Linux OS. Please see SysAdmin if you want to connect with another OS. They may be able to assist with this.
Contact SysAdmin if system is not responding. Do NOT turn power off to machine.
Password protection. When changing your password make sure it is at least 8 characters long and uses at least one non-letter or number character (example: hur!ry@1). Do not use your username in the password. To change password just enter 'passwd' in terminal window.
The terminal window (command line) is used often. It can be started either through:
- 'Applications' ->'System tools' ->'Terminal',
- Or clicking the right mouse button and selecting 'Terminal'.
Commonly used applications.
Recovering nightly backed up files: Backups of your user folders are done nightly. You may access and recover them from server arwen (arwen.bioeng.washington.edu):
- ssh to arwen ('ssh arwen'). Now just copy the files from the backup directory to your user directory. The backup directories are correlated as follows:
- Detailed Instructions: Use the 'pwd' command to confirm which user share you are on (ex: 'pwd' gives /user1/bartj/backedup)
- Now cd to the backed up share of the same user# (ex: for /user1/bartj cd to /user1.BK/bartj, /userA/username go to /userA.BK/username) and confirm the files you want to recover are there.
- Next go to the directory where you want the backed up files to be copied to (Ex: 'cd ~/backedup')
- Use the 'pwd' command to confirm which user share you are on (ex: 'pwd' gives /user1/bartj/backedup), you want to make sure you are no longer in the backup directory.
- Now just copy the files you want to it (ex: cp -v /user1.BK/bartj/Desktop/physiol_term.pdf .) This will copy the pdf file into the current working directory.
You may recover folders/files from our external backups which are run weekly. We keep the last four weeks, monthly, and quarterly backups. To get files from weekly backups just follow instructions from nightly backups except go to arwen:/wklyBKUP/ to recover the files. Please see a system administrator if you need files restored from a tape.
No local mail service available. Use webpine or some other web based email.
Bash is the Linux shell used. Type 'man bash' in terminal window for info ('q' to exit man).
A few basic command line commands:

'cp': copies files, 'cp --help' for more info.
'ls': lists files, directories, 'ls --help' for more info.
'pwd': outputs current working directory (the directory you are currently in).
'cd': change directory, ex: 'cd subdir', Go up a dir: 'cd ..'

Basic linux command reference (External site). Bart Jardine has a few Intro level Unix guides available in his office.
Currently all your user files are stored in your home subdirectory on the fileserver (not on your local machine). To get there from within the terminal window just type 'cd ~' and you will be there.
To log on remotely to a computer, use ssh (ex: 'ssh username@aragorn').
To work remotely at home: use ssh to connect ('ssh username@samwise.bioeng.washington.edu'), this will put in you in your home directory at NSR.
- For MS Windows users you will have to install some type of ssh compatible software to connect. Mac users have ssh in the terminal window.
- Note:When working at home it is often easier to work on files on your home computer and then copy them back to work when done (using vi or emacs may be cumbersome). To do this just use 'scp' (MS Windows users may need to install this if not available with the ssh program previously installed).
  Ex: ' scp username@samwise.bioeng.washington.edu:~/work/file.txt . ' <-- This will copy file.txt to your current working dir at home.
  To copy back to work just use:
  ' scp file.txt username@samwise.bioeng.washington.edu:~/work/ '

[This page was last modified 20Feb19, 11:16 am.]

Model development and archiving support at physiome.org provided by the following grants: NIH U01HL122199 Analyzing the Cardiac Power Grid, 09/15/2015 - 05/31/2020, NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.