Log into bayes

Your accounts on bayes have been created. By default, they use your nsid and password on paws for bayes. You can change your password with terminal command "passwd" if you want after you use ssh client (Putty on windows, or terminal on mac) to log into bayes.usask.ca.

Use VPN to access bayes from off-campus. As required by the U of S and CFI, you can only use bayes on campus. If you need to use bayes from home, you need to download vpn client (http://www.usask.ca/ict/services/network-services/vpn/index.php). It may be very slow though to use bayes from home.

How to use rstudio server on bayes

To use R, you can use rstudio server with your browser, such as firefox, safari. The url to log into rstudio on bayes is:

http://bayes.usask.ca:8787

rstudio is only for developing and testing your R code. It cannot do parallel computing.

Basic commands in linux terminal to manage your files:

To understand basic linux terminal (shell) commands, you are recommended to read this webpage:

http://www.comptechdoc.org/os/linux/usersguide/linux_ugbasics.html

You are in terminal if the line starts with $, which is different from R console that starts a line with > unless you configure it to be something else (if you know how to do so, you do not need to read this file).

How to use bayes to do parallel computing with R

  1. log in bayes using ssh client (putty on windows, terminal in linux and mac) with your user and password. To transfer files between bayes and your desktop, you need to install "winscp" on windows, or "macfusion" on macOS. Rstudio web interface provides the function to transfer files too, but that is less efficient than winscp or macfusion.

  2. suppose you want to run test.r simultaneously 100 times, do this:

    1. upload the “test.r” file (http://math.usask.ca/~longhai/useBayes/bayesfiles/test.r) to a directory, for example ``test'' under your home directory ((which you need to create with mkdir test)

    2. change to test directory from your home directory ~ in terminal($), type: cd test

    3. Run test.r 100 times:

      cvqsubR test.r 100

      Explanation of cvqsubR test.r 100: It creates 100 R jobs by adding an R expression “ifold <- i” (for i = 1, …, 100) to the top of “test.r” then submit the 100 modified “test.r” to the cluster. All the 100 new “test.r” will be run simultaneously. To distinguish the 100 job outputs, use “ifold” as the identity in each job. More explanations are contained in “test.r” file.

Basic commands to control your jobs

Read more about the command cvqsubR and mqdel?

Type which cvqsubR, then read the file for details. It has two more arguments to specify the memory and walltime needed for your jobs. Using less walltime and less memory than the default settings may place your jobs in higher priority.