Important .bashrc guidelines

The file .bashrc, located in your home directory, is read-in and executed whenever a bash script or bash shell is started. The exception is for login shells, in which case .bash_profile is started. The default .bash_profile calls .bashrc so that many scinet users never need to edit .bash_profile.

This means in particular that the file .bashrc is read in

• when you log in
• when you run compute jobs
• when you run certain commands such as mpirun
• at the end of a job, when copying output and error files.

And that both on the GPS and the TCS, which nonetheless often require quite a different setup.

Guidelines

To avoid difficulties, you are advised to follow these guidelines in .bashrc:

• Sourcing /etc/profile and /etc/bashrc is required for various SciNet routines to work!
• Do not execute any commands that write to standard output, because that would breaks things like copying-out output files and scp. So for instance, no echo or module list.
• Load only commonly used modules.
• Distinguish, especially for the module command, between the gpc and tcs.
• If you're trying out different implementations or versions of a module (e.g. mpi), you should not load them in the .bashrc, but explicitly on the command line before compiling and once more explicitly in your job script.
• To avoid accidentally compiling on the login nodes, you can 'shield' yourself from the compilers by wrapping the module load commands with hostname check in the .bashrc file, e.g. as follows: <source lang="bash">

HOSTNAME=$(hostname) if [ "${HOSTNAME:0:6}" != "scinet" ]; then

   module load intel openmpi  # and any other modules

fi </source> or as follows: <source lang="bash"> HOSTNAME=$(hostname) if [ "${HOSTNAME:0:6}" == "scinet" ]; then

   alias nocompiler="echo 'Cannot use compilers on login nodes'"
   alias gcc=nocompiler
   alias g++=nocompiler
   alias gfortran=nocompiler
   alias icc=nocompiler
   alias icpc=nocompiler
   alias ifort=nocompiler
   alias mpicc=nocompiler
   alias mpic++=nocompiler
   alias mpif77=nocompiler
   alias mpif90=nocompiler

fi </source>

Default .bashrc/.bash_profile

The default startup scripts provided by SciNet are as follows. Certain things - like sourcing /etc/profile and /etc/bashrc are required for various SciNet routines to work!

.bash_profile <source lang="bash"> if [ -f /etc/profile ]; then

      . /etc/profile

fi

1. commands which work for both GPC and TCS can go here

alias passwd='echo "Please use the SciNet portal to change password: https://portal.scinet.utoronto.ca/change_password"'

HOST=$(uname)

if [ "${HOST}" == "AIX" ] then

       # do things for the TCS machine
       alias llq1='/xcat/tools/tcs-scripts/LL/jobState.sh'
       alias llstat='/xcat/tools/tcs-scripts/LL/jobSummary.sh'

       if [ "${TERM}" = "xterm-color" ]; then
               export TERM=xterm
       fi

       # user environment for login shells goes here
       # replace colon with your own commands
       :

else

       # do things for the GPC machine
       # user environment for login shells goes here
       # replace colon with your own commands
       :

fi

PS1="\h-\$ "

if [ -f ~/.bashrc ]; then

      . ~/.bashrc

fi </source>

.bashrc <source lang="bash"> if [ -f /etc/bashrc ]; then

      . /etc/bashrc

fi

1. commands which work for both GPC and TCS can go here

export BASH_ENV=~/.bashrc

HOST=$(uname)

if [ "${HOST}" == "AIX" ]; then

       # do things for the TCS machine
       # user environment for all shells goes here
       # replace colon with your own commands
       :

else

       # do things for the GPC machine

       module load intel openmpi

       # user environment for all shells goes here
       # replace colon with your own commands
       :

fi </source>