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:

HOSTNAME=$(hostname)
if [ "${HOSTNAME:0:6}" != "scinet" ]; then
    module load intel openmpi  # and any other modules
fi

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

if [ -f /etc/profile ]; then
       . /etc/profile
fi
 
# 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"'
 
# what machine/architecture
HOSTNAME=$(hostname)
case $(uname -p) in
    'ppc64')    MACHINE='p7';;
    'powerpc')  MACHINE='tcs';;
    'x86_64')   MACHINE='gpc';;
    *)          MACHINE='unknown';;
esac
 
if uname -r | grep -q el5 
then
     OS='centos5'
elif uname -r | grep -q el6 
then
     OS='centos6'
elif uname -o | grep -q AIX
then
     OS='aix'
else
     OS='unknown'
fi
 
if [ "${MACHINE}" == "tcs" ] 
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
        :
elif [ "${MACHINE}" == "p7" ]
then
        # do things for the P7 machine
        # user environment for login shells goes here
        # replace colon with your own commands
        :
elif [ "${MACHINE}" == "gpc" ]
then
        # do things for the GPC machine
        # user environment for login shells goes here
        # replace colon with your own commands
        :
        # os specific commands next
        if [ "${OS}" == "centos5" ]
        then
            #centos 5 specific login commands
            :
        elif [ "${OS}" == "centos6" ]
        then
            #centos 6 specific login commands
            :
        fi
else 
   echo "Not a recognized system"
fi
 
PS1="\h-\$ "
 
 
if [ -f ~/.bashrc ]; then
       . ~/.bashrc
fi

.bashrc

if [ -f /etc/bashrc ]; then
       . /etc/bashrc
fi
 
# commands which work for both GPC and TCS can go here
 
export BASH_ENV=~/.bashrc
 
# what machine/architecture
HOSTNAME=$(hostname)
case $(uname -p) in
    'ppc64')    MACHINE='p7';;
    'powerpc')  MACHINE='tcs';;
    'x86_64')   MACHINE='gpc';;
    *)          MACHINE='unknown';;
esac
 
if uname -r | grep -q el5 
then
     OS='centos5'
elif uname -r | grep -q el6 
then
     OS='centos6'
elif uname -o | grep -q AIX
then
     OS='aix'
else
     OS='unknown'
fi
 
if [ "${MACHINE}" == "tcs" ]
then
        # do things for the TCS machine
        # user environment for all shells goes here
        # replace colon with your own commands
        :
elif [ "${MACHINE}" == "p7" ]
then
        # do things for the P7 machine
 
        module load pe vacpp xlf
 
        # user environment for all shells goes here
        # replace colon with your own commands
        :
elif [ "${MACHINE}" == "gpc" ]
then
        # do things for the GPC machine
 
        module load intel openmpi
 
        # user environment for all shells goes here
        # replace colon with your own commands
        :
 
        # os specific commands/modules can be loaded next
        if [ "${OS}" == "centos5" ]
        then
            #centos 5 specific modules
            :
        elif [ "${OS}" == "centos6" ]
        then
            #centos 6 specific modules
            :
        fi
 
else
        echo "Not a recognized system"
fi