scheduler-env.tex

%  2.1.2 Environment Set Up
% --------------------------
% TMP scheduler-specific section

After creating an SSH connection to Speed, you will need to
make sure the \tool{srun}, \tool{sbatch}, and \tool{salloc}
commands are available to you.
To check this, type each command at the prompt and press Enter.
If ``command not found'' is returned, you need to make sure your \api{\$PATH} 
includes \texttt{/local/bin}.
You can check your \api{\$PATH} by typing:
\begin{verbatim}
    echo $PATH
\end{verbatim}

%
%source 
%the ``Altair Grid Engine (AGE)'' scheduler's settings file. 
%Sourcing the settings file will set the environment variables required to 
%execute scheduler commands.
%
%Based on the UNIX shell type, choose one of the following commands to source
%the settings file. 
%
%csh/\tool{tcsh}:
%\begin{verbatim}
%source /local/pkg/uge-8.6.3/root/default/common/settings.csh 
%\end{verbatim}
%
%Bourne shell/\tool{bash}:
%\begin{verbatim}
%. /local/pkg/uge-8.6.3/root/default/common/settings.sh 
%\end{verbatim}
%
%In order to set up the default ENCS bash shell, executing the following command 
%is also required:
%\begin{verbatim}
%printenv ORGANIZATION | grep -qw ENCS || . /encs/Share/bash/profile 
%\end{verbatim}
%
%To verify that you have access to the scheduler commands execute 
%\texttt{qstat -f -u "*"}. If an error is returned, attempt sourcing 
%the settings file again.

\noindent The next step is to set up your cluster-specific storage ``speed-scratch'', to do so, execute the following command from within your
home directory. 
\begin{verbatim}
    mkdir -p /speed-scratch/$USER && cd /speed-scratch/$USER
\end{verbatim}

\noindent Next, copy a job template to your cluster-specific storage
\begin{itemize}
    \item From Windows drive G: to Speed:\\ 
    \verb|cp /winhome/<1st letter of $USER>/$USER/example.sh /speed-scratch/$USER/|
    \item From Linux drive U: to Speed:\\
    \verb|cp ~/example.sh /speed-scratch/$USER/|
\end{itemize}

\noindent \textbf{Tip:} the default shell for GCS ENCS users is \tool{tcsh}.
If you would like to use \tool{bash}, please contact \texttt{rt-ex-hpc AT encs.concordia.ca}.\\

%\textbf{Tip:} Add the source command to your shell-startup script. 

%For \textbf{new GCS ENCS Users}, and/or those who don't have a shell-startup script, 
%based on your shell type use one of the following commands to copy a start up script 
%from \texttt{nul-uge}'s home directory to your home directory. (To move to your home
%directory, type \tool{cd} at the Linux prompt and press \texttt{Enter}.)

%csh/\tool{tcsh}:
%\begin{verbatim}
%cp /home/n/nul-uge/.tcshrc . 
%\end{verbatim}

%Bourne shell/\tool{bash}:
%\begin{verbatim}
%cp /home/n/nul-uge/.bashrc . 
%\end{verbatim}

%Users who already have a shell-startup script, can use a text editor, such as
%\tool{vim} or \tool{emacs}, to add the source request to your existing
%shell-startup environment (i.e., to the \file{.tcshrc} file in your home directory). 

%csh/\tool{tcsh}:
%Sample \file{.tcshrc} file:
%\begin{verbatim}
%# Speed environment set up 
%if ($HOSTNAME == speed-submit.encs.concordia.ca) then
   %source /local/pkg/uge-8.6.3/root/default/common/settings.csh
%endif
%\end{verbatim}
%
%Bourne shell/\tool{bash}:
%Sample \file{.bashrc} file:
%\begin{verbatim}
%# Speed environment set up 
%if [ $HOSTNAME = "speed-submit.encs.concordia.ca" ]; then
    %. /local/pkg/uge-8.6.3/root/default/common/settings.sh
    %printenv ORGANIZATION | grep -qw ENCS || . /encs/Share/bash/profile
%fi
%\end{verbatim}

\noindent \textbf{Note:} If you encounter a ``command not found'' error after logging in to Speed, 
your user account may have defunct Grid Engine environment commands. 
See \xa{appdx:uge-to-slurm} for instructions on how to resolve this issue.