[manual][7.2] editorialize most sections.

This includes formatting, proofreading, factual things.
WIP the GPU section.

doc/scheduler-directives.tex

@@ -15,23 +15,18 @@
 Directives that start with \verb|#SBATCH| set the options for the cluster's 
 SLURM job scheduler. The following provides an example of some essential directives:
 
-%\begin{verbatim}
-%#$ -N <jobname>
-%#$ -cwd
-%#$ -m bea
-%#$ -pe smp <corecount>
-%#$ -l h_vmem=<memory>G
-%\end{verbatim}
-
+\small
 \begin{verbatim}
     #SBATCH --job-name=<jobname>        ## or -J. Give the job a name 
     #SBATCH --mail-type=<type>          ## set type of email notifications
     #SBATCH --chdir=<directory>         ## or -D, set working directory for the job
     #SBATCH --nodes=1                   ## or -N, node count required for the job
     #SBATCH --ntasks=1                  ## or -n, number of tasks to be launched
     #SBATCH --cpus-per-task=<corecount> ## or -c, core count requested, e.g. 8 cores
-    #SBATCH --mem=<memory>              ## assign memory for this job, e.g., 32G memory per node 
+    #SBATCH --mem=<memory>              ## assign memory for this job,
+                                        ## e.g., 32G memory per node 
 \end{verbatim}
+\normalsize
 
 \noindent Replace the following to adjust the job script for your project(s)
 \begin{itemize}
@@ -43,28 +38,26 @@
     Valid options are: NONE, BEGIN, END, FAIL, REQUEUE, ALL.
     \item \verb+<corecount>+ with the degree of multithreaded parallelism (i.e., cores) allocated to your job. Up to 32 by default.
     \item \verb+<memory>+ with the amount of memory, in GB, that you want to be allocated per node. Up to 500 depending on the node.\\
-    \textbf{Note}: All jobs MUST set a value for the \verb|--mem| option.
+    \textbf{Note}: All jobs MUST set a value for the \option{--mem} option.
 \end{itemize}
 
 \noindent Example with short option equivalents:
+\small
 \begin{verbatim}
-    #SBATCH -J myjob                    ## Job's name set to 'myjob'
-    #SBATCH --mail-type=ALL             ## Receive all email type notifications
-    #SBATCH -D ./                       ## Use current directory as working directory
-    #SBATCH -N 1                        ## Node count required for the job
-    #SBATCH -n 1                        ## Number of tasks to be launched
-    #SBATCH -c 8                        ## Request 8 cores
-    #SBATCH --mem=32G                   ## Allocate 32G memory per node 
+    #SBATCH -J myjob              ## Job's name set to 'myjob'
+    #SBATCH --mail-type=ALL       ## Receive all email type notifications
+    #SBATCH -D ./                 ## Use current directory as working directory
+    #SBATCH -N 1                  ## Node count required for the job
+    #SBATCH -n 1                  ## Number of tasks to be launched
+    #SBATCH -c 8                  ## Request 8 cores
+    #SBATCH --mem=32G             ## Allocate 32G memory per node 
 \end{verbatim}
+\normalsize
 
 \noindent \textbf{Tip:} If you are unsure about memory footprints, err on assigning a generous
 memory space to your job, so that it does not get prematurely terminated.
-%(the value given to \api{h\_vmem} is a hard memory ceiling).
 You can refine \option{--mem} values for future jobs by monitoring the size of a job's active
 memory space on \texttt{speed-submit} with:
-%\begin{verbatim}
-%qstat -j <jobID> | grep maxvmem
-%\end{verbatim}
 
 \begin{verbatim}
     sacct -j <jobID>
@@ -78,15 +71,15 @@
     sstat -o jobid,maxvmsize,ntasks%7,tresusageouttot%25 -j <jobID>
 \end{verbatim}
 
-\noindent Memory-footprint values are also provided for completed jobs in the final
+\noindent Memory-footprint efficiency values (\tool{seff}) are also provided for completed jobs in the final
 email notification as ``maxvmsize''.
 \emph{Jobs that request a low-memory footprint are more likely to load on a busy
 cluster.}\\
 
-\noindent Other essential options are \option{--time}, or \verb|-t|, and \option{--account}, or \verb|-A|.
+\noindent Other essential options are \option{--time}, or \option{-t}, and \option{--account}, or \option{-A}.
 \begin{itemize}
     \item \option{--time=<time>} -- is the estimate of wall clock time required for your job to run. 
-    As preiviously mentioned, the maximum is 7 days for batch and 24 hours for interactive jobs. 
+    As previously mentioned, the maximum is 7 days for batch and 24 hours for interactive jobs. 
     Jobs with a smaller \texttt{time} value will have a higher priority and may result in your job being scheduled sooner. 
 
     \item \option{--account=<name>} -- specifies which Account, aka project or association, 

doc/scheduler-faq.tex

@@ -1,65 +1,77 @@
-% ------------------------------------------------------------------------------
+% -----------------------------------------------------------------------------
 %						B Frequently Asked Questions 
-% ------------------------------------------------------------------------------
+% -----------------------------------------------------------------------------
 \section{Frequently Asked Questions}
 \label{sect:faqs}
 
 % B.1 Where do I learn about Linux?
-% -------------------------------------------------------------
+% -----------------------------------------------------------------------------
 \subsection{Where do I learn about Linux?}
 \label{sect:faqs-linux}
 
 All Speed users are expected to have a basic understanding of Linux and its commonly used commands.
 Here are some recommended resources:
 
+% -----------------------------------------------------------------------------
 \paragraph*{Software Carpentry}
+
 Software Carpentry provides free resources to learn software, including a workshop on the Unix shell.
 Visit \href{https://software-carpentry.org/lessons/}{Software Carpentry Lessons} to learn more.
 
+% -----------------------------------------------------------------------------
 \paragraph*{Udemy}
+
 There are numerous Udemy courses, including free ones, that will help you learn Linux. 
 Active Concordia faculty, staff and students have access to Udemy courses. 
 A recommended starting point for beginners is the course ``Linux Mastery: Master the Linux Command Line in 11.5 Hours''.
 Visit \href{https://www.concordia.ca/it/services/udemy.html}{Concordia's Udemy page} to learn how Concordians can access Udemy.
 
 % B.2 How to bash shell on Speed?
-% -------------------------------------------------------------
-\subsection{How to use bash shell on \tool{Speed}?}
+% -----------------------------------------------------------------------------
+\subsection{How to use bash shell on Speed?}
 \label{sect:faqs-bash}
 
 This section provides comprehensive instructions on how to utilize the bash shell on the Speed cluster.
 
 % B.2.1 How do I set bash as my login shell?
+% -----------------------------------------------------------------------------
 \subsubsection{How do I set bash as my login shell?}
+
 To set your default login shell to bash on Speed, your login shell on all GCS servers must be changed to bash.
 To make this change, create a ticket with the Service Desk (or email \texttt{help at concordia.ca}) to
 request that bash become your default login shell for your ENCS user account on all GCS servers.
 
 % B.2.2 How do I move into a bash shell on Speed?
-\subsubsection{How do I move into a bash shell on \tool{Speed}?}
+% -----------------------------------------------------------------------------
+\subsubsection{How do I move into a bash shell on Speed?}
+
 To move to the bash shell, type \textbf{bash} at the command prompt:
 \begin{verbatim}
 	[speed-submit] [/home/a/a_user] > bash
 	bash-4.4$ echo $0
 	bash
 \end{verbatim}	
 
-\noindent \textbf{Note} how the command prompt changes from 
+\noindent
+\textbf{Note} how the command prompt changes from 
 ``\verb![speed-submit] [/home/a/a_user] >!'' to ``\verb!bash-4.4$!'' after entering the bash shell.
 
 % B.2.3 How do I use the bash shell in an interactive session on Speed?
-\subsubsection{How do I use the bash shell in an interactive session on \tool{Speed}?}
+% -----------------------------------------------------------------------------
+\subsubsection{How do I use the bash shell in an interactive session on Speed?}
+
 Below are examples of how to use \tool{bash} as a shell in your interactive job sessions 
 with both the \tool{salloc} and \tool{srun} commands.
 
 \begin{itemize}
 	\item \texttt{salloc -ppt --mem=100G -N 1 -n 10 /encs/bin/bash}
-	\item \texttt{srun  --mem=50G -n 5 --pty /encs/bin/bash}
+	\item \texttt{srun --mem=50G -n 5 --pty /encs/bin/bash}
 \end{itemize}
 
 \noindent\textbf{Note:} Make sure the interactive job requests memory, cores, etc.
 
 % B.2.4 How do I run scripts written in bash on Speed?
+% -----------------------------------------------------------------------------
 \subsubsection{How do I run scripts written in bash on \tool{Speed}?}
 
 To execute bash scripts on Speed:
@@ -74,8 +86,10 @@ \subsubsection{How do I run scripts written in bash on \tool{Speed}?}
 % B.3 How to resolve “Disk quota exceeded” errors?
 % -------------------------------------------------------------
 \subsection{How to resolve ``Disk quota exceeded'' errors?}
+\label{sect:quota-exceeded}
 
 % B.3.1 Probable Cause
+% -----------------------------------------------------------------------------
 \subsubsection{Probable Cause}
 
 The ``\texttt{Disk quota exceeded}'' error occurs when your application has 
@@ -87,6 +101,7 @@ \subsubsection{Probable Cause}
 \end{enumerate}
 
 % B.3.2 Possible Solutions
+% -----------------------------------------------------------------------------
 \subsubsection{Possible Solutions}
 
 \begin{enumerate}
@@ -119,6 +134,7 @@ \subsubsection{Possible Solutions}
 \noindent In the above example, \verb!$USER! is an environment variable containing your ENCS username.
 
 % B.3.3 Example of setting working directories for COMSOL
+% -----------------------------------------------------------------------------
 \subsubsection{Example of setting working directories for \tool{COMSOL}}
 
 \begin{itemize}
@@ -137,6 +153,7 @@ \subsubsection{Example of setting working directories for \tool{COMSOL}}
 \noindent In the above example, \verb!$USER! is an environment variable containing your ENCS username.
 
 % B.3.4 Example of setting working directories for Python Modules
+% -----------------------------------------------------------------------------
 \subsubsection{Example of setting working directories for \tool{Python Modules}}
 
 By default when adding a Python module, the \texttt{/tmp} directory is set as the temporary repository for files downloads.
@@ -156,7 +173,7 @@ \subsubsection{Example of setting working directories for \tool{Python Modules}}
 \noindent In the above example, \verb!$USER! is an environment variable containing your ENCS username.
 
 % B.4 How do I check my job's status?
-% -------------------------------------------------------------
+% -----------------------------------------------------------------------------
 \subsection{How do I check my job's status?}
 
 %When a job with a job id of 1234 is running, the status of that job can be tracked using \verb!`qstat -j 1234`!.
@@ -181,33 +198,16 @@ \subsection{How do I check my job's status?}
 \end{itemize}
 
 % B.5 Why is my job pending when nodes are empty?
-% -------------------------------------------------------------
+% -----------------------------------------------------------------------------
 \subsection{Why is my job pending when nodes are empty?}
 
 % B.5.1 Disabled nodes
+% -----------------------------------------------------------------------------
 \subsubsection{Disabled nodes}
+
 It is possible that one or more of the Speed nodes are disabled for maintenance.
 To verify if Speed nodes are disabled, check if they are in a draining or drained state:
 
-%\begin{verbatim}
-%qstat -f -qs d
-%queuename                      qtype resv/used/tot. load_avg arch          states
-%---------------------------------------------------------------------------------
-%[email protected] BIP   0/0/32         0.27     lx-amd64      d
-%---------------------------------------------------------------------------------
-%[email protected] BIP   0/0/32         0.01     lx-amd64      d
-%---------------------------------------------------------------------------------
-%[email protected] BIP   0/0/32         0.01     lx-amd64      d
-%---------------------------------------------------------------------------------
-%[email protected] BIP   0/0/32         0.02     lx-amd64      d
-%---------------------------------------------------------------------------------
-%[email protected] BIP   0/0/32         0.03     lx-amd64      d
-%---------------------------------------------------------------------------------
-%[email protected] BIP   0/0/32         0.01     lx-amd64      d
-%---------------------------------------------------------------------------------
-%[email protected] BIP   0/0/32         0.03     lx-amd64      d
-%\end{verbatim}
-
 \small
 \begin{verbatim}
 [serguei@speed-submit src] % sinfo --long --Node
@@ -260,6 +260,7 @@ \subsubsection{Disabled nodes}
 and the disabled nodes have a state of \textbf{idle}.
 
 % B.5.2 Error in job submit request.
+% -----------------------------------------------------------------------------
 \subsubsection{Error in job submit request.}
 
 It is possible that your job is pending because it requested resources that are not available within Speed. 
@@ -268,5 +269,5 @@ \subsubsection{Error in job submit request.}
 	sacct -j 1234
 \end{verbatim}
 
-\noindent A summary of the reasons can be obtained via the \tool{squeue} command.
-%and review the messages in the \textbf{scheduling info:} section.
+\noindent
+A summary of the reasons can be obtained via the \tool{squeue} command.