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Merge pull request #52 from NAG-DevOps/manual-update
Manual updates for 7.2
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,79 @@ | ||
| #!/encs/bin/bash | ||
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| # Generates .tex and .md versions of the software list | ||
| # Serguei Mokhov | ||
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| GENERATED_ON=`date` | ||
| OUTFILE="software-list" | ||
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| # Generate the LaTeX version first | ||
| cat > "$OUTFILE.tex" << LATEX_HEADER | ||
| % ----------------------------------------------------------------------------- | ||
| % $0 | ||
| \section{Software Installed On Speed} | ||
| \label{sect:software-details} | ||
| This is a generated section by a script; last updated on \textit{$GENERATED_ON}. | ||
| We have two major software trees: Scientific Linux 7 (EL7), which is | ||
| outgoing, and AlmaLinux 9 (EL9). After major synchronization of software | ||
| packages is complete, we will stop maintaining the EL7 tree and | ||
| will migrate the remaining nodes to EL9. | ||
| Use \option{--constraint=el7} to select EL7-only installed nodes for their | ||
| software packages. Conversely, use \option{--constraint=el9} for the EL9-only | ||
| software. These options would be used as a part of your job parameters | ||
| in either \api{\#SBATCH} or on the command line. | ||
| \noindent | ||
| \textbf{NOTE:} this list does not include packages installed directly on the OS (yet). | ||
| % ----------------------------------------------------------------------------- | ||
| \subsection{EL7} | ||
| \label{sect:software-el7} | ||
| Not all packages are intended for HPC, but the common tree is available | ||
| on Speed as well as teaching labs' desktops. | ||
| \scriptsize | ||
| \begin{multicols}{3} | ||
| \begin{itemize} | ||
| LATEX_HEADER | ||
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| ls -1 /encs/ArchDep/x86_64.EL7/pkg/ \ | ||
| | egrep -v HIDE \ | ||
| | sed 's/^/\\item \\verb|/g' \ | ||
| | sed 's/$/|/g' \ | ||
| >> "$OUTFILE.tex" | ||
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| cat >> "$OUTFILE.tex" << LATEX_EL9_HEADER | ||
| \end{itemize} | ||
| \end{multicols} | ||
| \normalsize | ||
| % ----------------------------------------------------------------------------- | ||
| \subsection{EL9} | ||
| \label{sect:software-el9} | ||
| \scriptsize | ||
| \begin{multicols}{3} | ||
| \begin{itemize} | ||
| LATEX_EL9_HEADER | ||
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| ls -1 /encs/ArchDep/x86_64.EL9/pkg/ \ | ||
| | egrep -v HIDE \ | ||
| | sed 's/^/\\item \\verb|/g' \ | ||
| | sed 's/$/|/g' \ | ||
| >> "$OUTFILE.tex" | ||
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| cat >> "$OUTFILE.tex" << LATEX_FOOTER | ||
| \end{itemize} | ||
| \end{multicols} | ||
| \normalsize | ||
| % EOF | ||
| LATEX_FOOTER | ||
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| # Get .md version of the same from LaTeX | ||
| pandoc -s "$OUTFILE.tex" -o "$OUTFILE.md" | ||
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| # EOF |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,115 +1,96 @@ | ||
| % ------------------------------------------------------------------------------ | ||
| \subsubsection{Directives} | ||
| \label{sect:directives} | ||
| % 2.2.1 Directives | ||
| % ------------------- | ||
| % TMP scheduler-specific section | ||
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| Directives are comments included at the beginning of a job script that set the shell | ||
| and the options for the job scheduler. | ||
| and the options for the job scheduler. | ||
| % | ||
| The shebang directive is always the first line of a script. In your job script, | ||
| this directive sets which shell your script's commands will run in. On ``Speed'', | ||
| we recommend that your script use a shell from the \texttt{/encs/bin} directory. | ||
| we recommend that your script use a shell from the \texttt{/encs/bin} directory.\\ | ||
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| To use the \texttt{tcsh} shell, start your script with \verb|#!/encs/bin/tcsh|. | ||
| % | ||
| For \texttt{bash}, start with \verb|#!/encs/bin/bash|. | ||
| % | ||
| Directives that start with \verb|#SBATCH|, set the options for the cluster's | ||
| Slurm job scheduler. The script template, \texttt{template.sh}, | ||
| provides the essentials: | ||
| For \texttt{bash}, start with \verb|#!/encs/bin/bash|.\\ | ||
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| 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: | ||
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| %\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 where output files will go | ||
| #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 --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 | ||
| \end{verbatim} | ||
| \normalsize | ||
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| Replace the following to adjust the job script for your project(s) | ||
| \begin{enumerate} | ||
| \item \verb+<jobname>+ with a job name for the job | ||
| \item \verb+<directory>+ with the fullpath to your job's working directory, e.g., where your code, | ||
| source files and where the standard output files will be written to. By default, \verb+--chdir+ | ||
| sets the current directory as the job's working directory | ||
| \item \verb+<type>+ with the type of e-mail notifications you wish to receive. 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. | ||
| NOTE: All jobs MUST set a value for the \verb|--mem| option. | ||
| \end{enumerate} | ||
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| Example with short option equivalents: | ||
| \noindent Replace the following to adjust the job script for your project(s) | ||
| \begin{itemize} | ||
| \item \verb+<jobname>+ with a job name for the job. This name will be displayed in the job queue. | ||
| \item \verb+<directory>+ with the fullpath to your job's working directory, e.g., where your code, | ||
| source files and where the standard output files will be written to. | ||
| By default, \verb+--chdir+ sets the current directory as the job's working directory. | ||
| \item \verb+<type>+ with the type of e-mail notifications you wish to receive. | ||
| 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 \option{--mem} option. | ||
| \end{itemize} | ||
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| \noindent Example with short option equivalents: | ||
| \small | ||
| \begin{verbatim} | ||
| #SBATCH -J tmpdir ## Job's name set to 'tmpdir' | ||
| #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 | ||
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| % | ||
| If you are unsure about memory footprints, err on assigning a generous | ||
| \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 | ||
| %\api{h\_vmem} | ||
| \option{--mem} | ||
| values for future jobs by monitoring the size of a job's active | ||
| 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: | ||
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| %\begin{verbatim} | ||
| %qstat -j <jobID> | grep maxvmem | ||
| %\end{verbatim} | ||
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| \begin{verbatim} | ||
| sacct -j <jobID> | ||
| sstat -j <jobID> | ||
| sacct -j <jobID> | ||
| sstat -j <jobID> | ||
| \end{verbatim} | ||
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| \noindent | ||
| This can be customized to show specific columns: | ||
| \noindent This can be customized to show specific columns: | ||
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| \begin{verbatim} | ||
| sacct -o jobid,maxvmsize,ntasks%7,tresusageouttot%25 -j <jobID> | ||
| sstat -o jobid,maxvmsize,ntasks%7,tresusageouttot%25 -j <jobID> | ||
| sacct -o jobid,maxvmsize,ntasks%7,tresusageouttot%25 -j <jobID> | ||
| sstat -o jobid,maxvmsize,ntasks%7,tresusageouttot%25 -j <jobID> | ||
| \end{verbatim} | ||
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| Memory-footprint values are also provided for completed jobs in the final | ||
| e-mail notification as ``maxvmsize''. | ||
| % | ||
| \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.} | ||
| cluster.}\\ | ||
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| 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. | ||
| Jobs with a smaller \texttt{time} value will have a higher priority and may result in your job being scheduled sooner. | ||
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| \item | ||
| \option{--account=<name>} -- specifies which Account, aka project or association, | ||
| that the Speed resources your job uses should be attributed to. When moving from | ||
| GE to SLURM users most users were assigned to Speed's two default accounts | ||
| \texttt{speed1} and \texttt{speed2}. However, users that belong to a particular research | ||
| group or project are will have a default Account like the following | ||
| \texttt{aits}, | ||
| \texttt{vidpro}, | ||
| \texttt{gipsy}, | ||
| \texttt{ai2}, | ||
| \texttt{mpackir}, | ||
| \texttt{cmos}, among others. | ||
| \item \option{--time=<time>} -- is the estimate of wall clock time required for your job to run. | ||
| 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. | ||
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| \item \option{--account=<name>} -- specifies which Account, aka project or association, | ||
| that the Speed resources your job uses should be attributed to. When moving from | ||
| GE to SLURM users most users were assigned to Speed's two default accounts | ||
| \texttt{speed1} and \texttt{speed2}. However, users that belong to a particular research | ||
| group or project are will have a default Account like the following | ||
| \texttt{aits}, | ||
| \texttt{vidpro}, | ||
| \texttt{gipsy}, | ||
| \texttt{ai2}, | ||
| \texttt{mpackir}, | ||
| \texttt{cmos}, among others. | ||
| \end{itemize} |
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