View source for Submitting jobs and compiling programs on Magnolia cluster

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= Description =

'''Topics in this workshop:'''

# Introduction to Magnolia cluster
# Using Modules to select programs
# Submitting/running jobs using SLURM scheduler
# Compiling MPI programs
# Compiling CUDA programs



Questions? Email [mailto:Brian.Olson@usm.edu?Subject=Linux%20Workshop%20Part%20I Brian Olson]

= Workshop Notes =

The following is a a summary of topics covered in the workshop.

{{WIP|author=bgo}}
== Check hostname ==

Connecting to {{C|magnolia.usm.edu}} will result in access to one of two (2) login nodes, {{C|magnolia01}} or {{C|magnolia02}}, chosen randomly each time a connection is requested. The {{C|hostname}} command will show the host name of the system:
 
{{Cmd|hostname|output=<pre>magnolia01</pre>}}

== Create a Script/Program ==

To create a very simply script for {{C|bash}}, load up a next editor. To use the {{C|nano}} text editor, type:

{{Cmd|nano myscript.sh}}

Type the following, and save it.

{{FileBox|title=First script|filename=myscript.sh|lang=bash|1=#!/bin/sh

hostname}}


=== Mark as Executable, and Run ===
 
The script has been created, however it is currently a plain text file; to mark the script as executable, the {{C|chmod}} command is used.

{{Cmd|chmod a+x myscript.sh|./myscript.sh|output=<pre>magnolia01</pre>}}

=== Comments ===

Bash scripts allow for comments to be placed within the files by preceding them with a '#'

{{FileBox|title=First script with a comment|filename=myscript.sh|lang=bash|1=#!/bin/sh

# This is my first script, and a comment.

hostname}}

The script has previously been marked as executable, so it can be run directly.

{{Cmd|./myscript.sh|output=<pre>magnolia01</pre>}}

The output is the same as before, since comments are ignored by Bash.

== Slurm ==

The Slurm Workload Manager is used for submitting and monitoring jobs to the {{C|Magnolia}} cluster.

=== Partitions ===

Nodes of the {{C|Magnolia}} cluster is separated into partitions. These partitions can be viewed with the {{C|sinfo}} command.

{{Cmd|sinfo|output=<pre>PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
node*        up   infinite     69  alloc node[001-026,032-036,038-041,043-076]
node*        up   infinite      7   idle node[027-031,037,042]
gpu          up   infinite      2   idle gpu[001-002]
himem        up   infinite      4   idle himem[001-004]
phi          up   infinite      4   idle phi[001-004]</pre>}}

=== Job Information ===

The {{C|squeue}} command is used show infomation of jobs currently in the Slurm queue.

{{Cmd|squeue|output=<pre>   JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
    2151      node concorde     cpan  R 2-06:33:11     23 node[001-011,016,018,020,032-036,038-041]
    2162      node concorde     cpan  R 1-14:58:40     23 node[011-015,043-060]
    2208      node concorde     cpan  R    4:51:02     24 node[017,019,021-026,061-076]</pre>}}

=== Submit a Job ===

To submit a job, the {{C|sbatch}} command is used. The script made previously can be sent to the cluster for running:

{{Cmd|sbatch myscript.sh|output=<pre>Submitted batch job 2210</pre>}}

When the job is finished, the output will by default will be placed in a {{Path|slurm-####.out}} file, where '####' is the batch job number shown after the script was submitted with {{C|sbatch}}.

{{Cmd|cat slurm-2210.out|output=<pre>node028.cluster</pre>}}

{{Cmd|sbatch -n 2 -N 2 myscript.sh|output=<pre>Submitted batch job 2211</pre>}}

{{Cmd|cat slurm-2211.out|output=<pre>node028.cluster</pre>}}

{{FileBox|title=First script with a comment|filename=myscript.sh|lang=bash|1=#!/bin/sh

# This is my first script

srun hostname}}

{{Cmd|sbatch -n 2 -N 2 myscript.sh|output=<pre>Submitted batch job 2213</pre>}}

{{Cmd|cat slurm-2213.out|output=<pre>node028.cluster
node037.cluster</pre>}}

{{FileBox|title=First script with a comment|filename=myscript.sh|lang=bash|1=#!/bin/sh

#SBATCH --nodes=2
#SBATCH --ntasks-per-node=2
#SBATCH --mail-user=myemail@example.com
##SBATCH --mail-type=END
#SBATCH --time=0-00:10:00
#SBATCH --job-name=hostname

# This is my first script

srun hostname}}

{{Cmd|sbatch myscript.sh|output=<pre>Submitted batch job 2214</pre>}}

{{Cmd|cat slurm-2214.out|output=<pre>node028.cluster
node028.cluster
node037.cluster
node037.cluster</pre>}}


== Modules ==

{{Cmd|module avail|output=<pre>
------------------------ /usr/share/Modules/modulefiles ------------------------
dot         module-git  module-info modules     null        use.own

------------------------------- /act/modulefiles -------------------------------
impi               mpich/intel        openmpi-1.6/gcc    openmpi-1.8/intel
intel              mvapich2-2.2/gcc   openmpi-1.6/intel  openmpi-2.0/gcc
mpich/gcc          mvapich2-2.2/intel openmpi-1.8/gcc    openmpi-2.0/intel

----------------------------- /modules/modulefiles -----------------------------
atlas/3.10.3     hdf5/1.8.19      mkl/2017.0.3     python/3.6.2
cmake/3.9.1      lammps/20170811  molpro/2012.1.52 qe/6.0
ffmpeg/3.3.3     lapack/3.7.1     netcdf/4.4.1.1   qe/6.1
fftw/3.3.6       libxc/4.0.1      python/3.5.4     scalapack/2.0.2
</pre>}}

{{Cmd|python3.5 --version|output=<pre>bash: python3.5: command not found...</pre>}}

{{Cmd|module load python/3.5.4}}

{{Cmd|python3.5 --version|output=<pre>Python 3.5.4></pre>}}

{{Cmd|module help python/3.5.4|output=<pre>----------- Module Specific Help for 'python/3.5.4' ---------------

Description - Python is a widely used high-level programming language for general-purpose programming.
Docs        - https://www.python.org/
</pre>}}

{{Cmd|module unload python/3.5.4}}

== Example Job using LAMMPS ==

== Using the Lustre Storage ==

== Array Jobs ==

== Compiling MPI Programs ==

== Compiling CUDA Programs ==

== Compiling a Package ==

=== Download and Extract Package ===

=== Interactive Job ===

=== Configure Package ===

=== Build and Install Package ===

== Python Modules ==

=== pip ===

=== virtualenv ===

[[Category:Workshops]]