Magnolia HPC Cluster Workshop (July 2023): Difference between revisions

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This workshop is intended as an introduction to logging into and submitting jobs to the Magnolia computer cluster.
Workshop on using the Magnolia HPC cluster.
{|
{| class="table-striped"
|'''When:'''
|'''When:''' ||''July 18, 2023 10 am — 12 pm''
|''July 18, 2023 10 am — 12 pm''
|-
|-
|'''Where:'''
|'''Where:''' ||''[//map.usm.edu/campus_map.php?id=27801 PSRC 105]''
|''[https://map.usm.edu/campus_map.php?id=27801 PSRC 105]''
|-
|-
|'''Watch Recording:''' ||''[//smttt-my.sharepoint.com/:v:/g/personal/w498149_usm_edu/EQF4NjQbdAlBn5Zpp-RSuKIB108dIXynlhbZ1khof1Rtpg USM SharePoint Video Link].''
|}
|}


= Description =
= Description =


'''Topics in this workshop:'''
This workshop is intended for users that have used the cluster and wish to learn how to use it more efficiently. Topics include the following:


* Introduction to Magnolia cluster
* Introduction to the Magnolia High Performance Computing (HPC) cluster
* Submitting and running jobs
* HPC workflow
** SLURM scheduler
* Quick review of Linux shell commands
* Using Modules to select programs
* Using pre-installed programs and software (Linux Environment Modules)
* Running Python programs
* Python
* Compiling C/C++ programs
* Compiling C/C++ programs
** MPI and CUDA
* How serial (single threaded) programs can take advantage of HPC Clusters
* Running serial programs `faster`.
 
{{Note|This workshop is focused on how to use an HPC cluster, not how to use the individual software packages discussed. For example, during the ''Python'' topic, ways to use python on the cluster will be explored, not how to code in the Python programming language.}}
 
=Requirements=
Prior knowledge of the Magnolia HPC cluster will be useful, but is not required.
 
Bring a laptop that can connect to the Magnolia HPC Cluster (see the [[#Check connection to the cluster|Check connection to the cluster]] section below).


{{Important|Workshop participants '''MUST''' configure the SSH connection between their computer and Magnolia '''BEFORE''' the day of the workshop.}}
=In-person and Virtual=
In-person attendance is preferred, but for those who are not at the Hattiesburg Campus a Zoom link will be posted in the header of this page.


=Pre-Workshop Checklist=
=Registration=
*Fill out the registration form
Please fill out the [//redcap.usm.edu/surveys/?s=33D4LKAWY8NLX9X3 registration form] to reserve a seat.
*Configure the SSH connection between your computer and Magnolia
*Bring your computer to the workshop


=Fill out registration form=
Direct link to the registration form: https://redcap.usm.edu/surveys/?s=33D4LKAWY8NLX9X3
Those planning to attend need to fill out the registration form. [//redcap.usm.edu/surveys/?s=NWJH493JAL Registration Page]


=Configure the SSH connection=
=Check connection to the cluster=
If you are using Linux or OSX, SSH is used from the terminal. Type the command shown below to check the host key fingerprint. Do not enter any passwords. Instead, cancel by typing {{Key|Control+C}}. For Windows users, install an SSH client like PuTTY (http://www.putty.org) and follow the directions given in the following link. [[Connect_to_Magnolia#Windows|Windows Specific Directions]]
Please check that you can connect to the cluster before attending the workshop. Connecting to the cluster is typically done using [//wikipedia.org/wiki/Secure_Shell {{C|ssh}}] (see [[Connect_to_Magnolia#Connecting_/_Login|Connecting/Login]] for more details). If you are using Linux or OSX, {{C|ssh}} is used from the terminal. Type the command shown below to check the host key fingerprint. Do not enter any passwords. Instead, cancel by typing {{Key|Control+C}}. For Windows users, install an {{C|ssh}} client like PuTTY (https://www.putty.org) and follow the directions given in the following link: [[Connect_to_Magnolia#Windows|Windows Specific Directions]]


{{Cmd|ssh -o VisualHostKey{{=}}yes check@magnolia.usm.edu|output=<pre>
{{Cmd|ssh -o VisualHostKey{{=}}yes check@magnolia.usm.edu|output=<pre>
Line 51: Line 55:
</pre>}}
</pre>}}


Make sure that the host key fingerprint (In this case: SHA256:glQIZZKlsAwf3QJNNDQSxFpRzE2rKs4GfxByO6ZBzis) matches one of the fingerprints given in the list of SSH fingerprints for Magnolia. [[SSH_Fingerprints/magnolia.usm.edu]]
Make sure that the host key fingerprint (In this case: <tt>SHA256:glQIZZKlsAwf3QJNNDQSxFpRzE2rKs4GfxByO6ZBzis</tt>) matches one of the fingerprints given in the list of [[SSH_Fingerprints/magnolia.usm.edu|SSH Fingerprint for Magnolia]].


If you have any questions, please contact [mailto:brian.olson@usm.edu?subject=Magnolia%20Cluster:%20Workshop%20Question%20 Brian G. Olson].
If you have any questions, please contact [mailto:brian.olson@usm.edu?subject=Magnolia%20Cluster:%20Workshop%20Question%20 Brian G. Olson].


[[Category:Workshops]]
[[Category:Workshops]]

Latest revision as of 16:08, 3 August 2023

Workshop on using the Magnolia HPC cluster.

When:  July 18, 2023 10 am — 12 pm
Where:  PSRC 105
Watch Recording:  USM SharePoint Video Link.


Description

This workshop is intended for users that have used the cluster and wish to learn how to use it more efficiently. Topics include the following:

  • Introduction to the Magnolia High Performance Computing (HPC) cluster
  • HPC workflow
  • Quick review of Linux shell commands
  • Using pre-installed programs and software (Linux Environment Modules)
  • Python
  • Compiling C/C++ programs
  • How serial (single threaded) programs can take advantage of HPC Clusters
Note
This workshop is focused on how to use an HPC cluster, not how to use the individual software packages discussed. For example, during the Python topic, ways to use python on the cluster will be explored, not how to code in the Python programming language.

Requirements

Prior knowledge of the Magnolia HPC cluster will be useful, but is not required.

Bring a laptop that can connect to the Magnolia HPC Cluster (see the Check connection to the cluster section below).

In-person and Virtual

In-person attendance is preferred, but for those who are not at the Hattiesburg Campus a Zoom link will be posted in the header of this page.

Registration

Please fill out the registration form to reserve a seat.

Direct link to the registration form: https://redcap.usm.edu/surveys/?s=33D4LKAWY8NLX9X3

Check connection to the cluster

Please check that you can connect to the cluster before attending the workshop. Connecting to the cluster is typically done using ssh (see Connecting/Login for more details). If you are using Linux or OSX, ssh is used from the terminal. Type the command shown below to check the host key fingerprint. Do not enter any passwords. Instead, cancel by typing Control+C. For Windows users, install an ssh client like PuTTY (https://www.putty.org) and follow the directions given in the following link: Windows Specific Directions

user $ssh -o VisualHostKey=yes check@magnolia.usm.edu
Host key fingerprint is SHA256:glQIZZKlsAwf3QJNNDQSxFpRzE2rKs4GfxByO6ZBzis
+---[ECDSA 256]---+
|ooX^@=o          |
|o++*B+o.         |
|.+o ...          |
|o.o. o           |
|+o oo . S        |
|oo=.   .         |
|o=oo             |
|E+. .            |
|oo .             |
+----[SHA256]-----+
check@magnolia.usm.edu's password:

Make sure that the host key fingerprint (In this case: SHA256:glQIZZKlsAwf3QJNNDQSxFpRzE2rKs4GfxByO6ZBzis) matches one of the fingerprints given in the list of SSH Fingerprint for Magnolia.

If you have any questions, please contact Brian G. Olson.

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