Rocky 8 Transition Guide - Revision history

Isaiah: Updated description of how to remove old hosts in ~/.ssh/known_hosts file

2023-10-04T19:44:21Z

Updated description of how to remove old hosts in ~/.ssh/known_hosts file

← Older revision		Revision as of 15:44, 4 October 2023
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	</pre>		</pre>

	To fix this problem, ~~open~~ the ~~known_hosts file on '''your local machine''' (in~~ the ~~example above~~ the ~~full path to this file is '''~~/~~Users/jsmith~~/.ssh/known_hosts~~'''~~, ~~as shown in~~ the ~~error message above). Then delete the line that has~~ sapelo2.gacrc.uga.edu ~~and save the file.~~		To fix this problem, you will need to remove the keys belonging to the host, <code>sapelo2.gacrc.uga.edu</code>. This can be done by manually deleting all lines corresponding to the host, <code>sapelo2.gacrc.uga.edu</code>, in the <code>~/.ssh/known_hosts</code> file, or by executing the command:<syntaxhighlight lang="bash">
			ssh-keygen -R sapelo2.gacrc.uga.edu
	Once you have done this, you should be able to ssh into sapelo2.gacrc.uga.edu. You might still get a message like this:		</syntaxhighlight>Once you have done this, you should be able to ssh into sapelo2.gacrc.uga.edu. You might still get a message like this:

	<pre class="gcomment">		<pre class="gcomment">

Shtsai at 18:28, 7 September 2023

2023-09-07T18:28:42Z

← Older revision		Revision as of 14:28, 7 September 2023
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	If your are attempting to load a module that was available on CentOS 7, but no longer available on Rocky 8, the module will not be loaded, and the commands provided by that module will not be available for the job. Please check the correct name of the modules on the Rocky 8 system. If the software is not available on the updated cluster, please feel free to [https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=25850 submit a software installation request ticket] and we will try to get it installed for you.		If your are attempting to load a module that was available on CentOS 7, but no longer available on Rocky 8, the module will not be loaded, and the commands provided by that module will not be available for the job. Please check the correct name of the modules on the Rocky 8 system. If the software is not available on the updated cluster, please feel free to [https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=25850 submit a software installation request ticket] and we will try to get it installed for you.

			===Python scripts not working anymore===

			Please note that the updated Sapelo2 does not have /usr/bin/python installed. The OS comes with a default /usr/bin/python2 (v. 2.7.18) and a default /usr/bin/python3 (v. 3.6.8). Scripts that have the first line:

			<pre class="gscript">
			#!/usr/bin/python
			</pre>

			will not work on Sapelo2 (with the Rocky 8 OS). We recommend that you change this line to

			<pre class="gscript">
			#!/usr/bin/env python
			</pre>

			and load one of the Python modules before running the script. The following command on Sapelo2 will show all the Python modules installed centrally:
			<pre class="gscript">
			ml spider Python
			</pre>

Shtsai: /* Compiler toolchains */

2023-09-07T18:11:33Z

Compiler toolchains

← Older revision		Revision as of 14:11, 7 September 2023
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	*GCCcore/11.3.0, GCC/11.3.0, gompi/2022a, foss/2022a		*GCCcore/11.3.0, GCC/11.3.0, gompi/2022a, foss/2022a
	*CUDA versions 11.4, 11.7, and 12.0		*CUDA versions 11.4, 11.7, and 12.0
	*OpenMPI versions 4.1.2 and 4.1.4		*OpenMPI versions 4.1.1 and 4.1.4

	====Centrally installed modules====		====Centrally installed modules====

Shtsai: /* Queueing System */

2023-09-07T18:11:10Z

Queueing System

← Older revision		Revision as of 14:11, 7 September 2023
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	===Queueing System===		===Queueing System===

	The Slurm queueing system will be updated from version 21.08.8 to version 23.02.2. Most compute nodes available on the CentOS 7 system will continue to be available after the transition to Rocky 8, and the Slurm partitions will remain the same.		The Slurm queueing system will be updated from version 21.08.8 to version 23.02.4. Most compute nodes available on the CentOS 7 system will continue to be available after the transition to Rocky 8, and the Slurm partitions will remain the same.


	===Software===		===Software===

Shtsai at 18:10, 7 September 2023

2023-09-07T18:10:51Z

← Older revision		Revision as of 14:10, 7 September 2023
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	==Introduction==		==Introduction==

	As part of our ~~August 29~~-31,2023 maintenance window, the GACRC will be upgrading the Sapelo2 cluster operating system from CentOS 7 to Rocky 8.		As part of our September 5-7,2023 maintenance window, the GACRC will be upgrading the Sapelo2 cluster operating system from CentOS 7 to Rocky 8.

	==Why is a major Operating System (OS) update necessary?==		==Why is a major Operating System (OS) update necessary?==

Shtsai: /* Centrally installed modules */

2023-07-30T13:48:52Z

Centrally installed modules

← Older revision		Revision as of 09:48, 30 July 2023
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	====Centrally installed modules====		====Centrally installed modules====

	Centrally installed software modules will continue to have the format <b>Name/Version-Toolchain</b>, but for most software packages the <b>Version</b> and <b>Toolchain</b> will be updated. Some module names have an optional <b>Versionsuffix</b> ~~and it~~ might change or be dropped on the new system. There are modules whose names will remain the same on the Rocky 8 system. Some examples:		Centrally installed software modules will continue to have the format <b>Name/Version-Toolchain</b>, but for most software packages the <b>Version</b> and <b>Toolchain</b> will be updated. Some module names have the format <b>Name/Version-Toolchain-Versionsuffix</b> with an optional <b>Versionsuffix</b> that might change or be dropped on the new system. There are also some modules whose names will remain the same on the Rocky 8 system. Some examples:

	{\| class="wikitable"		{\| class="wikitable"

Shtsai at 13:46, 30 July 2023

2023-07-30T13:46:07Z

← Older revision		Revision as of 09:46, 30 July 2023
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	====Centrally installed modules====		====Centrally installed modules====

	Centrally installed software modules will continue to have the format <b>Name/Version-Toolchain</b>, but for most software packages the <b>Version</b> and <b>Toolchain</b> will updated. Some module names have an optional <b>Versionsuffix</b> and it might change or be dropped on the new system. There are modules whose names will remain the same on the Rocky 8 system. Some examples:		Centrally installed software modules will continue to have the format <b>Name/Version-Toolchain</b>, but for most software packages the <b>Version</b> and <b>Toolchain</b> will be updated. Some module names have an optional <b>Versionsuffix</b> and it might change or be dropped on the new system. There are modules whose names will remain the same on the Rocky 8 system. Some examples:

	{\| class="wikitable"		{\| class="wikitable"

Shtsai: /* Centrally installed modules */

2023-07-28T18:14:23Z

Centrally installed modules

← Older revision		Revision as of 14:14, 28 July 2023
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	\| Trinity \|\| Trinity/2.10.0-foss-2019b-Python-3.7.4 \|\| Trinity/2.15.1-foss-2022a \|\| version, toolchain, versionsuffix		\| Trinity \|\| Trinity/2.10.0-foss-2019b-Python-3.7.4 \|\| Trinity/2.15.1-foss-2022a \|\| version, toolchain, versionsuffix
	\|}		\|}

			A list of the modules already installed on the Rocky 8 system is available at [[Software installed on Rocky 8]].

	====Conda environments====		====Conda environments====

Shtsai at 17:06, 28 July 2023

2023-07-28T17:06:49Z

← Older revision		Revision as of 13:06, 28 July 2023
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	Many software modules have been updated with a new version and/or a new toolchain version. The modules your jobs loaded on the CentOS 7 system might not be available on Rocky 8. Please check the name of the modules on the updated cluster. You can search for a module using the <code>ml spider NAME</code> command, where NAME needs to be replaced by the software package name that you are searching for. You can also see a list of all installed software with the command <code>ml avail</code>.		Many software modules have been updated with a new version and/or a new toolchain version. The modules your jobs loaded on the CentOS 7 system might not be available on Rocky 8. Please check the name of the modules on the updated cluster. You can search for a module using the <code>ml spider NAME</code> command, where NAME needs to be replaced by the software package name that you are searching for. You can also see a list of all installed software with the command <code>ml avail</code>.

	===Job gets command not found errors, but module load command included===		===Job gets command not found errors, but module load command included in job submission script===

	If your are attempting to load a module that was available on CentOS 7, but no longer available on Rocky 8, the module will not be loaded, and the commands provided by that module will not be available for the job. Please check the correct name of the modules on the Rocky 8 system. If the software is not available on the updated cluster, please feel free to [https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=25850 submit a software installation request ticket] and we will try to get it installed for you.		If your are attempting to load a module that was available on CentOS 7, but no longer available on Rocky 8, the module will not be loaded, and the commands provided by that module will not be available for the job. Please check the correct name of the modules on the Rocky 8 system. If the software is not available on the updated cluster, please feel free to [https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=25850 submit a software installation request ticket] and we will try to get it installed for you.

Shtsai at 17:06, 28 July 2023

2023-07-28T17:06:20Z

← Older revision		Revision as of 13:06, 28 July 2023
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	</pre>		</pre>

	===~~My job~~ gets module not found errors, the same script used to work on Sapelo2===		===Job gets module not found errors, the same script used to work on Sapelo2===

	Many software modules have been updated with a new version and/or a new toolchain version. The modules your jobs loaded on the CentOS 7 system might not be available on Rocky 8. Please check the name of the modules on the updated cluster. You can search for a module using the <code>ml spider NAME</code> command, where NAME needs to be replaced by the software package name that you are searching for. You can also see a list of all installed software with the command <code>ml avail</code>.		Many software modules have been updated with a new version and/or a new toolchain version. The modules your jobs loaded on the CentOS 7 system might not be available on Rocky 8. Please check the name of the modules on the updated cluster. You can search for a module using the <code>ml spider NAME</code> command, where NAME needs to be replaced by the software package name that you are searching for. You can also see a list of all installed software with the command <code>ml avail</code>.

	===~~My job~~ gets command not found errors, but ~~I did~~ load ~~the module~~===		===Job gets command not found errors, but module load command included===

	If your are attempting to load a module that was available on CentOS 7, but no longer available on Rocky 8, the module will not be loaded, and the commands provided by that module will not be available for the job. Please check the correct name of the modules on the Rocky 8 system. If the software is not available on the updated cluster, please feel free to [https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=25850 submit a software installation request ticket] and we will try to get it installed for you.		If your are attempting to load a module that was available on CentOS 7, but no longer available on Rocky 8, the module will not be loaded, and the commands provided by that module will not be available for the job. Please check the correct name of the modules on the Rocky 8 system. If the software is not available on the updated cluster, please feel free to [https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=25850 submit a software installation request ticket] and we will try to get it installed for you.