Rocky 9 Transition Guide - Revision history

Shtsai at 16:00, 2 August 2025

2025-08-02T16:00:58Z

← Older revision		Revision as of 12:00, 2 August 2025
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	If you are attempting to load a module that was available on Rocky 8, but no longer available on Rocky 9, 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 9 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 you are attempting to load a module that was available on Rocky 8, but no longer available on Rocky 9, 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 9 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.

			===Errors when running MPI applications===

			Please launch the MPI-enabled executable with srun, without using the --mpi=pmi2 option. For example, if your job submission script used

			<code> srun --mpi=pmi2 ./programname [options] </code>

			please use the following now

			<code> srun ./programname [options] </code>

			where [options] stand for any options that need to be passed to the program.

			If the executable you are running was compiled on Sapelo2 prior to the maintenance (on Rocky 8), please recompile the code on Sapelo2, to ensure that it uses the libraries on the current Rocky 9 OS.

	===I cannot find Anaconda3 or Miniconda3 modules===		===I cannot find Anaconda3 or Miniconda3 modules===

Shtsai at 15:26, 2 August 2025

2025-08-02T15:26:26Z

← Older revision		Revision as of 11:26, 2 August 2025
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	If you are attempting to load a module that was available on Rocky 8, but no longer available on Rocky 9, 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 9 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 you are attempting to load a module that was available on Rocky 8, but no longer available on Rocky 9, 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 9 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.

			===I cannot find Anaconda3 or Miniconda3 modules===

			Anaconda3 and Miniconda3 will no longer be available on Sapelo2.

			If you need to install conda environments, we suggest using Miniforge3. Miniforge is a community-driven, open-source distribution that provides conda package management without the licensing constraints of Anaconda and Miniconda.

			You can install and manage environments with Miniforge in much the same way as with Anaconda or Miniconda.

			If you need help transitioning to Miniforge or recreating your existing environments, please feel free to reach out.


	===Python scripts not working anymore===		===Python scripts not working anymore===

Shtsai: /* Job gets command not found errors, but module load command included in job submission script */

2025-06-30T17:38:14Z

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

← Older revision		Revision as of 13:38, 30 June 2025
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	===Job gets command not found errors, but module load command included in job submission script===		===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 Rocky 8, but no longer available on Rocky 9, 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 9 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 you are attempting to load a module that was available on Rocky 8, but no longer available on Rocky 9, 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 9 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===		===Python scripts not working anymore===

Shtsai: /* Python packages */

2025-06-30T17:37:01Z

Python packages

← Older revision		Revision as of 13:37, 30 June 2025
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	====Python packages====		====Python packages====

	Python libraries and virtual environments need to be reinstalled as well, using versions of Python available ~~there~~.		Python libraries and virtual environments need to be reinstalled as well, using versions of Python available on the updated system.

	====R packages====		====R packages====

Shtsai: /* Conda environments */

2025-06-30T17:36:18Z

Conda environments

← Older revision		Revision as of 13:36, 30 June 2025
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	====Conda environments====		====Conda environments====

	Some users have conda environments installed in their home ~~directory~~ or group shared directories. These environments should be reinstalled on the Rocky 9 system, using versions of Miniforge available there. Because of changes in Anaconda licenses, the updated cluster does not provide a central installation of Anaconda and Miniconda. We suggest that users use Miniforge to create conda environments.		Some users have conda environments installed in their home directories or group shared directories. These environments should be reinstalled on the Rocky 9 system, using versions of Miniforge available there. Because of changes in Anaconda licenses, the updated cluster does not provide a central installation of Anaconda and Miniconda. We suggest that users use Miniforge to create conda environments.

	Mamba and Micromamba are available on the the Rocky 9 system as well.		Mamba and Micromamba are available on the the Rocky 9 system as well.

Shtsai: /* Why is a major Operating System (OS) update necessary? */

2025-06-30T17:15:33Z

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

← Older revision		Revision as of 13:15, 30 June 2025
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	==Why is a major Operating System (OS) update necessary?==		==Why is a major Operating System (OS) update necessary?==

	* Existing OS (Rocky 8) is End of Life - There are no more ~~full version~~ updates being released for the existing operating system and newer versions of some software applications are not supported by the current OS version.		* Existing OS (Rocky 8) is End of Life - There are no more feature updates being released for the existing operating system and newer versions of some software applications are not supported by the current OS version.

	* Updated system libraries (glibc 2.34) - The upgrade to Rocky 9 includes a newer glibc version, which is required by newer applications. This ensures better compatibility and performance for current and future software.		* Updated system libraries (glibc 2.34) - The upgrade to Rocky 9 includes a newer glibc version, which is required by newer applications. This ensures better compatibility and performance for current and future software.

Shtsai: /* Why is a major Operating System (OS) update necessary? */

2025-06-30T17:03:12Z

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

← Older revision		Revision as of 13:03, 30 June 2025
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	* Existing OS (Rocky 8) is End of Life - There are no more full version updates being released for the existing operating system and newer versions of some software applications are not supported by the current OS version.		* Existing OS (Rocky 8) is End of Life - There are no more full version updates being released for the existing operating system and newer versions of some software applications are not supported by the current OS version.

	* Updated system libraries (glibc 2.34) - The upgrade to Rocky 9 includes a newer glibc version, which is required by ~~many modern scientific and HPC~~ applications. This ensures better compatibility and performance for current and future software.		* Updated system libraries (glibc 2.34) - The upgrade to Rocky 9 includes a newer glibc version, which is required by newer applications. This ensures better compatibility and performance for current and future software.

	* Newer kernel (5.14) - the updated Linux kernel enable us to better support new CPUs, GPUs, and storage devices.		* Newer kernel (5.14) - the updated Linux kernel enable us to better support new CPUs, GPUs, and storage devices.

	* Security improvement - to retain compliance with current and future security requirements, we must keep using a supported version of the operating system.		* Security improvement - to retain compliance with current and future security requirements, we must keep using a supported version of the operating system.


	==What does this mean to you and your workflows?==		==What does this mean to you and your workflows?==

Shtsai: /* Introduction */

2025-06-30T17:01:06Z

Introduction

← Older revision		Revision as of 13:01, 30 June 2025
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	* Update the cluster Linux operating system from Rocky 8 to Rocky 9.		* Update the cluster Linux operating system from Rocky 8 to Rocky 9.

	* Migrate ~~the~~ home directories to a new storage device.		* Migrate user home directories (/home) to a new storage device.

	* Update firmware of some computing and network hardware.		* Update firmware of some computing and network hardware.


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

Shtsai: /* Centrally installed modules */

2025-06-30T16:57:50Z

Centrally installed modules

← Older revision		Revision as of 12:57, 30 June 2025
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	\|}		\|}

	A list of the modules already installed on the Rocky 9 system is available at [[Software installed on Rocky 8]].		A list of the modules already installed on the Rocky 9 system is available at [[Software installed on Rocky 9]].

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

Shtsai at 16:22, 30 June 2025

2025-06-30T16:22:09Z

← Older revision		Revision as of 12:22, 30 June 2025
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	===Storage===		===Storage===

	The home directories will be migrated to a new storage device. All existing /home, /scratch, /work, /project, and /db spaces will be available after the maintenance and they will retain their existing data.		The home directories will be migrated to a new storage device. Prior to the maintenance, files from /home were copied to the new storage device and periodic synchronization processes are run. At the start of the maintenance window, while no users are logged in and no jobs are running, we will perform one last synchronization of the files in /home from the old storage device to the new one.

			All existing /home, /scratch, /work, /project, and /db spaces will be available after the maintenance and they will retain their existing data.


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	*GCCcore/12.3.0, GCC/12.3.0, gompi/2023a, foss/2023a		*GCCcore/12.3.0, GCC/12.3.0, gompi/2023a, foss/2023a
	*GCCcore/13.3.0, GCC/13.3.0, gompi/2024a, foss/2024a		*GCCcore/13.3.0, GCC/13.3.0, gompi/2024a, foss/2024a
	*CUDA versions 12.1, 12.4, 12.6		*CUDA versions 12.1, 12.4, 12.6, 12.8
	*OpenMPI versions 4.1.5 and 5.0.3		*OpenMPI versions 4.1.5 and 5.0.3

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	! Software !! Module name on Rocky 8 !! Module name on Rocky 9 !! Changes		! Software !! Module name on Rocky 8 !! Module name on Rocky 9 !! Changes
	\|-		\|-
	\| ~~ABySS~~ \|\| ~~ABySS~~/2.3.1-foss-~~2019b~~ \|\| ~~ABySS~~/2.3.5-foss-~~2021b~~ \|\| version, toolchain		\| AlphaFold \|\| AlphaFold/2.3.1-foss-2022a-CUDA-11.7.0 \|\| AlphaFold/2.3.2-foss-2023a-CUDA-12.1.1 \|\| version, toolchain, CUDA version
	\|-		\|-
	\| BLAST+ \|\| BLAST+/2.12.0-gompi-~~2020b~~ \|\| BLAST+/2.13.0-gompi-~~2022a~~ \|\| version, toolchain		\| BLAST+ \|\| BLAST+/2.13.0-gompi-2022a \|\| BLAST+/2.16.0-gompi-2024a \|\| version, toolchain
	\|-		\|-
	\| ~~BWA~~ \|\| ~~BWA~~/0.~~7.17~~-~~GCC~~-~~10.3.0~~ \|\| ~~BWA~~/0.~~7.17~~-~~GCCcore~~-~~11.2.0~~ \|\| toolchain		\| BRAKER \|\| BRAKER/3.0.8-foss-2022a \|\| BRAKER/3.0.8-foss-2022a \|\| toolchain
	\|-		\|-
	\| ~~DeepAffinity~~ \|\| ~~DeepAffinity~~/0.1 \|\| \|\| ~~not available (yet)~~		\| SAMtools \|\| SAMtools/1.18-GCC-12.3.0 \|\| SAMtools/1.18-GCC-12.3.0 \|\| no changes
	\|-		\|-
	\| SAMtools \|\| SAMtools/1.~~16.1~~-GCC-11.3.0 \|\| SAMtools/1.~~16.1~~-GCC-11.3.0 \|\| ~~no changes~~		\| SAMtools \|\| SAMtools/1.18-GCC-12.3.0 \|\| SAMtools/1.21-GCC-13.3.0 \|\| version, toolchain, though old version still available
	\|-		\|-
	\| ~~STAR~~ \|\| ~~STAR~~/2.7.~~10a~~-GCC-8.3.0 \|\| ~~STAR/2.7.10b-GCC-11.3.0~~ \|\| ~~version, toolchain~~		\| SpaceRanger \|\| SpaceRanger/2.1.0-GCC-11.3.0 \|\| \|\| not available (yet)
	\|-		\|-
	\| ~~Trinity~~ \|\| ~~Trinity~~/2.10.0-foss-~~2019b~~-Python-3.7.4 \|\| ~~Trinity~~/2.15.1-foss-~~2022a~~ \|\| version, toolchain, versionsuffix		\| STAR \|\| STAR/2.7.10b-GCC-11.3.0 \|\| STAR/2.7.11b-GCC-13.3.0 \|\| version, toolchain
			\|-
			\| UMI-tools \|\| UMI-tools/1.1.2-foss-2022a-Python-3.10.4 \|\| UMI-tools/1.1.4-foss-2023a \|\| version, toolchain, versionsuffix
	\|}		\|}

	A list of the modules already installed on the Rocky 8 system is available at [[Software installed on Rocky 8]].		A list of the modules already installed on the Rocky 9 system is available at [[Software installed on Rocky 8]].

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

	Some users have conda environments installed in their home directory or group shared directories. These environments should be reinstalled on the Rocky 8 system, using versions of Miniconda ~~or Anaconda~~ available ~~there~~. Documentation on how to install conda environments on the cluster is available at https://wiki.gacrc.uga.edu/wiki/Installing_Applications_on_Sapelo2		Some users have conda environments installed in their home directory or group shared directories. These environments should be reinstalled on the Rocky 9 system, using versions of Miniforge available there. Because of changes in Anaconda licenses, the updated cluster does not provide a central installation of Anaconda and Miniconda. We suggest that users use Miniforge to create conda environments.

			Mamba and Micromamba are available on the the Rocky 9 system as well.

			Documentation on how to install conda environments on the cluster is available at https://wiki.gacrc.uga.edu/wiki/Installing_Applications_on_Sapelo2

	====Python packages====		====Python packages====

	Python libraries and virtual environments need to be reinstalled as well, using versions of Python~~, Miniconda, or Anaconda~~ available there.		Python libraries and virtual environments need to be reinstalled as well, using versions of Python available there.

	====R packages====		====R packages====
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	====Singularity containers====		====Singularity containers====

	Singularity containers that you used on ~~CentOS 7~~ should continue to work on the Rocky 8 system. The containers installed centrally in /apps/singularity-images will be available after the maintenance.		Singularity containers that you used on Rocky 8 should continue to work on the Rocky 9 system. The containers installed centrally in /apps/singularity-images will be available after the maintenance.


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	===Modules in your .bashrc no longer work or give errors on login===		===Modules in your .bashrc no longer work or give errors on login===

	If you have edited your .bashrc file to include commands to load modules automatically when you login, you may find that some ~~CentOS 7~~ modules will not be found or may not work on Rocky 8. You will need to edit your .bashrc and comment out or remove any such lines. You can also replace the module load commands in your .bashrc file with new module names. If you can no longer log in because of something in your .bashrc, contact us and we can rename your .bashrc and copy in a default version for you.		If you have edited your .bashrc file to include commands to load modules automatically when you login, you may find that some Rocky 8 modules will not be found or may not work on Rocky 9. You will need to edit your .bashrc and comment out or remove any such lines. You can also replace the module load commands in your .bashrc file with new module names. If you can no longer log in because of something in your .bashrc, contact us and we can rename your .bashrc and copy in a default version for you.

	If you’d like to start from scratch, a default .bashrc contains the following:		If you’d like to start from scratch, a default .bashrc contains the following:
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	===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 Rocky 8 system might not be available on Rocky 9. 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 in job submission script===		===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 Rocky 8, but no longer available on Rocky 9, 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 9 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===		===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:		Please note that the updated Sapelo2 does not have /usr/bin/python or /usr/bin/python2 installed. The OS comes with a default /usr/bin/python3 (v. 3.9.21). Scripts that have the first line:

	<pre class="gscript">		<pre class="gscript">
	#!/usr/bin/python		#!/usr/bin/python
			</pre>
			or
			<pre class="gscript">
			#!/usr/bin/python2
	</pre>		</pre>

	will not work on Sapelo2 (with the Rocky 8 OS). We recommend that you change this line to		will not work on Sapelo2 (with the Rocky 9 OS). We recommend that you change this line to

	<pre class="gscript">		<pre class="gscript">