Software Update Information

Software update frequency

• For shared nodes.
  • Twice a year, the software is updated. (around June each year and during scheduled maintenance following legal power outages around December each year.)
• For occupied nodes.
  • Once a year only during routine maintenance (around December), the software is updated.

Software update details

• During scheduled maintenance, an overall upgrade is performed by apt upgrade of Ubuntu Linux and software updates outside the control of apt are performed.
• Around June each year, software updates are performed only for software such as CUDA.

info

If it is a problem that the analysis results change due to software updates, please consider the following options.

• Use Biocontaier's Apptainer container.
• Use Conda, spack, etc. to install the analysis software by yourself and manage the version.

info

You can check the list of software installed with apt using apt list --installed.

Update history

The following table describes the update dates and versions of software installed except for apt.

1. CUDA

Directory path: /usr/local/cuda*

Update Date	Version (The General Analysis Division)	Version (The Personal Genome Analysis Division)	Currently Available Versions	notes
17/12/2024	12.6.3	12.6.3	〇
08/10/2024	12.4	12.4	〇
30/11/2023	12.1	12.1	〇	Downgraded at scheduled maintenance in 2023. *Downgrade from 12.2 as the supported version of the Ubuntu Linux 22.04 LTS GA kernel is 12.1.
06/09/2023	CUDA Version: 12.2 NVIDIA-SMI 535.54.03 Driver Version: 535.54.03 (GPU queues)	CUDA Version: 12.2 NVIDIA-SMI 535.54.03 Driver Version: 535.54.03 (Slurm GPU partitions)	×	Updated from CUDA Version: 11.6 NVIDIA-SMI 510.47.03 Driver Version: 510.47.03. GPU login nodes are currently being updated (2023.09.06).

2. Apptainer

Directory path: /opt/pkg/apptainer

Update Date	Version (The General Analysis Division)	Version (The Personal Genome Analysis Division)	Currently Available Versions	notes
18/12/2024	1.3.5	1.3.5	〇
02/07/2024	1.3.2	1.3.2	〇
30/11/2023	1.2.4	1.2.4	〇	Updated from 1.1

3. SingularityCE

Directory path: /opt/pkg/singularity-ce

Update Date	Version (The General Analysis Division)	Version (The Personal Genome Analysis Division)	Currently Available Versions	notes
18/12/2024	4.2.1	4.2.1	〇
02/07/2024	4.1.3	4.1.3	〇
30/11/2023	4.0.0	4.0.0	〇	Updated from 3.10.2.

4. NVIDIA HPC SDK (旧 PGI コンパイラ)

Directory path: /opt/pkg/nvidia/hpc_sdk/Linux_x86_64

Update Date	Version (The General Analysis Division)	Version (The Personal Genome Analysis Division)	Currently Available Versions	notes
Scheduled for 16-17/12/2024	24.11	24.11	〇
02/07/2024	24.3	24.3	〇
30/11/2023	23.7	23.7	〇	Updated from 22.9

5. Intel OneAPI

Directory path: /opt/pkg/intel_2024/intel_ubuntu_2024/oneapi

Update Date	Version (The General Analysis Division)	Version (The Personal Genome Analysis Division)	Currently Available Versions	notes
18/12/2024	2025.0.0	2025.0.0	〇
02/07/2024	2024.1.0	2024.1.0	〇
30/11/2023	2023.2.0	2023.2.0	×	Updated from 2022.2.0

6. Altair Grid Engine

Directory path: /home/geadmin/AGER

Update Date	Version (The General Analysis Division)	Version (The Personal Genome Analysis Division)	Currently Available Versions	notes
30/11/2023	2023.1.1	2023.1.1	〇	Updated from 8.6.19/8.6.4

7. Slurm server

Update Date	Version (The General Analysis Division)	Version (The Personal Genome Analysis Division)	Currently Available Versions	notes
30/11/2023	21.08	21.08	〇	Updated from 21.08.8

8. Archaea tools　(formerly HCPtools) server

Update Date	Version (The General Analysis Division)	Version (The Personal Genome Analysis Division)	Currently Available Versions	notes
22/07/2024	1.5.5_28	1.5.5_28	〇	Updated from 1.4.6-2

9. Archaea tools　(formerly HCPtools) client

It will be installed in the future.

10. NVIDIA Clara Parabricks

Directory path: /opt/pkg/nvidia/parabricks

Update Date	Version (The General Analysis Division)	Version (The Personal Genome Analysis Division)	Currently Available Versions	notes
Scheduled for 16-17/12/2024	4.4.0	4.4.0	〇
02/07/2024	4.3.1	4.3.1	〇
07/08/2023	4.1	4.1	〇

11. Aspera server

Update Date	Version (The General Analysis Division)	Version (The Personal Genome Analysis Division)	Currently Available Versions	notes
01/03/2017	4.1.0	unavailable	〇

12. Aspera client

It will be installed in the future.

13. AMD Optimizing C/C++ and Fortran Compilers (AOCC)

Directory path: /opt/pkg/aocc

Update Date	Version (The General Analysis Division)	Version (The Personal Genome Analysis Division)	Currently Available Versions	notes
Scheduled for 18/12/2024	5.0	5.0	〇
02/07/2024	4.2.0	4.2.0	〇	newly introduced

14. Apache Guacamole

Update Date	Version (The General Analysis Division)	Version (The Personal Genome Analysis Division)	Currently Available Versions	notes
14/05/2021	unavailable	1.4.0	〇