The NIG Supercomputer
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 upgradeof Ubuntu Linux and software updates outside the control ofaptare 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 interactive 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 |