Changelog¶
All notable changes to Orfeo infrastructure will be documented here
2025-04-24¶
Changed¶
- Moved all computational nodes without accelerator from F40 to F41, the following core package were affected:
| module | previous version | new version |
|---|---|---|
| Python | 3.12 | 3.13 |
| Linux kernel | <=6.12 | 6.13 |
| Glibc | 2.39 | 2.40 |
-
Cluster wide slurm update from 24.05 to 24.11. The number of changes featurewise is considerable; please consider visiting the official news file for more details. For more details on the server deployment visit this link
-
Modules update, among the most relevant:
| module | old version | new version | comments |
|---|---|---|---|
| openmpi | 4.1.6 | 5.0.5 | |
| openblas | 0.3.26 | 0.3.29 | |
| cuda | 12.6 | 12.8 | |
| cutapt | 4.2 | 5.0 | |
| R | 4.3.3 | 4.5.0 | |
| hwloc | 2.10.0 | 2.12.0 | |
| picard | 3.2.0 | 3.4.0 | |
| foldseek | 9-427df8a | 10-941cd33 | |
| singularity | 3.11.5 | 4.3.1 | |
| trim_galore | 0.6.10 | ||
| bcftools | 1.17 | 1.21 | |
| bcl2fastq2 | 2.20.0 | ||
| bedtools2 | 2.31.1 | ||
| bwa-mem2 | 2.2.1 | ||
| igv | 2.16.2 | 2.18.0 | |
| samtools | 1.17 | 1.21 | |
| sambamba | 1.0 | 1.0.1 | |
| fastp | 0.23.4 | 0.24.1 | |
| fastqc | 0.12.1 | ||
| foldseek | 8-ef4e960 | 10-941cd33 | |
| gromacs | 2022.6 | 2025.1 | |
| guppy-cpu | 6.2.1 | 6.5.7 | |
| guppy-gpu | 6.2.1 | 6.5.7 | |
| plink | 1.90 | ||
| star | 2.7.9a | 2.7.11b |
If you are interested in a particular module and how it was compiled please visit the following link. We will open source repositories as they reach a stable state.
- GPU nodes are equipped with the following CUDA drivers:
| Card | CUDA driver |
|---|---|
| H100 | 12.7 |
| A100 | 12.2 (as per DGX OS) |
| V100 | >= 12.3 |
We expect the CUDA runtime 12.2 to work everywhere on the cluster, but compatibility with other runtimes may vary.
Tested¶
- Slurm/MPI essential feature performances, results are in line with previous measurements
- IO performances, results are in line with previous measurements
User Impact
- Codes compiled by you that rely on older versions of libraries will need to be recompiled (this might include some R modules)
- Python virtual environment that relies on the OS python version will need to be recompiled
- Some older codes may stop working due to their deprecated dependency. Please use newer versions whenever possible or transition to a containerized approach
2025-04-17¶
Changed¶
- Service Migration:
- HOME storage migrated from HDD to SSD
- FAST storage migrated from SSD to NVMe
User Impact
- Reduced storage latency and increased throughput
2025-04-15¶
Added¶
- Ceph Metadata Server (MDS) Update:
- Dedicated node for Ceph Metadata Server (MDS)
- Increased RAM allocation for MDS to cache more metadata
User Impact
- Faster metadata operations
- More reliable file system access during heavy usage
- Resolved bug where commands like
findorlswould hang in certain directories
2025-01-20¶
Added¶
- DGX H100 Production Deployment:
- 8 NVIDIA H100 GPUs per node (Hopper architecture)
- Internal NVLink and InfiniBand connectivity to the cluster
- Up to 32 PFLOPS FP8 performance per node
User Impact
- Enhanced throughput for large-scale model workloads
2025-01-10¶
Added¶
“Genoa” Servers Production Deployment:
- AMD EPYC 9654 “Genoa” CPUs with 96 cores each
- 768 GB of high-speed DDR5 RAM per node