garnatxa-hpclisted

Use whenever the user is working on, connecting to, submitting jobs to, troubleshooting, or asking about the Garnatxa HPC cluster at I2SysBio (UV/CSIC, Valencia). Covers SSH/VPN setup, SLURM submission and monitoring (sbatch, srun, sacct, squeue, scancel, sinfo, plotjob, squeue_/sacct_), choosing the right QoS, writing efficient job scripts (serial, threaded, MPI, array, dependencies), the Lmod module system, mamba/conda environments, Singularity containers, Nextflow and Snakemake pipelines on SLURM, /home + /storage + /scr filesystems, tape archive via merlot/tapecopy, the self-hosted GitLab + VSCode workflow, usage policies and quotas, and the required acknowledgment in publications. Trigger this skill for any mention of Garnatxa, garnatxa.srv.cpd, i2sysbio HPC, or when a user is clearly working on a CSIC/UV HPC at I2SysBio — even when the user does not name the cluster explicitly but is asking about job scripts, SLURM, tape, GitLab on garnatxagitlab.uv.es, or VPN config files like i2sysbi.ovpn.
TianYuan-Liu/garnatxa-hpc-skill · ★ 1 · AI & Automation · score 72

Install: claude install-skill TianYuan-Liu/garnatxa-hpc-skill

# Garnatxa HPC Cluster — I2SysBio (UV/CSIC) Garnatxa is a shared SLURM cluster at the Institute for Integrative Systems Biology (I2SysBio, joint UV/CSIC, Valencia). Use this skill to give the user concrete, copy-pasteable answers grounded in how Garnatxa is actually configured — not generic SLURM advice. ## Cluster facts at a glance - **Login host**: `garnatxa.srv.cpd` (SSH only). Prompt after login: `[USERNAME@master ~]$`. - **Scheduler**: SLURM. Module manager: Lmod. - **External access**: blocked. Connect from inside the UV network or via VPN (`i2sysbio.ovpn` with Garnatxa credentials, or `vpn_uv_es.ovpn` for UV staff). - **Tape access host**: `merlot` (you `ssh merlot` from the login node). - **Self-hosted GitLab**: <https://garnatxadoc.uv.es/gitlab> (LDAP tab, Garnatxa creds). - **Support / tickets**: <https://garnatxadoc.uv.es/support>; email `i2sysbiohpc@uv.es`. - **Compute**: 14 compute nodes (`cn00-cn13`), 1232 hardware threads, mixed 64/80/128-CPU generations, ~18 TB RAM, ~20.5 TFLOPS. **No GPUs** — Garnatxa is a CPU-only cluster. - **Storage**: CEPH (4.1 PB raw, ~3.5 PB usable); tape library is LTO-9 16 TB tapes (~720 TB online; `/tape2/<TAPE_CODE>/` is only readable by the owning group). ### Partitions and the QoS table — pick the right one or jobs sit forever | Partition | Use for | Time | Default mem | Notes | |-----------|---------|------|-------------|-------| | `interactive` | Interactive shells, light work | up to 1 d | 4 GB | Use `interactive`