Psc Bridges2

PSC Bridges-2 User Guide

Reference for running work on the Pittsburgh Supercomputing Center's Bridges-2 system. See partitions.md, job-scripts.md, filesystems.md, airlab-fast-setup.md (AirLab-specific workflow: Singularity, ROBO/H100, Rerun, <allocation-id>), docker-to-singularity.md (running Docker images on PSC via the bundled scripts/singularity_pull_docker_local.sh + scripts/start_sif.sh), and remote-workspace.md (pinned rsync bridge: .psc-config + scripts/sync_local_to_psc.sh / scripts/sync_psc_to_local.sh, with mandatory workspace safety checks).

Connecting

• SSH: ssh username@bridges2.psc.edu (port 22, HPN-SSH supported)
• Web: OnDemand portal for Jupyter, RStudio, file management
• Set/reset PSC password at apr.psc.edu (8+ chars, 3 of 4 char groups, annual change)
• Data transfers must use data.bridges2.psc.edu DTNs, not login nodes

Allocations and Accounting

• projects — list allocations, balances, IDs, Ocean usage
• my_quotas — check $HOME and $PROJECT quotas
• Specify allocation in SLURM: -A <allocation-id>
• newgrp <group> — temporary Unix group switch
• change_primary_group <account-id> — permanent default switch

Service Unit (SU) charging:

• RM / RM-shared / RM-512 / EM: 1 core-hour = 1 SU
• GPU V100 / L40S: 1 GPU-hour = 1 SU (8 SUs/node-hour)
• GPU H100: 1 GPU-hour = 2 SUs (16 SUs/node-hour)
• RM (full) always charges all 128 cores regardless of use
• ROBO allocation balance shown by projects is always negative (e.g. -168,249 / 0 SU) — this is normal and the allocation remains usable

Filesystems

Exceeding $PROJECT quota blocks job submission.

Path Discipline (REQUIRED)

Ask the user to indicate the workspace — an absolute Ocean path under /ocean/projects/<group>/<PSC-user>/... — before doing anything on PSC. Do not guess. If .psc-config exists locally, read PSC_WORKSPACE and confirm with the user.

Allowed paths:

• Login nodes: the pinned Ocean workspace only. Avoid ~ / $HOME whenever possible (only for things that belong there, e.g. SSH keys, dotfiles, module config).
• Compute nodes (interact / sbatch): the pinned Ocean workspace and $LOCAL. Nothing else.
• /tmp is never allowed, on any node. If a tool defaults there, redirect it (TMPDIR, APPTAINER_TMPDIR, cache flags).

If the workspace has not been specified yet, stop and ask — don't cd, mkdir, download, singularity pull, or sbatch first.

Modules

• module avail — list available
• module load <name> / module unload <name> / module list
• module spider <name> — search
• Typing bioinformatics lists bio software

Partitions (quick view)

See partitions.md for full specs.

Interactive Jobs

interact                                       # RM-shared default: 1 core, 60 min
interact -p RM-shared --ntasks-per-node=32 -t 5:00:00
interact -p GPU-shared --gres=gpu:v100-32:1 -t 2:00:00

Options: -p, -t, -N, --ntasks-per-node, --gres=gpu:<type>:<n>, -A.

Important constraints when using interact:

• Max wall time is 8 hours (-t 8:00:00), regardless of the partition's batch limit (RM/RM-shared 72h and GPU/GPU-shared 48h apply only to sbatch). Default is 60 min, and idle sessions are auto-logged-out after 30 min — always pass -t explicitly.
• EM partition does not allow interactive sessions — use sbatch for EM.
• Effectively one active interact session per user (observed: a second interact while one is already running will queue behind it; not explicitly documented in the PSC user guide). Before launching, check squeue -u $USER for an existing interactive job and reuse it (re-attach via the original terminal / tmux) instead of spawning another.
• Even for longer jobs, interact (up to 8h) is often the right tool — but if the work needs >8h or must survive disconnects, use sbatch.
• Wrap interact in tmux/screen on the login node so SSH drops don't kill the session.

Batch Jobs

sbatch -p RM -t 5:00:00 -N 1 script.job
squeue -u $USER
scancel <jobid>

Output: slurm-<jobid>.out. States: PD (pending), R (running), CA (cancelled), F (failed).

Interactive uses --gres=gpu:<type>:<n>; batch uses --gpus=<type>:<n> (multiple of 8 on GPU full-node).

See job-scripts.md for ready-to-adapt templates (RM, RM-shared, EM, GPU, GPU-shared, MPI, OpenMP).

Parallel Allocation / Partition Racing (reduce queue wait)

Queues on Bridges-2 vary dramatically by allocation and partition. A single -A <alloc> submission can sit in PD for hours while another allocation/partition would start in minutes. When wait time matters, submit the same job to multiple allocations or compatible partitions in parallel and cancel the losers once one starts.

When to use:

• You have access to 2+ allocations (check with projects), or the job can run on multiple partitions (e.g. GPU-shared vs ROBO for H100 work).
• A first submission has been PD for noticeably longer than the job's own runtime, or longer than ~15–30 min.
• The job is idempotent from a clean start (no side effects from duplicate starts before cancel).

How to do it:

1. Submit the same script to each viable (allocation, partition) pair. Tag each with a recognizable --job-name so you can find them:

   sbatch -A <alloc-A> -p GPU-shared --gres=gpu:h100-80:1 -J race_h100_A job.sh
   sbatch -A <alloc-B> -p GPU-shared --gres=gpu:h100-80:1 -J race_h100_B job.sh
   sbatch -A <alloc-B> -p ROBO     --gres=h100:1          -J race_h100_R job.sh
   

2. Poll: squeue -u $USER -n race_h100_A,race_h100_B,race_h100_R.
3. As soon as one enters state R, cancel the rest:

   RUNNING=$(squeue -u $USER -n race_h100_A,race_h100_B,race_h100_R -h -t R -o %i | head -1)
   squeue -u $USER -n race_h100_A,race_h100_B,race_h100_R -h -t PD -o %i | xargs -r scancel
   

4. Record which (allocation, partition) won so later jobs can start there directly.

Rules / cautions:

• Cancel PD duplicates the instant one starts running — otherwise multiple copies will run and burn SUs on every allocation.
• Be patient — do NOT cancel siblings just because waiting feels long. The cancel trigger is "another sibling entered state R," not "I've been waiting a few minutes." Racing only works if every sibling stays alive until exactly one starts; killing PD jobs early to "settle" on one defeats the purpose, since the one you kept may itself be the slowest. If no sibling has started yet, keep waiting.
• Prefer interact for small / short / exploratory tasks. A single interact -p RM-shared ... or interact -p GPU-shared --gres=gpu:<type>:<n> ... session is usually better than batch racing for debug work, quick checks, or anything under ~15–30 min — lower overhead, no duplicate-job SU risk, and the user can drive it directly. Reach for racing only when the job is long enough that queue wait actually dominates.
• Only race allocations that are actually valid for the work; don't submit to an EM allocation for a GPU job.
• Every job consumes SUs — be thoughtful and make sure the code and submission script are checked and good to run before launching.
• Don't race more than ~3–4 copies; beyond that the SU-loss risk from a missed cancel outweighs the queue savings.
• For very short jobs (< 15 min) skip racing; overhead of submit+cancel isn't worth it — use interact instead.

Compilers and MPI

MPI implementations: MVAPICH2, OpenMPI, Intel MPI. Load compiler module + MPI module, then use mpicc / mpicxx / mpifort.

Data Transfer (from your local machine)

# rsync (recommended: faster MAC)
rsync -rltDvp -oMACS=umac-64@openssh.com source/ user@data.bridges2.psc.edu:/ocean/projects/<group>/<PSC-user>/dest/

# scp
scp file user@data.bridges2.psc.edu:/ocean/projects/<group>/<PSC-user>/

# sftp
sftp user@data.bridges2.psc.edu

Globus: endpoint PSC Bridges-2 /ocean and /jet filesystems. Best for large/resumable transfers.

Pinned-workspace rsync (recommended for project code): use the bundled scripts/sync_local_to_psc.sh / scripts/sync_psc_to_local.sh. Both read .psc-config in the project root, which fixes the remote path ONCE (PSC_WORKSPACE=...); the loader rejects unsafe destinations ($HOME roots, allocation roots, other users' trees). Agents must NEVER construct a remote path by hand — use these scripts, never pass a remote arg, and fix .psc-config if a check fails. Full rules and exclude list in remote-workspace.md.

Software

• Anaconda-based AI/ML/Big Data environments curated by PSC
• Singularity/Apptainer containers supported; singularity exec --nv -B /ocean:/ocean <img.sif> <cmd>
• Pre-built NGC images at /ocean/containers/ngc
• Set APPTAINER_CACHEDIR / APPTAINER_TMPDIR under $PROJECT before pulling/building
• Docker → Singularity bridge: the skill ships two helper scripts at scripts/singularity_pull_docker_local.sh (pull a Docker image on an allocated node using $LOCAL scratch, then save the .sif to the working dir) and scripts/start_sif.sh (fuzzy-match a .sif by keyword and start/exec it with --nv + /local bind). Full usage in docker-to-singularity.md. For a bare Docker-on-PSC workflow, copy those two scripts to the cluster — nothing else is required.
• Install requests: help@psc.edu

For lab-standard container workflows, tmux-pinning to a login node, job arrays, and Rerun visualization, see airlab-fast-setup.md.

Common Mistakes

• Running transfers from login nodes — use data.bridges2.psc.edu.
• Submitting tiny jobs to RM — you pay for all 128 cores. Use RM-shared.
• EM with non-multiple-of-24 core counts — will reject.
• GPU batch with --gres=gpu:... — batch uses --gpus=<type>:<n>.
• Forgetting -A <allocation> when multiple allocations exist.
• Storing important files in $LOCAL/$RAMDISK — wiped at job end.
• Filling $PROJECT — blocks further submissions until under quota.

Support

• Email: help@psc.edu
• Phone: 412-268-4960

Useful Links

Official PSC Bridges-2

• User Guide: https://www.psc.edu/resources/bridges-2/user-guide/
• Getting Started with HPC: https://www.psc.edu/resources/bridges-2/getting-started-with-hpc/
• Introduction to Unix: https://www.psc.edu/resources/introduction-to-unix/
• Glossary: https://www.psc.edu/resources/glossary/
• Password utility (APR): https://apr.psc.edu
• OnDemand portal: https://ondemand.bridges2.psc.edu/pun/sys/dashboard
• Login host: bridges2.psc.edu
• Data transfer host: data.bridges2.psc.edu

Access / allocations

• ACCESS-CI identity: https://identity.access-ci.org
• ACCESS allocations: https://allocations.access-ci.org

Tooling

• SLURM docs: https://slurm.schedmd.com/documentation.html
• Apptainer (Singularity) docs: https://apptainer.org/docs/user/latest/
• Sylabs Cloud (remote builds): https://cloud.sylabs.io
• NVIDIA NGC catalog: https://catalog.ngc.nvidia.com
• Globus: https://www.globus.org — endpoint name "PSC Bridges-2 /ocean and /jet filesystems"
• Weights & Biases: https://wandb.ai
• Rerun docs: https://www.rerun.io/docs/getting-started/data-in/python

AirLab

• Cloud repo template: https://github.com/castacks/Cloud-Computing-Repository-Template
• Private container registry: airlab-storage.andrew.cmu.edu:5001
• Fast Setup doc (source): https://airlab.slite.page/p/-1w-EGD7QgqnQO/Fast-Setup-on-PSC

Source: JakoError/claude-research-skills — distributed by TomeVault.