Interactive Sessions with sinteractive¶

sinteractive gives you a shell on a compute node that survives an SSH disconnect. It submits a batch job that starts a terminal multiplexer on the allocated node and connects you to it; when your laptop sleeps or the VPN drops, the job keeps running and you reattach where you left off.

It is maintained at rnabioco/sinteractive, with the full reference — every command, every environment variable, the Claude Code integration — at https://rnabioco.github.io/sinteractive/. This page covers what a Bodhi user needs.

Why not just srun --pty bash?¶

Use srun --pty bash for a quick throwaway command. Use sinteractive for anything you would be annoyed to lose.

Installation¶

Check what you have, and whether it can actually start a session:

sinteractive --version
sinteractive doctor      # is this install able to run a session from here?

doctor is the answer to "why did that not work" — it checks the binary, the cache directory, the Slurm commands and whether the compute nodes can see the binary. If it reports a problem, or sinteractive is missing or old, install your own copy from the releases page (built for Rocky 8 / glibc 2.28, x86_64):

mkdir -p ~/.local/bin
mv sinteractive-x86_64-linux-gnu-glibc2.28 ~/.local/bin/sinteractive
chmod +x ~/.local/bin/sinteractive
sinteractive doctor

Make sure ~/.local/bin is on your $PATH (add export PATH="$HOME/.local/bin:$PATH" to ~/.bashrc if it is not).

Launching a session¶

sinteractive

That is a 1-day session on the interactive partition with 2 CPUs and 8 GB. Override any of it:

Anything else is passed straight through to sbatch, in any order — so --gres=gpu:1, --qos=long, --account=... all work.

# Named, 8 hours, 4 CPUs, 16 GB
sinteractive -n rna-seq -t 8h -j 4 -m 16G

# A GPU session
sinteractive -p gpu --gres=gpu:1 -m 16G

# Launch it now, come back to it later
sinteractive --detach -n build
sinteractive attach build

Bodhi's interactive partition¶

Because the partition imposes no QoS, a session here runs under the default normal QoS and is bounded by the partition's own MaxTime. The interactive QoS — 12 hours, 16 CPUs, 8 GB — applies only if you ask for it with --qos=interactive.

The partition is small and it carries everyone's shells, so treat a session as a place to orchestrate work, not to run it. Heavy jobs belong in their own allocation on a compute partition:

srun -p rna -c 16 --mem 64G -t 4:00:00 -J bwa-align --comment=bwa-align -- ./run.sh

Managing sessions¶

sinteractive list
sinteractive attach rna-seq

Inside a session¶

Ctrl+b is the only chord: press it, then one key. Ctrl+b h shows this legend in the status bar.

The status bar reads like this:

● sint 261172 · bodhi · compute07 · 22h left · jobs 3R · ^b h help

The dot spins while the session starts, then turns yellow and red as the walltime runs down. jobs counts your running and pending jobs, and a ⚠ N notices counter appears when the session has something to tell you — red while you are over your storage quota.

Mouse mode is on: scroll with the wheel, click to focus a pane, drag borders to resize, and select text to copy it to your local clipboard. Hold Shift to select with the terminal instead.

Ending a session¶

Exiting the last shell (exit or Ctrl+d) ends the job. From the login node, sinteractive cancel NAME|JOBID — or scancel JOBID — does the same.

Personal defaults¶

Set these in ~/.bashrc; explicit flags always win.

export SINTERACTIVE_MEM=16G
export SINTERACTIVE_CPUS=4

The full list covers the cache directory, warning thresholds, quota daemons and the Claude Code hooks.

Scripting and coding agents¶

Every reporting command takes --json, and a session can be driven from outside it — which is how a coding agent such as Claude Code works on the cluster without running anything on the login node:

# Reuse the session named 'agent', or launch it if it isn't there
sinteractive session ensure agent

# Read the last 40 lines of its screen
sinteractive session peek agent -n 40

# Type a command into it
sinteractive session send agent 'make test'

# Machine-readable state
sinteractive list --json
sinteractive status agent --json

To run a command in a session's allocation and get its exit code back:

srun --overlap --jobid=JOBID -- bash -lc 'make test'