compute-backend

name	compute-backend
description	Use when a workflow stage subagent has prepared computation scripts and needs to submit the job to a local or HPC backend via DPDispatcher

Compute Backend

Overview

Unified dispatch interface for superscientist workflow stages. All computations — local and remote — go through DPDispatcher.

Core principle: One code path. No branching between local bash wrappers and HPC submission. DPDispatcher handles everything.

NEVER run the computation command directly. This means no bash script.sh, no python run.py, no command < input, no subprocess, no shell exec — nothing that bypasses dpdisp submit. Local backends use batch_type: Shell, which still runs through DPDispatcher. There are zero exceptions to this rule, regardless of how simple, local, or fast the job appears.

REQUIRED CONTEXT: The orchestrator includes the backend profile in the subagent prompt under "Backend". Read it before using this skill.

Quick Reference

Operation	Command
Schema docs	uvx --with dpdispatcher dargs doc dpdispatcher.entrypoints.submit.submission_args
Validate	uvx --with dpdispatcher dargs check [--allow-ref] -f dpdispatcher.entrypoints.submit.submission_args stage-{id}/submission.json
Dry-run	uvx --from dpdispatcher dpdisp submit --dry-run [--allow-ref] stage-{id}/submission.json
Submit	uvx --from dpdispatcher dpdisp submit [--allow-ref] stage-{id}/submission.json

Decision	Sync	Async
Backend	Local	Remote (always)
Runtime	< 2 min	> 2 min or remote
Method	dpdisp submit directly	Wrapper script in tmux
tmux session	None	dpdisp_stage-{id}
Markers	None	DPDISP_DONE, DPDISP_EXIT_CODE

--allow-ref is REQUIRED on all dargs check and dpdisp submit commands when $ref is used in the machine block.

Workflow

Step 1: Resolve Backend Profile

Read the profile from the "Backend" section of the subagent prompt:

• Profile name (e.g., "local", "hpc-cluster")
• Type ("local" or "remote")
• Machine config (inline for local, config_path for remote)
• Resource defaults (merged with any stage-level resource_overrides)

Step 2: Acquire Schema (optional)

If using the templates below, skip this step. Otherwise, run:

uvx --with dpdispatcher dargs doc dpdispatcher.entrypoints.submit.submission_args

This defines valid fields, types, and defaults for submission.json.

Step 3: Build submission.json

Before building: Copy any dependency outputs from prior stages into stage-{id}/ so paths resolve correctly (see File Transfer Heuristics).

Write to {workflow_root}/stage-{id}/submission.json. The JSON is flat — no "submission": { ... } wrapper (causes dargs check to fail with "undefined key submission").

Working directory: The command runs in {local_root}/{work_base}/{task_work_path}, which for local jobs resolves to {workflow_root}/stage-{id}/.

Local backend template

{
  "work_base": ".",
  "machine": {
    "batch_type": "Shell",
    "context_type": "LocalContext",
    "local_root": "/absolute/path/to/workflow/root",
    "remote_root": "/absolute/path/to/workflow/root"
  },
  "resources": {
    "number_node": 1,
    "cpu_per_node": 1,
    "gpu_per_node": 0,
    "group_size": 1,
    "queue_name": ""
  },
  "task_list": [
    {
      "command": "<command from stage parameters>",
      "task_work_path": "stage-1",
      "forward_files": ["<input files for this stage>"],
      "backward_files": ["<expected output files>", "log", "err"]
    }
  ]
}

• task_list field names above are descriptive placeholders, not literal filenames. Replace with actual files from the stage spec. log and err are DPDispatcher standard outputs — always include them. Add software-specific log files to backward_files.
• local_root and remote_root: REQUIRED even for LocalContext (without them, dpdisp submit crashes with KeyError: 'remote_root'). Both are the workflow root absolute path. Resolve via $(pwd).
• resources: Start from the profile's resource_defaults. If none provided, use the values above as defaults. Apply any stage-level resource_overrides on top.

Remote backend template

{
  "work_base": ".",
  "machine": {
    "$ref": "/home/user/.dpdisp/hpc_config.json"
  },
  "resources": {
    "queue_name": "gpu",
    "number_node": 4,
    "cpu_per_node": 16,
    "gpu_per_node": 2,
    "group_size": 1,
    "custom_flags": ["#SBATCH --qos=4gpus", "#SBATCH --mem-per-gpu=10G"],
    "module_list": ["cuda/12.0", "openmpi/4.1"],
    "source_list": ["/path/to/env_setup.sh"],
    "prepend_script": ["bash stage-3/validate_env.sh || exit 1"]
  },
  "task_list": [
    {
      "command": "<command from stage parameters>",
      "task_work_path": "stage-3",
      "forward_files": ["<input files>", "<dependency outputs>", "validate_env.sh"],
      "backward_files": ["<expected output files>", "<restart/checkpoint files>", "log", "err"]
    }
  ]
}

• $ref is a plain file path — NOT a JSON Pointer ($ref:/path#/key is WRONG). NEVER read the referenced file (contains credentials).
• All dargs check and dpdisp submit commands MUST include --allow-ref when $ref is used.
• custom_flags: Extra scheduler-header lines inserted verbatim by DPDispatcher. Each entry MUST include the scheduler prefix (e.g., #SBATCH for Slurm). See Custom Flags Validation below.
• module_list: HPC modules loaded before the command runs.
• source_list: Shell scripts sourced before the command. Does NOT abort on failure — use for non-critical environment setup only.
• prepend_script: Shell lines executed before the task command at the submission root (NOT inside task_work_path). Use || exit 1 to abort on failure. Since forward_files are placed under task_work_path, reference them with the path prefix: bash stage-{id}/validate_env.sh, not bash validate_env.sh. See Pre-flight Validation below.
• validate_env.sh: Include in forward_files so it is uploaded to the remote under task_work_path.

envsubst (conditional)

If non-machine fields use ${VAR} placeholders (e.g., resource paths from env vars):

1. Write stage-{id}/submission.template.json with placeholders
2. Run: envsubst '${VAR1} ${VAR2}' < stage-{id}/submission.template.json > stage-{id}/submission.json
3. NEVER read submission.json after envsubst — it contains resolved secrets

Custom Flags Validation

DPDispatcher inserts custom_flags entries verbatim into the generated submission script. It does NOT auto-prepend the scheduler directive prefix. Entries without the correct prefix appear as bare shell lines and are silently ignored by the scheduler.

Before building submission.json, validate every custom_flags entry:

1. Look up batch_type from the backend profile:

   • Local: config.batch_type (inline in profile)
   • Remote: top-level batch_type field in the profile (set by workflow-planning)

2. Check the required prefix:

batch_type	Required prefix	Example
Slurm / SlurmJobArray	#SBATCH	"#SBATCH --qos=4gpus"
PBS / Torque	#PBS	"#PBS -l walltime=24:00:00"
LSF	#BSUB	"#BSUB -R rusage[mem=10000]"
SGE	#$	"#$ -l h_vmem=10G"
Shell	N/A	Warn if custom_flags is non-empty (local Shell has no scheduler)

3. If any entry lacks the correct prefix, stop and report to the orchestrator. Do not proceed to validation or submission.

Auto-generated directive reference (Slurm): These resources fields automatically generate Slurm directives. Do NOT duplicate them in custom_flags:

Resource field	Auto-generated directive (as of DPDispatcher v0.6+)
number_node	#SBATCH --nodes N
cpu_per_node	#SBATCH --ntasks-per-node N
gpu_per_node	#SBATCH --gres=gpu:N
queue_name	#SBATCH --partition NAME

This mapping is internal to DPDispatcher and may change across versions. It is a reference for human awareness, not automated validation.

Pre-flight Validation (remote backends)

For remote backend stages, generate a stage-specific validation script based on the stage's parameters (software, required packages, flags). This catches environment mismatches before the actual computation runs, inside the same Slurm allocation — zero extra jobs.

How it works:

1. Write a validation script to stage-{id}/validate_env.sh based on the stage's software and flags:

#!/bin/bash
# validate_env.sh — uploaded as forward_file, executed via prepend_script
# Checks generated from stage parameters — adapt per software

# Check binary exists (required for every stage)
command -v <binary> >/dev/null 2>&1 || { echo "FAIL: <binary> not found in PATH"; exit 1; }

# Check software-specific requirements (examples — adapt per tool):
#   lmp -h 2>&1 | grep -q "GPU"                                    # LAMMPS GPU package
#   python -c "import torch; assert torch.cuda.is_available()"      # PyTorch GPU
#   simpleFoam -help 2>&1 | head -1                                 # OpenFOAM binary
#   gmx --version 2>&1 | grep -q "GROMACS"                          # GROMACS availability

echo "ENV_VALIDATION_PASSED"

2. Add validate_env.sh to forward_files so DPDispatcher uploads it to the remote.
3. Add "bash stage-{id}/validate_env.sh || exit 1" to the prepend_script array in resources. The stage-{id} prefix is required because prepend_script runs at the submission root, while forward_files are placed under task_work_path.

Why prepend_script and not source_list: DPDispatcher renders source_list entries as bare source {file} lines with no error checking. A failing source does not abort execution. prepend_script lines run as shell commands with explicit || exit 1, which aborts the job immediately on failure.

When to generate: For every remote backend stage. The validation checks are derived from:

• parameters.software → check binary exists in PATH
• Command flags that depend on optional features → check those features are available
• [UNVERIFIED] annotations in the experiment design → mandatory validation

When to skip: Local backend stages (batch_type: Shell) do not need pre-flight validation — init.sh already validates the local environment.

Step 4: Validate & Dry-Run

Run both in sequence. If either fails, stop and report to the orchestrator.

# Schema validation
uvx --with dpdispatcher dargs check [--allow-ref] \
  -f dpdispatcher.entrypoints.submit.submission_args \
  stage-{id}/submission.json

# Dry-run: parses config, validates paths — does NOT submit
uvx --from dpdispatcher dpdisp submit --dry-run [--allow-ref] \
  stage-{id}/submission.json

The dry-run catches path resolution issues that schema validation misses (e.g., invalid $ref targets).

Step 5: Dispatch

Sync path (local backend AND expected runtime < 2 min):

uvx --from dpdispatcher dpdisp submit [--allow-ref] stage-{id}/submission.json

Report results inline: exit code, output files, any warnings from logs.

Async path (remote backend always, OR local > 2 min):

Use these EXACT names — the orchestrator's poll protocol depends on them:

1. Write stage-{id}/dpdisp-run.sh:

   #!/bin/bash
   cd "$(dirname "$0")/.."
   uvx --from dpdispatcher dpdisp submit [--allow-ref] stage-{id}/submission.json
   echo $? > stage-{id}/DPDISP_EXIT_CODE
   touch stage-{id}/DPDISP_DONE
   

2. Launch in tmux as dpdisp_stage-{id}:

   tmux kill-session -t dpdisp_stage-{id} 2>/dev/null
   tmux new-session -d -s dpdisp_stage-{id} "bash stage-{id}/dpdisp-run.sh"
   

3. Verify: tmux has-session -t dpdisp_stage-{id} 2>/dev/null && echo "Running" || echo "FAIL"

4. Report to orchestrator: tmux session name, submission.json path.

File Transfer Heuristics

All paths in forward_files and backward_files are relative to task_work_path (i.e., relative to stage-{id}/).

forward_files — everything the job reads:

• Scripts/configs prepared for this stage (e.g., input scripts, data files)
• Dependency outputs from prior stages — copy into stage-{id}/ first, then list the copied filename:

  cp ../stage-2/output.data stage-{id}/input.data
  

• Auxiliary files referenced in scripts (parameter files, configuration files, data tables)

backward_files — everything that needs to come back:

• All expected output files from the stage spec's outputs
• Always include: log, err (DPDispatcher standard output)
• Restart/checkpoint files the computation produces

Important Notes

• DPDISP_EXIT_CODE reflects DPDispatcher's exit code, NOT scientific correctness. The orchestrator always proceeds to result-verification regardless.
• DPDispatcher polls internally every 30 s in blocking mode. The tmux session keeps this alive across session boundaries.
• Recovery: If tmux dies without DPDISP_DONE, re-launch dpdisp-run.sh in a new tmux session. DPDispatcher's idempotent recovery resumes monitoring without re-submitting.

Diagnostic Reproduction Run

When an HPC stage fails and DPDispatcher aborts the backward_files download (because a required output file doesn't exist on the remote), the orchestrator may dispatch a diagnostic reproduction run to obtain error logs.

Key constraint: This is a NEW job execution, not a file transfer. DPDispatcher creates a content-hashed remote directory per submission — it cannot access files from a previous job's directory. The reproduction run re-executes the command. This means:

• It consumes an HPC allocation
• It only works if the failure reproduces (configuration errors like missing packages, wrong flags, resource mismatches always reproduce)
• For intermittent failures, dpdispatcher.log (Level 1 diagnostics) may be the only option

When the orchestrator prompt says "This is a diagnostic run":

1. Write stage-{id}/submission.diagnostic.json — NOT submission.json. The original submission.json is preserved for the real fix retry.
2. Use the same command and forward_files as the original submission.json.
3. Set backward_files to ["log", "err"] only — no output files that might be missing.
4. Validate and submit submission.diagnostic.json using the same steps (dargs check → dry-run → submit).
5. For the wrapper script, reference the diagnostic file:

   uvx --from dpdispatcher dpdisp submit [--allow-ref] stage-{id}/submission.diagnostic.json
   

6. After the diagnostic run completes, leave submission.diagnostic.json in place for debugging reference.

Retry Modes

When retry_count > 0, the orchestrator prompt specifies one of two modes:

Reuse mode (default for retries after script-level fixes):

1. Check that stage-{id}/submission.json exists.
2. Validate and dry-run it (the fix was to the input script, not the submission configuration).
3. Submit the existing submission.json as-is.
4. Do NOT regenerate submission.json from scratch.

Regenerate mode (when the fix changes submission parameters):

1. Rebuild submission.json from the stage's updated parameters and resource_overrides.
2. Validate and dry-run.
3. Submit the new submission.json.

The orchestrator chooses the mode based on the nature of the fix:

• Input script fix (e.g., corrected a flag in the computation command) → reuse
• Submission parameter fix (e.g., change gpu_per_node, add custom_flags) → regenerate

Security Guardrails

• NEVER read external $ref config files — they contain credentials
• NEVER read submission.json after envsubst — it contains resolved secrets
• NEVER use direct SSH — all remote operations through DPDispatcher only
• NEVER run the computation command directly — not even for local, not even once to "test" it

Red Flags

Thought	Reality
"I'll SSH to check the job"	All remote operations go through DPDispatcher. No direct SSH.
"Let me read the machine config to verify it"	NEVER read $ref config files. They contain credentials.
"I'll skip the dry-run, validation passed"	Dry-run catches path issues validation misses. Always run both.
"This local job is fast, skip tmux"	Only skip tmux for local backend AND < 2 min expected runtime.
"I'll set forward_files later"	Build the complete file list now. Missing files = failed job on remote.
"I'll call bash validate_env.sh from prepend_script"	prepend_script runs at the submission root, not task_work_path. Use bash stage-{id}/validate_env.sh with the full path prefix.
"Let me read submission.json to verify envsubst worked"	NEVER read after envsubst. It contains resolved secrets.
"I'll write my own wrapper script"	Use the EXACT template. The orchestrator depends on dpdisp-run.sh, DPDISP_DONE, DPDISP_EXIT_CODE, and dpdisp_stage-{id} naming.
"The key is task not task_list"	It is task_list (array).
"I'll wrap it in {submission: {...}}"	No wrapper. Flat JSON. dargs check rejects a submission key.
"It's just a local job, I'll run the command directly"	NEVER. Local backends use batch_type: Shell — still submitted via dpdisp submit.
"DPDispatcher is slow/complex for this simple script"	Complexity is irrelevant. Every job goes through dpdisp submit. No exceptions.
"I'll run it directly first to test, then use DPDispatcher for real"	NEVER run directly. Validate with dargs check and --dry-run. That is sufficient.
"I'll just bash the run script I wrote"	Only valid script to run is dpdisp-run.sh inside tmux. Never bash the simulation script directly.
"The submission.json is ready, but dpdisp seems broken — I'll just run the command"	Stop and debug DPDispatcher. Do not bypass it. Report the failure to the orchestrator.
"I'll overwrite submission.json for the diagnostic run"	Write submission.diagnostic.json. The original is needed for the fix retry.
"Let me regenerate submission.json for the retry"	Check the orchestrator prompt: reuse or regenerate? Reuse is the default.
"custom_flags don't need #SBATCH"	DPDispatcher inserts them verbatim. Missing prefix = silently ignored by scheduler.