Make queue-executed ASE (UMA/fairchem) jobs runnable on a cluster

[alongd]

What

Make queue-executed ASEAdapter jobs actually run on a remote cluster. The ASE adapter had only ever been exercised incore; its queue path was latent and broke on the first real submission. This lets ASE-backed calculators (e.g. UMA / fairchem MLIPs) run hindered-rotor and other scans as ordinary PBS/Slurm jobs.

Why

Running a real ARC job that delegates its hindered-rotor scans to an ASE calculator on a cluster queue crashed the moment the first scan job was dispatched:

arc.exceptions.InputError: Cannot upload a non-existing file.
Check why file in path .../directed_scan_a2781/submit.sh is missing.

Two independent defects in the queue path, both masked because ASE had only ever run incore:

1. Files were never written. JobAdapter.execute() calls upload_files() before execute_queue(), and _initialize_adapter() calls set_files() while the job is constructed. The Gaussian/Orca/xTB adapters write submit.sh / input inside set_files(); ASEAdapter.set_files() only appended their names to files_to_upload and never wrote them, so the calcs dir was empty when ssh.upload_file() ran its os.path.isfile pre-flight.
2. Submission was dead code. ASEAdapter.execute_queue() guarded on self.server_adapter, an attribute nothing in ARC sets (hasattr → False), so even with the files present the job would never submit — the write fix alone just moves the crash one line down to an AttributeError.

Changes (confined to the ASE adapter)

• set_files() now writes submit.sh and input.yml for non-incore jobs, mirroring the other adapters. Incore is unchanged — it still writes its input in execute_incore().
• execute_queue() now delegates to the shared legacy_queue_execution() that every other adapter uses (which also records job_status / job_id), replacing the bespoke never-reached block.
• write_submit_script()'s non-queue branch falls back to local_path when remote_path is None (a server-less job), fixing a latent crash surfaced by writing at construction time.
• Adds test_set_files_writes_the_files_of_a_queue_job (red against the pre-fix adapter).

Verification

• New/updated unit tests: pytest arc/job/adapters/ase_test.py -q -n0 → 10 passed (the file requires serial -n0, a pre-existing xdist setUpClass race unrelated to this change).
• Incore path unregressed: full execute() → execute_incore() → ase_script.py → parse_results() reproduces the prior geometry/energy to 5 decimals.
• Live cluster run: an ARC job (DFT opt/freq/sp on the queue, hindered-rotor scans via a UMA/ASE calculator) now runs end-to-end — the DFT stage completes and the rotor jobs are written with their submit.sh + input.yml and submitted to the queue, where the pre-fix run crashed.

The diff is limited to arc/job/adapters/ase_adapter.py, arc/job/adapters/ase_test.py, and a 1-indexed→0-indexed constraint fix in arc/job/adapters/scripts/ase_script.py (ASE FixInternals is 0-indexed; ARC constraints are 1-indexed). No other adapter's submit path is touched.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 64.54%. Comparing base (db9136e) to head (6e97a32).
⚠️ Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #985      +/-   ##
==========================================
- Coverage   64.56%   64.54%   -0.03%     
==========================================
  Files         119      119              
  Lines       39706    39751      +45     
  Branches    10289    10294       +5     
==========================================
+ Hits        25638    25657      +19     
- Misses      11085    11107      +22     
- Partials     2983     2987       +4     

Flag	Coverage Δ
functionaltests	64.54% <ø> (-0.03%)	⬇️
unittests	64.54% <ø> (-0.03%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Copilot]

Pull request overview

This PR fixes the previously-latent “queue execution” path for ASEAdapter so ASE-backed calculators (e.g., UMA/fairchem MLIPs) can run as real cluster jobs, including rotor/directed-scan workloads that ARC dispatches via the scheduler.

Changes:

• Write submit + input.yml during adapter construction for non-incore ASE jobs so upload_files() succeeds.
• Replace ASE’s bespoke queue submission logic with the shared legacy_queue_execution() flow.
• Correct ASE internal constraint indexing by translating ARC’s 1-indexed constraints to ASE FixInternals’ 0-indexed expectations.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
arc/job/adapters/ase_adapter.py	Writes queue job files in set_files(), adds directed-scan constraints translation, and delegates queue submission to legacy_queue_execution().
arc/job/adapters/ase_test.py	Adds unit coverage asserting queue-job construction writes/uploadables exist on disk (and that incore does not).
arc/job/adapters/scripts/ase_script.py	Converts constraint atom indices from ARC’s 1-indexing to ASE’s 0-indexing before applying FixInternals.

Suppressed comments (1)

arc/job/adapters/ase_adapter.py:415

• This method always writes the submit script to submit.sh. On Slurm, ARC submits submit.sl (see settings['submit_filenames']), so Slurm jobs will still error unless the script is written under the Slurm filename.

        with open(os.path.join(self.local_path, 'submit.sh'), 'w') as f:
            f.write(content)

---

💡 Add a code-review agent skill or configure MCP servers for context-aware, tailored reviews. Learn more in the docs.

[alongd]

Added a third commit (dc23057): fix a stale directed-scan parser call site — check_directed_scan_job called parser.parse_e_elect(path=...) but the refactored API is log_file_path= (as every other call site uses). Without it, ARC crashes assembling V(φ) the moment a directed-scan job's energy is parsed. Verified by parsing a real UMA rotor output (−500058.16 kJ/mol). This is needed for ASE/UMA rotor scans to run end-to-end.

[Copilot]

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

Suppressed comments (6)

arc/job/adapters/ase_adapter.py:284

• Slurm jobs will still fail at submission: write_submit_script() writes submit.sh, and this entry uploads/registers that same name, but legacy_queue_execution() invokes the shared submit_filenames['Slurm'] (submit.sl; see arc/settings/settings.py:173-176). Thus sbatch submit.sl cannot find the file. Use the shared scheduler-specific filename consistently when writing and registering the script.

            self.files_to_upload.append(self.get_file_property_dictionary(file_name='submit.sh'))

arc/job/adapters/ase_adapter.py:354

• max_job_time is not propagated into these templates: format_kwargs has no t_max, and the PBS/Slurm templates have no walltime directive. Unlike the shared JobAdapter.write_submit_script() path (arc/job/adapter.py:287-315), an ASE queue job will use the scheduler default limit and can be killed before ARC's requested time. Add the scheduler-specific walltime directive and pass the formatted value.

        format_kwargs = {'name': self.job_server_name, 'cpus': self.cpu_cores, 'memory': memory,
                         'remote_path': self.remote_path, 'env_setup': config['env_setup'], 'command': command}

arc/job/adapters/ase_adapter.py:376

• queue_job is false for every non-incore scheduler other than PBS/Slurm, so OGE/HTCondor (and a no-queue local server) take the bare-script branch but are still submitted through legacy_queue_execution(). HTCondor then looks for submit.sub, while only submit.sh was written; other schedulers also lack their directives. Raise for unsupported schedulers or add templates instead of silently submitting an invalid script.

        queue_job = self.execution_type != 'incore' and cluster_soft in ('pbs', 'slurm')

arc/job/adapters/scripts/ase_script.py:127

• The new index conversion is not covered by the ASE tests: there is no test for apply_constraints() or for determine_constraints() generating a directed-scan constraint. A regression here would silently apply a constraint to the wrong atoms, so add a test that writes a 1-indexed four-atom dihedral constraint and verifies the FixInternals indices are 0-indexed.

        indices = [index - 1 for index in constraint[0]]

arc/settings/submit.py:128

• The PR description says the diff is confined to three ASE adapter files, but this change also adds arc/settings/submit.py and modifies arc/imports.py. Please update the description or explain these additional shared submission/configuration changes, since they materially expand the review scope.

# Submission scripts for queue-executed ASE (e.g. UMA/fairchem MLIP) jobs, keyed by cluster

arc/settings/submit.py:146

• ARC invokes sbatch after changing into the submission directory, but this script changes into remote_path as if the batch job starts at the remote home. When the server has no path, remote_path is relative, so this can resolve to a nested runs/.../runs/... directory; for a local queue it also points away from local_path. Use the scheduler's submission directory for the job directory instead.

cd "{remote_path}"
JOB_DIR="$(pwd)"  # absolute path (the path above is relative to the remote home, where the job starts)