T3 rmg zeus submit script#7
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Pull request overview
This PR adds Zeus-specific local T3 configuration files (submit script + settings) intended to be placed under ~/.t3/ for running RMG via PBS on the Zeus cluster, and it updates the Zeus .bashrc to avoid user-specific manual edits.
Changes:
- Add
Servers/Zeus/.t3/t3_submit.pydefining a PBS submit template for T3’srmgjobs. - Add
Servers/Zeus/.t3/t3_settings.pyoverriding T3 runtime/server settings for Zeus. - Update
Servers/Zeus/.bashrcto use$USERfor thestalias instead of a placeholder.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| Servers/Zeus/.t3/t3_submit.py | Adds a Zeus PBS submit-script template used by T3 when submitting RMG jobs. |
| Servers/Zeus/.t3/t3_settings.py | Adds Zeus-specific T3 settings overrides (execution mode, server resources, PBS commands). |
| Servers/Zeus/.bashrc | Removes the manual username placeholder by switching st to qstat -u $USER. |
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| touch initial_time | ||
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| python-jl $rmgpy_path/rmg.py -n {cpus} input.py{max_iterations} |
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| 'local': { # Each Zeus node has 80 cores and 378 GB RAM | ||
| 'cluster_soft': 'PBS', | ||
| 'cpus': 16, | ||
| 'max mem': 40, # GB | ||
| }, |
Adds Servers/Zeus/.t3/ — the T3 counterpart of the existing .arc config — so T3 runs on Zeus without hand-edited settings: - t3_settings.py: PBS server + Zeus /opt/pbs/bin command paths (matching the ARC Zeus config); RMG submitted to the queue, ARC run in-process. Keys/values match what T3 actually reads (execution_type incore|local, servers 'max mem', check_status/submit/submit_filenames). - t3_submit.py: PBS RMG submit template using $rmgpy_path, pinned to node n170 on alon_q like Servers/Zeus/ARC/submit.sh; filled by T3 via name/cpus/memory/workdir/max_iterations (max_iterations placed as its own token so spacing is safe). Files are named t3_settings.py / t3_submit.py, the names T3 loads from ~/.t3 (t3.imports); the earlier draft's settings.py would never load. Drops python-jl (no longer used): the RMG submit template, the RMG/submit.sh script, and the rmg/arkane .bashrc aliases now call plain python. RMG/submit.sh also now uses $rmgpy_path (the exported var) instead of the undefined $rmg_code. .bashrc: `st` alias uses `$USER` instead of a hand-edited <user>. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Adds the t3_submit and the settings file for .t3 folder. Also updates .bashrc so that no manual editing is required.