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https://github.com/patonlab/paton_group_workflows
Python Code, shell scripts, templates, submission scripts and compchem specific workflows for use in the Paton Lab
https://github.com/patonlab/paton_group_workflows
bash monitoring python slurm submission
Last synced: about 2 months ago
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Python Code, shell scripts, templates, submission scripts and compchem specific workflows for use in the Paton Lab
- Host: GitHub
- URL: https://github.com/patonlab/paton_group_workflows
- Owner: patonlab
- Created: 2021-02-10T18:08:06.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2023-06-05T15:41:42.000Z (over 1 year ago)
- Last Synced: 2023-08-21T09:20:53.199Z (over 1 year ago)
- Topics: bash, monitoring, python, slurm, submission
- Language: Python
- Homepage: http://patonlab.colostate.edu
- Size: 17.1 MB
- Stars: 9
- Watchers: 3
- Forks: 3
- Open Issues: 1
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Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
**Welcome to RSPGROUP on SUMMIT: congratulations - your path is set-up correctly!**
The following scripts are available:
- qstat_summit (monitor disk usage, queue status and jobs)
- qsub_summit (submit G16 and Orca jobs)
- ncisub_summit (submit NCIPlot jobs)
- qcosmo_summut (submit COSMO-RS jobs)
- AutoPrep (create input files from existing output files)
- RotMol (rotates molecules, creating new input files)
The following python modules are available (python -m module):
- goodvibes (thermochemical anaylsis) | https://github.com/bobbypaton/GoodVibes
- pyqrc (fast reaction coordinate) | https://github.com/bobbypaton/pyQRC
- pydftd3 (D3-dispersion corrections) | https://github.com/bobbypaton/pyDFTD3
- kinisot (kinetic isotope effects) | https://github.com/bobbypaton/Kinisot
- DBSTEP (steric parameters) | https://github.com/bobbypaton/DBSTEP
- ase (atomic simulation environment)
To activate a python environment where rdkit, openbabel etc are present:
- source activate DL_CPU (this may require edits to your .condarc file - ask RSP if this is an issue)
The following software is available:
- QChem 5.2.2 /projects/[email protected]/qchem
- Gaussian 16 rev C.01 - /projects/[email protected]/g16/g16
- Orca v4.2.1 - /projects/[email protected]/orca_4_2_1_linux_x86-64_openmpi216
- NBO v7 - /projects/[email protected]/nbo6/bin/gaunbo7
- NCIPlot v4 - /projects/[email protected]/nciplot/nciplot
- Turbomole v7.5 - /projects/[email protected]/turbomole/TURBOMOLE
- COSMOtherm2021 - /projects/[email protected]/BIOVIA/COSMOtherm2021/COSMOtherm/BIN-LINUX/cosmotherm
- TeraChem 1.93P - /projects/[email protected]/TeraChem/bin/terachem
- XTB v6.4.0 - /projects/[email protected]/xtb_6.4.0/bin/xtb
- CREST v2.11 - /projects/[email protected]/xtb_6.4.0/crest
- MECPRO - /projects/[email protected]/mecpro
- Jprogdyn - /projects/[email protected]/JPROGDYN
- AMBER18 - /projects/[email protected]/amber18
To see example usage: create a directory in your $PROJECTS folder and cd there, then type:
- RUNTEST all
This will submit several jobs. When finished, check they ran properly:
- CHECKTEST all
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\/__/ \/__/ \/__/ \/__/ \/__/ \/__/ \/__/ \/__/ ¯\_(ツ)_/¯ last update May 26 2021
- REMINDER: NEW SSKY QUEUE: qsub_summit -p ssky-preemptable