Many Jobs In Parallel

To execute this PLAMS script, make sure to download molecules.tar and extract it.

To follow along, either

Worked Example

Initial Imports

import multiprocessing
from scm.plams import JobRunner, config, Settings, read_molecules, AMSJob

Configure Job Runner

Set the default job runner to run in parallel. Run as many jobs simultaneously as there are cpu on the system. In addition, set the number of cores for each job to 1.

maxjobs = multiprocessing.cpu_count()
print("Running up to {} jobs in parallel simultaneously".format(maxjobs))

Running up to 12 jobs in parallel simultaneously

config.default_jobrunner = JobRunner(parallel=True, maxjobs=maxjobs)

config.job.runscript.nproc = 1

Load Molecules

Load set of molecules from directory containing xyz files.

molecules = read_molecules("molecules")

Set Up and Run Jobs

Configure the calculation settings in the Settings object. Run a geometry optimization job for each molecule in parallel.

settings = Settings()
settings.input.ams.Task = "GeometryOptimization"
settings.input.dftb.Model = "GFN1-xTB"

results = []
for name, molecule in sorted(molecules.items()):
    job = AMSJob(molecule=molecule, settings=settings, name=name)
    results.append(job.run())

[13.08|11:29:05] JOB Acetic_acid STARTED
[13.08|11:29:05] JOB Benzene STARTED
[13.08|11:29:05] JOB Butane STARTED
[13.08|11:29:05] JOB Ethane STARTED
[13.08|11:29:05] JOB Ethanol STARTED
[13.08|11:29:05] JOB Acetic_acid RUNNING
[13.08|11:29:05] JOB Formic_acid STARTED
[13.08|11:29:05] JOB Benzene RUNNING
[13.08|11:29:05] JOB Methanol STARTED
[13.08|11:29:05] JOB Butane RUNNING
[13.08|11:29:05] JOB Water STARTED
[13.08|11:29:05] JOB Ethane RUNNING
[13.08|11:29:05] JOB Ethanol RUNNING

Results

Print a table of results only for the successful calculations.

# Only print the results of the succesful caluclations:
for result in [r for r in results if r.ok()]:
    print("Energy for {:<12}: {:>10.3f} kcal/mol".format(result.name, result.get_energy(unit="kcal/mol")))

[13.08|11:29:05] JOB Formic_acid RUNNING
[13.08|11:29:05] Waiting for job Acetic_acid to finish
[13.08|11:29:05] JOB Methanol RUNNING
[13.08|11:29:05] JOB Water RUNNING
[13.08|11:29:05] JOB Acetic_acid FINISHED
[13.08|11:29:05] JOB Acetic_acid SUCCESSFUL
[13.08|11:29:05] Waiting for job Benzene to finish
[13.08|11:29:05] JOB Benzene FINISHED
[13.08|11:29:05] JOB Benzene SUCCESSFUL
[13.08|11:29:05] Waiting for job Butane to finish
[13.08|11:29:05] JOB Butane FINISHED
[13.08|11:29:05] JOB Butane SUCCESSFUL
[13.08|11:29:05] Waiting for job Ethane to finish
[13.08|11:29:05] JOB Ethane FINISHED
[13.08|11:29:05] JOB Ethane SUCCESSFUL
[13.08|11:29:05] Waiting for job Ethanol to finish
[13.08|11:29:06] JOB Ethanol FINISHED
[13.08|11:29:06] JOB Ethanol SUCCESSFUL
[13.08|11:29:06] Waiting for job Formic_acid to finish
[13.08|11:29:06] JOB Formic_acid FINISHED
[13.08|11:29:06] JOB Formic_acid SUCCESSFUL
[13.08|11:29:06] Waiting for job Methanol to finish
[13.08|11:29:06] JOB Methanol FINISHED
[13.08|11:29:06] JOB Methanol SUCCESSFUL
[13.08|11:29:06] Waiting for job Water to finish
[13.08|11:29:06] JOB Water FINISHED
[13.08|11:29:06] JOB Water SUCCESSFUL
Energy for Acetic_acid :  -9913.297 kcal/mol
Energy for Benzene     : -12039.482 kcal/mol
Energy for Butane      :  -8699.182 kcal/mol
Energy for Ethane      :  -4686.354 kcal/mol
Energy for Ethanol     :  -7629.287 kcal/mol
Energy for Formic_acid :  -7890.662 kcal/mol
Energy for Methanol    :  -5621.724 kcal/mol
Energy for Water       :  -3618.401 kcal/mol

Complete Python code

#!/usr/bin/env amspython
# coding: utf-8

# ## Initial Imports

import multiprocessing
from scm.plams import JobRunner, config, Settings, read_molecules, AMSJob


# ## Configure Job Runner
#
# Set the default job runner to run in parallel. Run as many jobs simultaneously as there are cpu on the system. In addition, set the number of cores for each job to 1.

maxjobs = multiprocessing.cpu_count()
print("Running up to {} jobs in parallel simultaneously".format(maxjobs))


config.default_jobrunner = JobRunner(parallel=True, maxjobs=maxjobs)


config.job.runscript.nproc = 1


# ## Load Molecules
#
# Load set of molecules from directory containing xyz files.

molecules = read_molecules("molecules")


# ## Set Up and Run Jobs
#
# Configure the calculation settings in the `Settings` object. Run a geometry optimization job for each molecule in parallel.

settings = Settings()
settings.input.ams.Task = "GeometryOptimization"
settings.input.dftb.Model = "GFN1-xTB"


results = []
for name, molecule in sorted(molecules.items()):
    job = AMSJob(molecule=molecule, settings=settings, name=name)
    results.append(job.run())


# ## Results
#
# Print a table of results only for the successful calculations.

# Only print the results of the succesful caluclations:
for result in [r for r in results if r.ok()]:
    print("Energy for {:<12}: {:>10.3f} kcal/mol".format(result.name, result.get_energy(unit="kcal/mol")))