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https://github.com/iximiel/plumed-bench-pp

A small collection of function to postprocess plumed benchmark output
https://github.com/iximiel/plumed-bench-pp

benchmarking plumber plumed2

Last synced: 2 months ago
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A small collection of function to postprocess plumed benchmark output

Host: GitHub
URL: https://github.com/iximiel/plumed-bench-pp
Owner: Iximiel
License: mit
Created: 2024-07-11T14:51:14.000Z (6 months ago)
Default Branch: main
Last Pushed: 2024-07-30T13:27:07.000Z (5 months ago)
Last Synced: 2024-10-02T20:17:57.919Z (3 months ago)
Topics: benchmarking, plumber, plumed2
Language: Python
Homepage:
Size: 44.9 KB
Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE.txt

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README

# Plumed-Bench-PP

[![PyPI - Version](https://img.shields.io/pypi/v/plumed-bench-pp.svg)](https://pypi.org/project/plumed-bench-pp)
[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/plumed-bench-pp.svg)](https://pypi.org/project/plumed-bench-pp)
[![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch)
[![Documentation Status](https://readthedocs.org/projects/plumed-bench-pp/badge/?version=latest)](https://plumed-bench-pp.readthedocs.io/en/latest/?badge=latest)

A small toolset for postprocess `plumed benchmark` and the plumed time report at the end of the simulations

as now it can extract a dict from a file like:
```
BENCH: Kernel: this
BENCH: Input: plumed.dat
BENCH: Comparative: 1.000 +- 0.000
BENCH: Cycles Total Average Minimum Maximum
BENCH: A Initialization 1 0.214297 0.214297 0.214297 0.214297
BENCH: B0 First step 1 0.062736 0.062736 0.062736 0.062736
BENCH: B1 Warm-up 199 12.618833 0.063411 0.055884 0.076860
BENCH: B2 Calculation part 1 400 25.567659 0.063919 0.054110 0.113234
BENCH: B3 Calculation part 2 400 25.594014 0.063985 0.059516 0.102646
PLUMED: Cycles Total Average Minimum Maximum
PLUMED: 1 64.054325 64.054325 64.054325 64.054325
PLUMED: 1 Prepare dependencies 1000 0.003443 0.000003 0.000001 0.000013
PLUMED: 2 Sharing data 1000 0.305915 0.000306 0.000015 0.037867
PLUMED: 3 Waiting for data 1000 0.003051 0.000003 0.000002 0.000013
PLUMED: 4 Calculating (forward loop) 1000 63.459357 0.063459 0.054012 0.091577
PLUMED: 5 Applying (backward loop) 1000 0.008520 0.000009 0.000005 0.000044
PLUMED: 6 Update 1000 0.043188 0.000043 0.000031 0.000080
BENCH:
BENCH: Kernel: ../../src/lib/install/libplumedKernel.so
BENCH: Input: plumed.dat
BENCH: Comparative: 0.941 +- 0.002
BENCH: Cycles Total Average Minimum Maximum
BENCH: A Initialization 1 0.216190 0.216190 0.216190 0.216190
BENCH: B0 First step 1 0.058967 0.058967 0.058967 0.058967
BENCH: B1 Warm-up 199 11.983512 0.060219 0.056412 0.102643
BENCH: B2 Calculation part 1 400 24.035510 0.060089 0.056539 0.113900
BENCH: B3 Calculation part 2 400 24.084369 0.060211 0.056866 0.097184
PLUMED: Cycles Total Average Minimum Maximum
PLUMED: 1 60.373083 60.373083 60.373083 60.373083
PLUMED: 1 Prepare dependencies 1000 0.003351 0.000003 0.000001 0.000014
PLUMED: 2 Sharing data 1000 0.329323 0.000329 0.000015 0.032672
PLUMED: 3 Waiting for data 1000 0.003078 0.000003 0.000001 0.000013
PLUMED: 4 Calculating (forward loop) 1000 59.752459 0.059752 0.056310 0.083841
PLUMED: 5 Applying (backward loop) 1000 0.008900 0.000009 0.000006 0.000034
PLUMED: 6 Update 1000 0.043015 0.000043 0.000032 0.000239
```

or
```
PLUMED: Cycles Total Average Minimum Maximum
PLUMED: 1 60.373083 60.373083 60.373083 60.373083
PLUMED: 1 Prepare dependencies 1000 0.003351 0.000003 0.000001 0.000014
PLUMED: 2 Sharing data 1000 0.329323 0.000329 0.000015 0.032672
PLUMED: 3 Waiting for data 1000 0.003078 0.000003 0.000001 0.000013
PLUMED: 4 Calculating (forward loop) 1000 59.752459 0.059752 0.056310 0.083841
PLUMED: 5 Applying (backward loop) 1000 0.008900 0.000009 0.000006 0.000034
PLUMED: 6 Update 1000 0.043015 0.000043 0.000032 0.000239
```

----

One way of extracting the timing from the ouput of the benchmark is:
`awk '/BENCH: Kernel: /,EOF' benchmark.out > times_benchmark.out`

-----

## Table of Contents

- [Installation](#installation)
- [License](#license)

## Installation

```console
pip install plumed-bench-pp
```

## License

`plumed-bench-pp` is distributed under the terms of the [MIT](https://spdx.org/licenses/MIT.html) license.