Summarize LSF job properties by parsing log files.

Related tags

Logginglsf_stats
Overview

lsf_stats

PyPI Tests

Summarize LSF job properties by parsing log files of workflows executed by Snakemake.

Installation

$ pip install lsf_stats

Usage

$ lsf_stats --help
Usage: lsf_stats [OPTIONS] COMMAND [ARGS]...

  Summarize LSF job properties by parsing log files.

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  gather     Aggregate information from log files in single dataframe.
  summarize  Summarize and visualize aggregated information.

Example

Assume that you executed your Snakemake workflow using the lsf-profile and all generated log files are stored in the directory ./logs/:

$ snakemake --profile lsf
[..]

You can then quickly aggregate resource, rule and other types of information about the workflow execution into a single dataframe:

$ lsf_stats gather -o workflow_stats.csv.gz ./logs/
[..]

This dataframe can then be summarized in various ways:

$ lsf_stats summarize \
    --query 'status == "Successfully completed."' \
    --split-wildcards \
    --grouping-variable category \
    workflow_stats.csv.gz
[..]

For example, the following plots will be generated:

Job execution Job resources
Job execution Job resources
Owner
Kim
:(){ :|: & };:
Kim
Greppin' Logs: Leveling Up Log Analysis

This repo contains sample code and example datasets from Jon Stewart and Noah Rubin's presentation at the 2021 SANS DFIR Summit titled Greppin' Logs. The talk was centered around the idea that Forens

Stroz Friedberg 20 Sep 14, 2022
The new Python SDK for Sentry.io

sentry-python - Sentry SDK for Python This is the next line of the Python SDK for Sentry, intended to replace the raven package on PyPI. from sentry_s

Sentry 1.4k Dec 31, 2022
Track Nano accounts and notify via log file or email

nano-address-notifier Track accounts and notify via log file or email Required python libs

Joohansson (Json) 4 Nov 08, 2021
Scout: an open-source version of the monitoring tool

Badger Scout Scout is an open-source version of the monitoring tool used by Badg

Badger Finance 2 Jan 13, 2022
ClusterMonitor - a very simple python script which monitors and records the CPU and RAM consumption of submitted cluster jobs

ClusterMonitor A very simple python script which monitors and records the CPU and RAM consumption of submitted cluster jobs. Usage To start recording

23 Oct 04, 2021
loghandler allows you to easily log messages to multiple endpoints.

loghandler loghandler allows you to easily log messages to multiple endpoints. Using Install loghandler via pip pip install loghandler In your code im

Mathias V. Nielsen 2 Dec 04, 2021
Log4j alternative for Python

Log4p Log4p is the most secure logging library ever created in this and all other universes. Usage: import log4p log4p.log('"Wow, this library is sec

Isaak Uchakaev 15 Dec 16, 2022
Json Formatter for the standard python logger

This library is provided to allow standard python logging to output log data as json objects. With JSON we can make our logs more readable by machines and we can stop writing custom parsers for syslo

Zakaria Zajac 1.4k Jan 04, 2023
Soda SQL Data testing, monitoring and profiling for SQL accessible data.

Soda SQL Data testing, monitoring and profiling for SQL accessible data. What does Soda SQL do? Soda SQL allows you to Stop your pipeline when bad dat

Soda Data Monitoring 51 Jan 01, 2023
Python script to scan log files/system for unauthorized access around system

checkLogs Python script to scan log files/system for unauthorized access around Linux systems Table of contents General info Getting started Usage Gen

James Kelly 1 Feb 25, 2022
Multi-processing capable print-like logger for Python

MPLogger Multi-processing capable print-like logger for Python Requirements and Installation Python 3.8+ is required Pip pip install mplogger Manual P

Eötvös Loránd University Department of Digital Humanities 1 Jan 28, 2022
A demo of Prometheus+Grafana for monitoring an ML model served with FastAPI.

ml-monitoring Jeremy Jordan This repository provides an example setup for monitoring an ML system deployed on Kubernetes.

Jeremy Jordan 176 Jan 01, 2023
Structured Logging for Python

structlog makes logging in Python faster, less painful, and more powerful by adding structure to your log entries. It's up to you whether you want str

Hynek Schlawack 2.3k Jan 05, 2023
Pretty-print tabular data in Python, a library and a command-line utility. Repository migrated from bitbucket.org/astanin/python-tabulate.

python-tabulate Pretty-print tabular data in Python, a library and a command-line utility. The main use cases of the library are: printing small table

Sergey Astanin 1.5k Jan 06, 2023
dash-manufacture-spc-dashboard is a dashboard for monitoring read-time process quality along manufacture production line

In our solution based on plotly, dash and influxdb, the user will firstly generate the specifications for different robots, and then a wide range of interactive visualizations for different machines

Dequn Teng 1 Feb 13, 2022
changedetection.io - The best and simplest self-hosted website change detection monitoring service

changedetection.io - The best and simplest self-hosted website change detection monitoring service. An alternative to Visualping, Watchtower etc. Designed for simplicity - the main goal is to simply

7.3k Jan 01, 2023
Logging system for the TPC software.

tpc_logger Logging system for the TPC software. The TPC Logger class provides a singleton for logging information within C++ code or in the python API

UC Davis Machine Learning 1 Jan 10, 2022
ScreenshotLogger works just like a keylogger but instead of capturing keystroke,it captures the screen, stores it or sends via email

ScreenshotLogger works just like a keylogger but instead of capturing keystroke,it captures the screen, stores it or sends via email. Scrapeasy is super easy to use and handles everything for you. Ju

Ifechukwudeni Oweh 17 Jul 17, 2022
Ultimate Logger - A Discord bot that logs lots of events in a channel written in python

Ultimate Logger - A Discord bot that logs lots of events in a channel written in python

Luca 2 Mar 27, 2022
Progressbar 2 - A progress bar for Python 2 and Python 3 - "pip install progressbar2"

Text progress bar library for Python. Travis status: Coverage: Install The package can be installed through pip (this is the recommended method): pip

Rick van Hattem 795 Dec 18, 2022