Jim GardnerOk I think I get it. numpy is base R
Christos Argyropoulos MD, PhD@jimgar but slower
@ChristosArgyrop The knives are out folks
@jimgar Somewhat tongue in cheek but this older benchmark shows a couple of things about base #Python vs base #Rstats vs #Perl and (surprisingly for those who don't know it exists) how fast the Perl authothreading library #PDL is vs #numba
Base #Rstats is highly optimized and the #Pythonistas unfortunately take a performance hit that they are mostly unaware about.
This and a few other other examples made me not transition to Python. #rstats ftw
The Quest for Performance Part II : Perl vs Python
Having run this toy performance example, we will now digress somewhat and contrast the performance against a few Python implementations. First let’s set up the stage for the calculations, and provide commandline capabilities to the Python script. ```python import argparse import time import math import numpy as np import os from numba import njit from joblib import Parallel, delayed
@ChristosArgyrop It’s funny you shred that, because I was thinking about Perl too. I’ve never used it, but 5 years ago when I started programming and doing basic bioinformatics, Perl was still spoken about wistfully. @scottishlass has been posting the Perl advent calendar https://perladvent.org/2025/index.html so there’s clearly still some interested parties around… including yourself!
@jimgar @scottishlass my stack nowadays is
#perl + #rstats on top of #clang , #sql .
I am using the former for application architecture development , management of data flows and for resource profiling of #rstats code
Given the extreme portability of both languages I don't have to worry about dependency hell (and CRAN/CPAN are better managed than any #Python repo).
#PDL is an extremely fascinating library especially for feature generation
Profiling Peak DRAM Use in R With Perl - Part 2
In the second part of this we implement the solution that was outlined at the end of Part 1: utilize a Perl application that probes the operating system in real time for the RSS (Resident Set Size), i.e. the DRAM footprint of an application fire the application from within R as a separate process, provide it with the PID (Process ID) of the R session and put it in the background do the long, memory hungry application upon the end of the calculation kill the Perl application and obtain DRAM usage for use within R
Allan Engelhardt@wiknin @jimgar @scottishlass Not only that but we just finished a two day hybrid conference Winter Perl Community Conference in applications (many scientific in nature).
https://perlcommunity.org/
(I delivered a talk on a GPU accelerated library that will be submitted to @joss at some point)
The community conference webpage gives an idea of the topics being discussed since its inception as a track of the Perl & Raku conference
https://www.papercall.io/perlcommunityconferencew25
Scottish Lass@jimgar @ChristosArgyrop wistful is a good way of putting it. My affection for Perl stems from the first wave of dynamically generated websites.The regex support ruled when you were dealing with the unholy mess of evolving HTML. Back in the day not unusual for packages to be written by true C gurus and Perl was a wrapper around highly performant low level code. Best of both worlds, easy to use and fast.
@scottishlass @jimgar The tradition of combining performant low level code in C and what-ever-abstraction-makes-more-sense-at-the-high-level in Perl continues.
@openmp_arb #openmp has opened wild opportunities for multithreading using the combo of a Perl script controlling the main thread and pushing things to C threads to shred.
I plan to revisit CGI sometime next year for fun!
Christos Argyropoulos MD, PhD (@[email protected])
@[email protected] @[email protected] @[email protected] Not only that but we just finished a two day hybrid conference Winter Perl Community Conference in applications (many scientific in nature). https://perlcommunity.org/ (I delivered a talk on a GPU accelerated library that will be submitted to @[email protected] at some point) The community conference webpage gives an idea of the topics being discussed since its inception as a track of the Perl & Raku conference https://www.papercall.io/perlcommunityconferencew25