Physics on ISciNumPy.dev

ROOT on Conda Forge

henryfs@princeton.edu (Henry Schreiner) — Wed, 13 Feb 2019 10:18:37 +0100

For High Energy Physics, the go-to framework for big data analysis has been CERN’s ROOT framework. ROOT is a massive C++ library that even predates the STL in some areas. It is¹ also a JIT C++ interpreter called Cling, probably the best in the business. If you have heard of the Xeus C++ Kernel for Jupyter, that is built on top of Cling. ROOT has everything a HEP physicist could want: math, plotting, histograms, tuple and tree structures, a very powerful file format for IO, machine learning, Python bindings, and more. It also does things like dictionary generation and arbitrary class serialization (other large frameworks like Qt have similar generation tools).

You may already be guessing one of the most common problems for ROOT. It is huge and difficult to install – if you build from source, that’s a several hour task on a single core. It has gotten much better in the last 6 years, and there are several places you can find ROOT, but there are still areas where it is challenging. This is especially true for Python; ROOT is linked to your distro’s Python (both python2 and python3 if your distro supports it, as of ROOT 6.22); but the common rule for using Python is “don’t touch your system Python” - so modern Python users should be in a virtual environment, and for that ROOT requires the system site-packages option be enabled, which is not always ideal. And, if you use the Anaconda Python distribution, which is the most popular scientific distribution of Python and massively successful for ML frameworks, the general rule even for people who build ROOT themselves has been: don’t. But now, you can get a fully featured ROOT binary package for macOS or Linux, Python 2.7, 3.6, 3.7, or 3.8 from Conda-Forge, the most popular Anaconda community channel! Many more HEP recipes have now been added to Conda-Forge, as well! ROOT now also provides a conda docker image, too!

ROOT Install Options

henryfs@princeton.edu (Henry Schreiner) — Mon, 04 Feb 2019 10:44:37 +0100

For particle physicists, ROOT is one of the most important toolkits around. It is a huge suite of tools that predates the C++ standard library, and has almost anything a particle physicist could want. It has driven developments in other areas too. ROOT’s current C++ interpreter, CLING, is the most powerful C++ interpreter available and is used by the Xeus project for Jupyter. The Python work has helped PyPy, with CPPYY also coming from ROOT. However, due to the size, complexity, and age of some parts of ROOT, it can be a bit challenging to install; and it is even more challenging when you want it to talk to Python. I would like to point to the brand-new Conda-Forge ROOT package for Linux and macOS, and point out a few other options for macOS installs. Note for Windows users: Due to the fact that ROOT expects the type long to match the system pointer size, 64-bit Windows cannot be supported for quite some time. While you can use it in 32 bit form, this is generally impossible to connect to Python, which usually will be a 64-bit build.

Announcing GooFit 2.1

henryfs@princeton.edu (Henry Schreiner) — Thu, 07 Dec 2017 03:20:00 -0500

GooFit 2.1 introduces the full-featured Python bindings to GooFit. These bindings mimic the C++ usage of GooFit, including bindings for all PDFs, and also provide NumPy-centric conversions, live Jupyter notebook printing, pip install, and more. Most of the examples in C++ are provided in Python form, as well.

Several other API changes were made. Observables are now distinguished from Variables and provided as a separate class. Both these classes are now passed around by copy everywhere.¹ The three and four body amplitude classes have been refactored and simplified. OpenMP is now supported via homebrew on macOS; GooFit is one of the only packages that currently can build with OpenMP on the default macOS compiler. Eigen is now available, and CLI11 has been updated to version 1.3.

GooFit 2.1 will receive continuing support while development on GooFit 2.2 presses on with a new indexing scheme for PDFs.

Announcing GooFit 2.0

henryfs@princeton.edu (Henry Schreiner) — Thu, 08 Jun 2017 17:54:00 -0700

The next version of the premier CUDA/OpenMP fitting program for HEP analysis, GooFit 2.0, has been released. GooFit is now easy to build on a wide variety of Unix systems, and supports debuggers and IDEs. GooFit is faster, has unit tests, and working examples. More PDFs and examples have been added, as well as newly released example datasets that are downloaded automatically. GooFit now has built in support for MPI, and can use that to deploy to multiple graphics cards on the same machine. A new command line parser (CLI11) and drastically improved logging and errors have made code easier to write and debug. Usage of GooFit specific terminology is now reduced, using standard Thrust or CUDA terms when possible, lowering the barrier for new developers. A new Python script has been added to assist users converting from pre 2.0 code.

The file structure of GooFit and the build system have been completely revamped. The fake nvcc features have been removed, as have the rootstuff copies of ROOT classes. PDFs are now organized by type and compile and link separately. Multiple PDF caching support has improved. The build system now uses CMake and manages external libraries.

A new feature of the CMake build system is GooFit Packages, which are complete packages that can be added to GooFit and built, allowing analysis code to live in a separate location from GooFit, rather than the old method of simply forking GooFit and adding your analysis manually. A GooFit Package can be made into an example trivially. See this package for an example.

GooFit 2.0 will receive continuing support while development on GooFit 2.1 presses on.

Links

GooFit on GitHub • GooFit webpage • API documentation

Uncertainty extension for IPython

henryfs@princeton.edu (Henry Schreiner) — Fri, 24 Jul 2015 06:45:00 -0700

Wouldn’t it be nice if we had uncertainty with a nice notation in IPython? The current method would be to use raw Python,

from uncertainties import ufloat

print(ufloat(12.34, 0.01))

12.340+/-0.010

Let’s use the infix library to make the notation easier. We’ll define |pm| to mean +/-.

Simple Overloading in Python

henryfs@princeton.edu (Henry Schreiner) — Tue, 07 Jul 2015 09:45:00 -0700

This is intended as an example to demonstrate the use of overloading in object oriented programming. This was written as a Jupyter notebook (aka IPython) in Python 3. To run in Python 2, simply rename the variables that have unicode names, and replace truediv with div.

While there are several nice Python libraries that support uncertainty (for example, the powerful uncertainties package and the related units and uncertainties package pint), they usually use standard error combination rules. For a beginning physics class, often ‘maximum error’ combination is used. Here, instead of using a standard deviation based error and using combination rules based on uncorrelated statistical distributions, we assume a simple maximum error and simply add errors.

To implement this, let’s build a Python class and use overloading to implement algebraic operations.