Benchmarks
==========

Overview
--------

The gene finding in Prodigal is based on dynamic programming, and the
performance critical part is actually the node connection scoring step,
which attempts to construct the highest-scoring chain of genes inside the
input sequence.

Profiling with Valgrind reveals that it represent two-thirds of
the total cycle count used for finding genes with the original Prodigal code
(647M cycles out of 965M on an example sequence), as seen below:

.. image:: _images/qcachegrind.prodigal.png

In Pyrodigal, the connection scoring step is being accelerated with a
pre-filtering step so that invalid connections can be skipped. This pre-filtering
step can be computed using SIMD instruction, processing several nodes at once.
Platform-accelerated code is available for SSE, AVX, and NEON instruction sets.
In addition, a "generic" implementation of the pre-filter is available in plain
C for testing purposes. The pre-filtering can be disabled, in which case
Pyrodigal will fall back to using the original Prodigal code.


Connection scoring is benchmarked using 50 bacterial contigs of various size
and content from the proGenomes v2.1 database. x86-64 Benchmarks were run on
an `Intel NUC <https://ark.intel.com/content/www/de/de/ark/products/188814/intel-nuc-10-performance-mini-pc-nuc10i7fnhja.html>`_
`i7-10710U CPU <https://ark.intel.com/content/www/us/en/ark/products/196448/intel-core-i7-10710u-processor-12m-cache-up-to-4-70-ghz.html>`_
@ 1.10GHz. Arm benchmarks were run on a `Raspberry Pi 4 Model B <https://www.raspberrypi.com/products/raspberry-pi-4-model-b/>`_
`ARM Cortex-A72 <https://developer.arm.com/Processors/Cortex-A72>`_ @ 1.5GHz.


x86-64
------

.. image:: _images/bench-x86-v1.1.2.svg



Arm
---

.. image:: _images/bench-arm-v1.1.2.svg