MacVector on Apple Silicon: benchmarks

MacVector 18.1 has just been released. MacVector 18.1 is a Universal Binary application, which means it runs natively on both Apple Silicon M1 Macs and Intel Macs. MacVector 18.1 also has graphical changes for a more authentic Big Sur look and feel. …and for the first time in many, many years the MacVector icon has changed to match the square look of macOS Big Sur icons.

Download the installer.

BigSurMV18 1

But it’s not just how it looks. It’s how well it runs. So we ran some benchmarks on the M1 Mac. We used an Apple Silicon MacBook Pro with 16GB of RAM. We ran using MacVector 18.0, which runs using Rosetta2 emulation (X86_64) and using MacVector 18.1 which runs natively on Apple Silicon (also known as ARM64).

For the benchmarks we used the following jobs:

  • A dotplot of a pair of E.coli genomes
  • A multiple sequence alignment of 16 mitochondria genomes (“Sample Files/Mammalian mtDNA genomes – DNA.msan”) with Clustalw, T-Coffee and Muscle.
  • Using Align to Reference to map sequencing reads against a subset of the L.paracasei genome (sequence are in “Tutorial Files/Contig Assembly/NextGen”)
  • Align to Folder of a section of the Campylobacter jejuni genome against a pair of compressed FASTQ files containing 750,000 pairs of reads.
  • Here are the benchmarks (times are in h:mm:ss):

    M1 BenchmarksTable

    In some cases you can see that the native Apple Silcon MacVector 18.1 runs 200% faster than the emulated MacVector 18.0. That’s an impressive speed increase!

    We also compared a Intel iMac* with the M1 MacBook Pro. Here we used Align To Reference to map a dataset of paired reads in compressed FASTQ files to the full Campylobacter jejuni genome.

    The iMac could map reads at 19,500 reads per minute. But the M1 Macbook Pro rattled through those reads at 39,400 per minute. The small 13“ ”consumer level" laptop runs faster than a considerably more expensive Desktop Mac! Wow!

    MacVector 18.1 will be released shortly.

    *iMac (Retina 5K, 27-inch, Late 2014) with a 4 GHz Intel Core i7, 32 GB RAM and a Fusion drive 12 TB.

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