ChimeraX on Apple M1 CPUs

Tom Goddard
November 2, 2021

We are making a version of our ChimeraX molecular graphics program that runs natively on Apple's new M1 CPUs for faster interactive calculations.
We'll report some speed-up timings and describe difficulties porting from Intel to the Apple M1 CPU.
A native Apple M1 version of ChimeraX is not yet available, but we expect to release it within 6 months.

About ChimeraX

New Mac Computers

Speed of Apple M1 ChimeraX vs Intel ChimeraX

Calculation1M1 CPU2M1 Pro CPU3Intel CPU4Notes
M1 ChimeraXIntel ChimeraXM1 ChimeraXIntel ChimeraXIntel ChimeraX
open PDB 3j3q3.8 sec5. 230 MByte text file in C++.
2.4 million atoms.
7n30 nucleotides slabs6.7 sec12.66.613.014.1Python calculation.
150,000 atom ribosome structure.
addh on 7n3018.0 sec28.716.928.838.7Mixed Python and C++ calculation.
compute surface for 7n308.9 sec9.68.09.511.4C++ calculation. Multithreaded.
Map contour calculation EMDB 22657 0.67 sec1.020.671.021.17C++ calculation on 300 MByte data set.
Apoferritin 420x420x420.
Rendering surface 7n30 full lighting12.8 frames/sec11.825.025.727Graphics rendering speed test.
Intel CPU column has AMD Vega 20 discrete GPU.
  1. Timings done using the ChimeraX time command. Benchmark details.
  2. 2021 Mac Mini (MacMini9,1), macOS 11.6, Apple M1 CPU, 16 Gbytes memory.
  3. 2021 MacBook Pro 16" (MacBookPro18,1), macOS 12.0.1, Apple M1 Pro CPU, 16 Gbytes memory.
  4. 2019 MacBook Pro (MacBookPro15,3), macOS 11.6, 32 Gbytes memory, Intel i9 8-core 2.4 GHz CPU, AMD Vega 20 GPU.

Difficulties porting ChimeraX to Apple M1 CPUs

Potential advantages of native Apple M1 ChimeraX