Installation

If you already have fulfilled the requirements for offloading to the GPU, the installation should be as easy as opening up a shell and typing

# To run on GPU
pip install powerfit-em[opencl]

If you are starting from a clean system, follow the instructions for your particular operating system as described below, they should get you up and running in no time.

Conda

If you do not have system admin rights, you likely cannot compile pyvkfft locally. However, by installing powerfit in a conda environment, you can still do computations on GPU. If you are on a Linux system and have Conda or Mamba available, follow these instructions;

Steps for running on GPU with Conda

For AMD or NVIDIA GPUs you can run the following command. Note that this relies on OpenCL drivers being available system wide (under `/etc/OpenCL/vendors/`).

conda create -n powerfit -c conda-forge python=3.12 ocl-icd ocl-icd-system pyopencl pyvkfft
conda activate powerfit
pip install powerfit-em[opencl]

On Intel integrated graphics you can use the following command. This includes the OpenCL runtime and does not rely on your system setup:

conda create -n powerfit -c conda-forge python=3.12 ocl-icd intel-compute-runtime pyopencl pyvkfft
conda activate powerfit
pip install powerfit-em[opencl]

Some older Intel processors might need to use `intel-opencl-rt` instead of `intel-compute-runtime`. After installation, you can check that the OpenCL installation is working by running

python -c 'import pyopencl as cl;from pyvkfft.fft import rfftn; ps=cl.get_platforms();print(ps);print(ps[0].get_devices())'

Usage in Docker

Powerfit can be run in a Docker container.

Install docker by following the instructions.

The Docker images of PowerFit are available in the GitHub Container Registry.

Running PowerFit in a Docker container with data located at a hypothetical /path/to/data on your machine can be done as follows

docker run --rm -ti --user $(id -u):$(id -g) \
    -v /path/to/data:/data ghcr.io/haddocking/powerfit:v4.0.4 \
    /data/<map> <resolution> /data/<pdb> \
    -d /data/<results-dir>

For <map>, <pdb>, <results-dir> use paths relative to /path/to/data.

To run tutorial example use

# cd into powerfit-tutorial repo
docker run --rm -ti --user $(id -u):$(id -g) \
    -v $PWD:/data ghcr.io/haddocking/powerfit:v4.0.4 \
    /data/ribosome-KsgA.map 13 /data/KsgA.pdb \
    -a 20 -p 2 -l -d /data/run-KsgA-docker

To run on NVIDIA GPU using NVIDIA container toolkit use

docker run --rm -ti \
    --runtime=nvidia --gpus all -v /etc/OpenCL:/etc/OpenCL \
    -v $PWD:/data ghcr.io/haddocking/powerfit:v4.0.4 \
    /data/ribosome-KsgA.map 13 /data/KsgA.pdb \
    -a 20 -l -d /data/run-KsgA-docker-nv --gpu

To run on Intel integrated graphics use

docker run --rm -ti \
    --device=/dev/dri \
    -v $PWD:/data ghcr.io/haddocking/powerfit:v4.0.4 \
    /data/ribosome-KsgA.map 13 /data/KsgA.pdb \
    -a 20 -l -d /data/run-KsgA-docker-nv --gpu

To run on AMD GPU use

sudo docker run --rm -ti \
    --device=/dev/kfd --device=/dev/dri \
    --security-opt seccomp=unconfined \
    --group-add video --ipc=host \
    -v $PWD:/data ghcr.io/haddocking/powerfit-rocm:v4.0.4 \
    /data/ribosome-KsgA.map 13 /data/KsgA.pdb \
    -a 20 -l -d /data/run-KsgA-docker-amd --gpu

Linux

Linux systems usually already include a Python3.10 or greater distribution. First make sure the Python header files, pip and git are available by opening up a terminal and typing for Debian and Ubuntu systems

sudo apt update
sudo apt install python3-dev python3-pip git build-essential

If you are working on Fedora, this should be replaced by

sudo yum install python3-devel python3-pip git development-c development-tools

Steps for running on GPU

If you want to use the GPU version of PowerFit, you need to install the drivers for your GPU. After installing the drivers, you need to install the OpenCL development libraries. For Debian/Ubuntu, this can be done by running

sudo apt install ocl-icd-opencl-dev ocl-icd-libopencl1

For Fedora, this can be done by running

sudo dnf install opencl-headers ocl-icd-devel

Install pyvkfft, a Python wrapper for the VkFFT library, using

pip install pyvkfft

Check that the OpenCL installation is working by running

python -c 'import pyopencl as cl;from pyvkfft.fft import rfftn; ps=cl.get_platforms();print(ps);print(ps[0].get_devices())'
# Should print the name of your GPU

Your system is now prepared, follow the general instructions here to install PowerFit.

MacOSX

First install git by following the instructions on their website, or using a package manager such as brew

brew install git

Next install pip, the Python package manager, by following the installation instructions on the website or open a terminal and type

python -m ensurepip --upgrade

To get faster score calculation, install the pyFTTW Python package in your conda environment with conda install -c conda-forge pyfftw.

Follow the general instructions here to install PowerFit.

Windows

First install git for Windows, as it comes with a handy bash shell. Go to git-scm, download git and install it. Next, install a Python distribution such as Anaconda. After installation, open up the bash shell shipped with git and follow the general instructions written above.

Tested platforms

Operating System	CPU single	CPU multi	GPU
Linux	Yes	Yes	Yes
MacOSX	Yes	Yes	No
Windows	Yes	Fail	No

The GPU version has been successfully tested on Linux and with a Docker container for the following devices;

NVIDIA GeForce GTX 1050 Ti
NVIDIA GeForce RTX 4070
AMD Radeon RX 7800 XT
AMD Radeon RX 7900 XTX
Intel Iris Xe Graphics (on a Core i7-1185G7)

The integrated graphics of AMD Ryzen CPUs do not officially support OpenCL. If they do seem available in PyOpenCL be aware that this may lead to incorrect results.