Installation¶
Conformational analysis of MD trajectories based on (pivot-based) Stochastic Proximity Embedding using dihedral distance as a metric.
Prerequisites¶
You need, at a minimum (requirements.txt):
- Python 2.7 or python 3
- NumPy
- H5py
- Pandas
- Matplotlib
- PyOpenCL
- MDAnalysis (>=0.17)
Installation on UNIX (Debian/Ubuntu)¶
I highly recommand you to install the Anaconda distribution (https://www.continuum.io/downloads) if you want a clean python environnment with nearly all the prerequisites already installed (NumPy, H5py, Pandas, Matplotlib).
1 . First, you have to install OpenCL:
- MacOS: Good news, you don’t have to install OpenCL, it works out-of-the-box. (Update: bad news, OpenCL is now depreciated in macOS 10.14. Thanks Apple.)
- AMD: You have to install the AMDGPU graphics stack.
- Nvidia: You have to install the CUDA toolkit.
- Intel: And of course it’s working also on CPU just by installing this runtime software package. Alternatively, the CPU-based OpenCL driver can be also installed through the package
`pocl`
(http://portablecl.org/) with the conda package manager.
For any other informations, the official installation guide of PyOpenCL is available here.
2 . As a final step, installation from PyPi server
pip install unrolr
Or from the source
# Get the package
wget https://github.com/jeeberhardt/unrolr/archive/master.zip
unzip unrolr-master.zip
rm unrolr-master.zip
cd unrolr-master
# Install the package
python setup.py install
And if somehow pip is having problem to install all the dependencies,
conda config --append channels conda-forge
conda install pyopencl mdanalysis
# Try again
python setup.py install
OpenCL context¶
Before running Unrolr, you need to define the OpenCL context. And it is a good way to see if everything is working correctly.
python -c 'import pyopencl as cl; cl.create_some_context()'
Here in my example, I have the choice between 3 differents computing device (2 graphic cards and one CPU).
Choose platform:
[0] <pyopencl.Platform 'AMD Accelerated Parallel Processing' at 0x7f97e96a8430>
Choice [0]:0
Choose device(s):
[0] <pyopencl.Device 'Tahiti' on 'AMD Accelerated Parallel Processing' at 0x1e18a30>
[1] <pyopencl.Device 'Tahiti' on 'AMD Accelerated Parallel Processing' at 0x254a110>
[2] <pyopencl.Device 'Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz' on 'AMD Accelerated Parallel Processing' at 0x21d0300>
Choice, comma-separated [0]:1
Set the environment variable PYOPENCL_CTX='0:1' to avoid being asked again.
Now you can set the environment variable.
export PYOPENCL_CTX='0:1'