Installation¶

from conda (Linux, OX)¶

We higly recommend install pytraj by conda

conda install -c ambermd pytraj-dev

This takes only less than 30 seconds.

If you don’t want to read long description about installing conda, just copy and paste below script to your terminal (for Linux). For Mac user, you need to follow conda website.

$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ sh Miniconda3-latest-Linux-x86_64.sh

from pip (Linux, OSX)¶

Note:

• Recommend to use python >= 3.4, pip >= 8.1
• osx: no wheel for python 2.7

pip install pytraj

from source code (easy way: Linux, OSX)¶

git clone https://github.com/Amber-MD/pytraj
cd pytraj

# linux
python ./setup.py install

# osx:
python setup.py install --disable-openmp

# note: pytraj will automatically install cpptraj first.

Depend on your machine, the fresh installation (libcpptraj + pytraj) could take 2 to 4 minutes.

from source code (hard way - expert only)¶

Sometimes you want to install libcpptraj.so by yourself.

• First, download cpptraj:

  git clone https://github.com/Amber-MD/cpptraj
  cd cpptraj
  bash configure -shared -openmp gnu
  
  # if you are AMBER user, you can add -amberlib
  bash configure -shared -openmp -amberlib gnu
  make libcpptraj -j4
  
  # please check bash configure --full-help for other options.
  # check: https://github.com/Amber-MD/cpptraj too
  export CPPTRAJHOME=`pwd`
  

• Then, install pytraj

  # cd to any folder you want to store pytraj code
  # then
  git clone https://github.com/Amber-MD/pytraj
  cd pytraj
  python ./setup.py install
  

from AMBER distribution (Linux, OSX)¶

pytraj is included in AMBER16, which will be released soon (2016): ambermd.org

from conda¶

If you install pytraj by conda, you can update it easily

conda update -c ambermd pytraj-dev libcpptraj-dev --force

from pip¶

pip install --upgrade pytraj

from github¶

if you install from source code and want to update the development code in github, try to follow below.

$ # make sure to go to pytraj folder (which has README.md, ./tests ...)
$ git pull
$ python ./setup.py install

if you install pytraj via github and want to update cpptraj

$ cd cpptraj
$ git pull
$ make libcpptraj

from conda¶

$ conda remove pytraj-dev libcpptraj-dev

from pip¶

$ pip uninstall pytraj

Permission denied¶

python setup.py install is standard process to install a new Python package. But if you are new to Python and got permission denied error, try to install pytraj in your home folder.

# install pytraj in $HOME/.local
python ./setup.py install --user

# or install pytraj in ``your_favorite_dir``
python ./setup.py install --prefix=your_favorite_dir
# if you do this, make sure to add ``your_favorite_dir`` to $PYTHONPATH
export PYTHONPATH=your_favorite_dir:$PYTHONPATH

If you want to see further options, check python setup.py install --help

Image not found (OSX)¶

Please try to install from conda or from AMBER distribution or from source code. No pip yet please.