Installation¶

from conda (Linux, OX)¶

We higly recommend install pytraj by conda

# install latest version
conda install -c ambermd pytraj

# install specific version
conda install -c ambermd pytraj==1.0.8

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)¶

# latest version
pip install pytraj

# specific version
pip install pytraj==1.0.8

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

# 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 AMBER (version >= 16): ambermd.org

From conda¶

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

conda update -c ambermd pytraj --force

From pip¶

pip install --upgrade pytraj

From github¶

if you install from source code and want to update the development code in github, you need to update both libcpptraj and pytraj

$ cd /to/pytraj/root/folder
$ cd cpptraj
$ git pull
$ make libcpptraj -j8

then

$ cd /to/pytraj/root/folder
$ git pull
$ python ./setup.py install

Update to AMBERHOME¶

$ amber.pip install pytraj --prefix=$AMBERHOME
# if you don't have amber.pip, just use pip

From conda¶

$ conda remove pytraj libcpptraj

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