Software installation

Software installation#

Conda is an open-source package and environment management system that runs on Windows, MacOS, and Linux. The conda repository contains a large number of open-source certified packages enabling scientific work. It is recommended that you install the minimal installer for conda named miniconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages, including pip, zlib and a few others.

Download and install miniconda#

Retrieve miniconda from the following website

Install the version for 64 bit computers.

Note

For MacOS, there are different downloads for Intel and M1 processors. Follow these steps to find out what is on your laptop:

  1. Click the Apple icon in the top-left corner of your Mac.

  2. This will bring up a drop-down menu. Pick the top option: About This Mac.

  3. The resulting window should show you the information you need: look for “Intel” or “M1”

Create conda environment and install packages#

You can create an environment step-by-step or directly with the use of a .yml file. Using the .yml file is the fastest and simplest way to get all the packages you need.

All in one step#

Get all packages needed for course in one step with use of a YML file by running the following command in your terminal (Mac)

conda env create -f ck1310.yml

or Anaconda Powershell (Windows)

conda env create -f ck1310_win.yml

where the file ck1310.yml* contains

name: ck1310
channels:
  - conda-forge
  - veloxchem
dependencies:
  - python>=3.10
  - jupyterlab
  - jupyterlab-spellchecker
  - jupyterlab_code_formatter
  - black
  - isort
  - numpy
  - scipy
  - matplotlib
  - veloxchem
  - k3d
  - py3dmol
  - rdkit
  - openmm
  - mdtraj

and the file ck1310_win.yml* contains

name: ck1310
channels:
  - conda-forge
  - veloxchem
dependencies:
  - python>=3.10
  - jupyterlab
  - jupyterlab-spellchecker
  - jupyterlab_code_formatter
  - black
  - isort
  - numpy
  - scipy
  - matplotlib
  - veloxchem
  - msmpi
  - k3d
  - py3dmol
  - rdkit
  - openmm
  - mdtraj

Some additional features are then made available in your notebooks such as a spell checker and a Python code formatter.

Note: Simply download the file, do not open it!

Step-by-step#

Start a conda terminal, or Anaconda Powershell as it is referred to on a Windows system. Conda supports multiple environments and you start in the one named base as is typically indicated by the prompt. To create a new and additional environment named ck1310, enter the following command line statement

conda create -n ck1310

You can list your conda environments

conda env list

The activated environment will be marked with an asterisk (the base environment to begin with) and you can activate your new environment with the command

conda activate ck1310

as should be indicated by getting a modified prompt.

Install packages into this environment

conda install numpy scipy matplotlib jupyterlab -c conda-forge

Try it out#

You should now be ready to start a Jupyter notebook with the command

jupyter-lab

which should open in your default web browser. A notebook allows for interactive execution of Python code written into cells.

If your notebook doesn’t run#

If you experience issues with a crashing kernel when running Veloxchem, this may relate to several OpenMP runtimes linked to the program, which causes the kernel to die. If your kernel dies, try rerunning the notebook with the below lines added in connection to the module imports. This is an undocumented, temporary solution, but we have so far not had any problems when using it.

import veloxchem as vlx
...

import os
os.environ["KMP_DUPLICATE_LIB_OK"] = "TRUE"
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