Anaconda linux mac

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Source code

Relax is available at

  1. https://sourceforge.net/projects/nmr-relax/
  2. https://github.com/nmr-relax/relax
  3. https://gitlab.com/nmr-relax/relax

Install on Redhat 7.3 or mac

We will install relax on Red Hat Enterprise Linux Workstation release 7.3
It should work for similar linux systems.

We will assume, that you do not have any sudo privileges to add rpm-packages.
Or, that you would like to make a standalone system.

Therefore, we need to be able to install a local version of python.
We will use anaconda for this.

Get anaconda python

  1. Head to: https://conda.io/miniconda.html
  2. Chose the minimal installer: Python 2.7, 64-bit (bash installer)

Start installation of anaconda

# Go to download
cd $HOME/Downloads
# Make installer executable
chmod +x Miniconda2-latest-Linux-x86_64.sh
./Miniconda2-latest-Linux-x86_64.sh

Add anaconda to your PATH

cd $HOME
touch .cshrc
echo '# Anaconda' >>.cshrc 
echo 'set path = (${HOME}/miniconda2/bin $path)' >> .cshrc

If you are using mac and BASH, then in $HOME/.bash_profile it should be:

# added by Anaconda2 4.4.0 installer
export PATH="$HOME/miniconda2/bin:$PATH"

Open a new terminal, to let the change take effect.

Install dependencies

Install wxpython

# Does not work yet! Version 4: https://anaconda.org/conda-forge/wxpython
#conda install -c conda-forge wxpython
# Version 3: https://anaconda.org/anaconda/wxpython
conda install -c anaconda wxpython
 
# Check version
python -c "import wx;print wx.__version__"

Install numpy. September 2017, there was a problem with numpy. Therefore this selection of version

# https://anaconda.org/anaconda/numpy
conda install -c anaconda numpy=1.12.1
 
# Check version
python -c "import numpy;print numpy.__version__"

Install scipy and matplotlib

# https://anaconda.org/anaconda/scipy
conda install -c anaconda scipy
 
# Check version
python -c "import scipy;print scipy.__version__"
 
# https://anaconda.org/anaconda/matplotlib
conda install -c anaconda matplotlib
 
# Check version
python -c "import matplotlib;print matplotlib.__version__"

Install mpi4py

# https://anaconda.org/anaconda/mpi4py
conda install -c anaconda mpi4py
 
# Check version
python -c "import mpi4py;print mpi4py.__version__"

Install Bmrblib

#In tcsh: set v=1.0.4
#In bash: v=1.0.4
set v=1.0.4
 
cd $HOME/Downloads
wget https://sourceforge.net/projects/bmrblib/files/$v/bmrblib-$v.tar.gz
tar -xzf bmrblib-$v.tar.gz
rm bmrblib-$v.tar.gz
cd bmrblib-$v
pip install .
cd ..
python -c "import bmrblib;print bmrblib.__version__, bmrblib.__file__"

Install Minfx

#In tcsh: set v=1.0.12
#In bash: v=1.0.12
set v=1.0.12
 
cd $HOME/Downloads
wget https://sourceforge.net/projects/minfx/files/$v/minfx-$v.tar.gz
tar -xzf minfx-$v.tar.gz
rm minfx-$v.tar.gz
cd minfx-$v
pip install .
cd ..
python -c "import minfx;print minfx.__version__, minfx.__file__"

Install scons

conda install -c anaconda scons

Restart terminal, to make scons available

Install relax

cd $HOME/Downloads
 
# Clone relax
git clone https://git.code.sf.net/p/nmr-relax/code nmr-relax-code
# OR
git clone https://github.com/nmr-relax/relax.git nmr-relax-code
 
cd nmr-relax-code
 
# Build
scons
 
# See version and package details
./relax -i
 
# The "main" branch is the developing branch. It can contain bugs and be unstable.
#You can also "check-out" the last "working version" of relax with
# This will show tags used for the numbering
git tag -l '[0-9]*' -n
 
# If the latest version is 4.0.3
git checkout tags/4.0.3
 
# See version and package details
./relax -i
 
# If you want to use the main branch
git branch --list
git checkout master
 
# Run unittest
./relax -u
 
# Try open GUI
./relax -g
# On a mac, if you get this error:
## This program needs access to the screen.
## Please run with a Framework build of python, and only when you are
## logged in on the main display of your Mac.
# Then you should use "pythonw" instead of "python"
pythonw ./relax -g
 
# Run system tests
./relax -s --time
# Run GUI tests
./relax --gui-tests --time

Make an alias to relax

cd $HOME/Downloads
mkdir -p $HOME/software
mv nmr-relax-code $HOME/software
 
echo '# nmr-relax' >> ${HOME}/.cshrc 
echo 'alias relax ${HOME}/software/nmr-relax-code/relax' >> ${HOME}/.cshrc

If you are using mac and BASH, then in $HOME/.bash_profile it should be with 'pythonw'.

alias relax="pythonw $HOME/software/nmr-relax-code/relax"

Restart terminal to take effect

See also