Full exemple : Anaconda Env : Stockwell

Install Anaconda

Get Anaconda

https://www.anaconda.com/download/#linux

$ cd /tmp
/tmp $ wget https://repo.anaconda.com/archive/Anaconda3-5.3.1-Linux-x86_64.sh
--2018-12-04 10:48:00--  https://repo.anaconda.com/archive/Anaconda3-5.3.1-Linux-x86_64.sh
Résolution de repo.anaconda.com (repo.anaconda.com)… 104.17.108.77, 104.17.109.77, 104.17.110.77, ...
Connexion à repo.anaconda.com (repo.anaconda.com)|104.17.108.77|:443… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 667976437 (637M) [application/x-sh]
Enregistre : «Anaconda3-5.3.1-Linux-x86_64.sh»

Anaconda3-5.3.1-Linux-x86_64.sh      100%[=============>] 637.03M  83.3MB/s    ds 7.4s    

2018-12-04 10:48:07 (86.2 MB/s) - «Anaconda3-5.3.1-Linux-x86_64.sh» enregistré [667976437/667976437]

/tmp $

Install Anaconda

/tmp $ sh Anaconda3-5.3.1-Linux-x86_64.sh 
[...]
Anaconda3 will now be installed into this location:
/home/mylogin/anaconda3

  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify a different location below

[/home/lecocq/anaconda3] >>> /localstorage/mylogin/Anaconda
PREFIX=/localstorage/nomad/Anaconda
installing: python-3.7.0-hc3d631a_0 ...
Python 3.7.0
[...]
installing: anaconda-5.3.1-py37_0 ...
installation finished.
Do you wish the installer to initialize Anaconda3
in your /home/lecocq/.bashrc ? [yes|no]
[no] >>> yes

Initializing Anaconda3 in /home/lecocq/.bashrc
A backup will be made to: /home/lecocq/.bashrc-anaconda3.bak


For this change to become active, you have to open a new terminal.

Thank you for installing Anaconda3!
[...]
Do you wish to proceed with the installation of Microsoft VSCode? [yes|no]
>>> no

Load Anaconda

Open a New terminal :

$ conda activate
(base) $

get last Anaconda update

$ conda update --prefix /localstorage/nomad/Anaconda anaconda
[...]
Proceed ([y]/n)? y
[...]
$

create new dedicated Anaconda env for stockwell

list your actual environments

$ conda activate
(base) $ conda env list
# conda environments:
#
base                  *  /localstorage/nomad/Anaconda

(base)

create env stockwell

(base) $ conda create --name stockwell
Solving environment: done

## Package Plan ##

  environment location: /localstorage/nomad/Anaconda/envs/stockwell


Proceed ([y]/n)? 

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate stockwell
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) $

list your new environments

(base) $ conda env list
# conda environments:
#
base                  *  /localstorage/nomad/Anaconda
stockwell                /localstorage/nomad/Anaconda/envs/stockwell

(base) $

activate your new environments

$ conda activate stockwell
(stockwell) $

install stockwell

https://github.com/synergetics/stockwell_transform

install Requirements

  • gcc

it’s already installed on sismologic computers :

$ which gcc
/usr/bin/gcc
nomad@saahre:~$ gcc --version
gcc (Ubuntu 7.3.0-27ubuntu1~18.04) 7.3.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$
  • fftw3 libraries
$ dpkg -l | grep fftw3-dev

If you have no result here, juste ask your administrator to install this package on your computer.

  • numpy
(stockwell) $ conda install numpy
[...]
Proceed ([y]/n)? y
[...]
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
$

clone stockwell repository

(stockwell) $ mkdir -p /localstorage/mylogin/GitHub
(stockwell) $ cd /localstorage/mylogin/GitHub
(stockwell) $ git clone https://github.com/synergetics/stockwell_transform.git
(stockwell) $ cd stockwell_transform

Build and install stockwell

(stockwell) $ pwd
/localstorage/mylogin/GitHub/stockwell_transform
(stockwell) python ./setup.py build
(stockwell) python ./setup.py install
[...]
Installed /localstorage/nomad/Anaconda/envs/stockwell/lib/python3.6/site-packages/stockwell-0.0.5-py3.6-linux-x86_64.egg
Processing dependencies for stockwell==0.0.5
Finished processing dependencies for stockwell==0.0.5
(stockwell) $

ckeck package list

(stockwell) $ conda list | grep stockwell
stockwell                 0.0.5                     <pip>
(stockwell) $