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Install Miniconda

Small tutorial on how to install and run miniconda on the HPC clusters.

    1.

  1. Login into you login machine
  2. 2. Download Miniconda into you local home

$ wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh

    3.

  1. Execute Miniconda

$ chmod +x Miniconda2-latest-Linux-x86_64.sh (give execution permission fo file)

$ ./Miniconda2-latest-Linux-x86_64.sh

Welcome to Miniconda2 4.6.14

In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue

.... 

Do you wish the installer to initialize Miniconda2
by running conda init? [yes|no]
[no] >>> no 

...

    4.

  1. Run miniconda

$ ./miniconda2/bin/conda

    5.

  1. Load conda environment

. /home/csys/jpina/miniconda2/etc/profile.d/conda.sh
  1. Load conda environment in your submission script
$ cat test_submit.sh 

#!/bin/bash
# Load user environment during job excution 
#$ -V   

# Start jobs at the submisssion path 
#$ -cwd 

# Call parallell environment "mp", and excute in 4 cores 
#$ -pe mp 4

# Queue selection 
#$ -q hpc

# Load miniconda 
.  /home/csys/jpina/miniconda2/etc/profile.d/conda.sh

NOTE Loading the conda environment can lead to conflits with the 'modules load' command, therefore users should test the environment on a running job when using both conda and modules environments. If possible, use only conda environment.

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