Miniconda within Singularity

Because lumière cluster is based on an old operating system (Centos 6.10), GLIBC errors may occur when installing or using new conda packages. For example:

./python3: /lib64/libc.so.6: version `GLIBC_2.15' not found (required by ./python3)
./python3: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./python3)
./python3: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by ./python3)''

Solution: the idea is to use a more recent version of GLIBC embedded in a singularity container.

advantage: access to the most recent version of Python and the majority of recent packages.

disadvantage: lack of conda activate and deactivate options.It is therefore impossible to use conda activate. command.

We have created a wrapper around conda called conda_sing.

This new command will replace the classical conda command.

First load the dedicated environment :

$ module load miniconda/singularity

$ module load miniconda/singularity
$ meso_setup_conda 

Create a new environment called myEnv

$ conda_sing create -n myEnv

To list conda environments

$ conda_sing env list

To install package inside environment:

$ conda_sing install -n myEnv package1 package2

To list installed packages:

$ conda_sing list -n myEnv 

To run program using Singularity :

$ conda_sing run -n myEnv python myProgram.py

anaconda.sge

#!/bin/bash
 
#$ -q all.q
 
#$ -l h_vmem=6G ## job will cancel if memory exceed
 
#$ -N Test_anaconda
 
module load miniconda/singularity
 
conda_sing run -n myEnv python myProgram.py