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Sabrina Sendel posted on 09. May. 2019 15:03h - last edited by Christopher Passow on 23. Nov. 2020 17:57h

Maxwell

TL;DR

The usual work flow, in case Anaconda is set-up:

(note that this is only tested for bash shell !)

$ source activate flash
(flash)$ ipython
[0]: import pydoocs
...
[999]: exit
(flash)$ conda deactivate

Anaconda Python environments and package installs at Maxwell

The default Pythons change frequently on Maxwell. We suggest to always load a specific Anaconda module and to add the module load command to your .bashrc file. The environments you create here, are then also selectable on Maxwell's central JupyterHub.

This example uses the Anaconda module anaconda3/5.2. This is loaded by the command

module load anaconda3/5.2

By the way, to check which modules are loaded do

module list

To list available Anaconda channels (i.e. Anaconda package sources):

conda info

To add the FLASH channels, i.e. the sources of the FLASH software not available in standard, preconfigured sources:  

BeamtimeDaqAccess (only within the DESY network):
conda config --add channels http://doocspkgs.desy.de/pub/flashconda
Pydoocs (only within the DESY network):
 conda config --add channels http://doocspkgs.desy.de/pub/doocsconda

To list available Anaconda virtual Python environments

conda info --envs

To create your own environment, e.g. named flash:

conda create -n flash python=3.6 ipykernel

Note, ipykernel is required, if you want to use the central JupyterHub installation on Maxwell. We do recommend to include ipykernel.

Also note, if you choose Python version 3.6 on any of the Maxwell nodes, you also have to downgrade the prompt_tookit to version 2.0.10. Execute the command

pip3 install --upgrade --user prompt_toolkit==2.0.10

To activate the environment named flash:

source activate flash

The active environment is shown enclosed in parentheses in front of the shell's command prompt.

To list the Anaconda packages available in your active environment:

conda list

To permanently install e.g. BeamtimeDaqAccess into your active environment:

conda install beamtimedaqaccess

To deactivate the environment:

conda deactivate

flashlxuser1 and 2, hasfcons0 to hasfcons15, haskcons0 to haskcons3


TL;DR

The usual work flow, in case Anaconda is set-up:

(note that this is only tested for bash shell !)

$ source activate flash
(flash)$ ipython
[0]: import pydoocs
...
[999]: exit
(flash)$ conda deactivate

Anaconda Python environments at flashlxuser[1, 2] and hasfcons[0-15], haskcons[0-3]

Anaconda is not the default on the user workstations and consoles in the FLASH halls or the FLASH servers flashlxuser1 and 2. On the consoles the module system does not contain an Anaconda module. Yet, a current Anaconda distribution is installed on all these machines at /opt/conda/.

To list available Anaconda channels (i.e. Anaconda package sources):

conda info

To add the FLASH channels, i.e. the sources of the FLASH software not available in standard, preconfigured sources:

BeamtimeDaqAccess, only with the DESY network
conda config --add channels http://doocspkgs.desy.de/pub/flashconda
Pydoocs, only within the DESY network
conda config --add channels http://doocspkgs.desy.de/pub/doocsconda

To list available Anaconda virtual Python environments

conda info --envs

To create your own environment, e.g. named flash, choosing your favourite Python version. Pydoocs packages are available for version 2.7, 3.6, and 3.7. Here we select the most recent 3.7. We recommend to include ipykernel for the IPython console and Jupyter Notebooks.

conda create -n flash python=3.7 ipykernel

To activate the environment named flash (note, this intentionally differs from the output of the previous command):

source activate flash

The active environment is shown in parentheses in front of the shell's command prompt.

To list the Anaconda packages available in your active environment:

conda list
To permanently install e.g. Pydoocs into your active environment:
conda install pydoocs

To deactivate the environment:

conda deactivate

To remove an environment named test permanently:

conda env remove --name test

Caveat - flashlxuser[1,2]

As no there is no alias for conda on flahlxuser1 & flashlxuser2 - Use:

/opt/conda/bin/conda

References