Wiki source code of Anaconda Python at FLASH

Last modified by sndueste on 2025/02/05 11:23
Hide last authors
sndueste 29.2 1 === ===
2
3 == (% style="color:#e74c3c" %)**OUTDATED (Dec 2024)  ... to be adapted to current situation ...**(%%) ==
4
5 === ===
6
7 === ===
8
9 === Maxwell ===
10
11 ==== TL;DR ====
12
13 The usual work flow, in case Anaconda is set-up:
14
15 (note that this is only tested for{{code language="none"}} bash{{/code}} shell !)
16
17 {{code language="bash"}}
18 $ source activate flash
19 (flash)$ ipython
20 [0]: import pydoocs
21 ...
22 [999]: exit
23 (flash)$ conda deactivate
24
25 {{/code}}
26
27 ==== Anaconda Python environments and package installs at Maxwell ====
28
29 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 {{code language="none"}}.bashrc{{/code}} file. The environments you create here, are then also selectable on Maxwell's central [[JupyterHub>>doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Online data analysis.Anaconda Python at FLASH.JupyterHub on Maxwell.WebHome]].
30
31 This example uses the Anaconda module {{code language="none"}}anaconda3/5.2{{/code}}. This is loaded by the command
32
33 {{code language="bash"}}
34 module load anaconda3/5.2
35
36 {{/code}}
37
38 By the way, to check which modules are loaded do
39
40 {{code language="bash"}}
41 module list
42 {{/code}}
43
44 To list available Anaconda channels (i.e. Anaconda package sources):
45
46 {{code language="bash"}}
47 conda info
48 {{/code}}
49
50 To add the FLASH channels, i.e. the sources of the FLASH software not available in standard, preconfigured sources:
51
52 {{code language="bash" title="lavue, opisgraph, ramanometer ..."}}
53 conda config --add channels http://doocspkgs.desy.de/pub/flashconda
54 {{/code}}
55
56 {{code language="bash" title="Pydoocs and Pydaq"}}
57 conda config --add channels http://doocspkgs.desy.de/pub/doocsconda
58 {{/code}}
59
60 To list available Anaconda virtual Python environments
61
62 {{code language="bash"}}
63 conda info --envs
64 {{/code}}
65
66 To create your own environment, e.g. named {{code language="none"}}flash{{/code}}:
67
68 {{code language="bash"}}
69 conda create -n flash python=3.6 ipykernel
70 {{/code}}
71
72 Note, {{code language="none"}}ipykernel{{/code}} is required, if you want to use the central [[JupyterHub>>doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Online data analysis.Anaconda Python at FLASH.JupyterHub on Maxwell.WebHome]] installation on Maxwell. We do recommend to include {{code language="none"}}ipykernel{{/code}}.
73
74 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
75
76 {{code language="bash"}}
77 pip3 install --upgrade --user prompt_toolkit==2.0.10
78 {{/code}}
79
80 To activate the environment named {{code language="none"}}flash{{/code}}:
81
82 {{code language="bash"}}
83 source activate flash
84 {{/code}}
85
86 The active environment is shown enclosed in parentheses in front of the shell's command prompt.
87
88 To list the Anaconda packages available in your active environment:
89
90 {{code language="bash"}}
91 conda list
92 {{/code}}
93
94 To permanently install e.g. [[pydoocs>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Online data analysis.PythonDOOCS.WebHome]] into your active environment:
95
96 {{code language="bash"}}
97 conda install pydoocs
98 {{/code}}
99
100 To deactivate the environment:
101
102 {{code language="bash"}}
103 conda deactivate
104 {{/code}}
105
106 === flashlxuser1 and 2, hasfcons0 to hasfcons15, haskcons0 to haskcons3 ===
107
108
109 ==== TL;DR ====
110
111 The usual work flow, in case Anaconda is set-up:
112
113 (note that this is only tested for{{code language="none"}} bash{{/code}} shell !)
114
115 {{code language="bash"}}
116 $ source activate flash
117 (flash)$ ipython
118 [0]: import pydoocs
119 ...
120 [999]: exit
121 (flash)$ conda deactivate
122
123 {{/code}}
124
125 ==== Anaconda Python environments at flashlxuser[1, 2] and hasfcons[0-15], haskcons[0-3] ====
126
127 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 {{code language="none"}}/opt/conda/{{/code}}.
128
129 To list available Anaconda channels (i.e. Anaconda package sources):
130
131 {{code language="bash"}}
132 conda info
133 {{/code}}
134
135 To add the FLASH channels, i.e. the sources of the FLASH software not available in standard, preconfigured sources:
136
137 {{code language="bash" title="lavue, opisgraph, ramanometer ..."}}
138 conda config --add channels http://doocspkgs.desy.de/pub/flashconda
139 {{/code}}
140
141 {{code language="bash" title="Pydoocs, only within the DESY network"}}
142 conda config --add channels http://doocspkgs.desy.de/pub/doocsconda
143 {{/code}}
144
145 To list available Anaconda virtual Python environments
146
147 {{code language="bash"}}
148 conda info --envs
149 {{/code}}
150
151 To create your own environment, e.g. named {{code language="none"}}flash{{/code}}, 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 {{code language="none"}}ipykernel{{/code}} for the IPython console and Jupyter Notebooks.
152
153 {{code language="bash"}}
154 conda create -n flash python=3.7 ipykernel
155 {{/code}}
156
157 To activate the environment named {{code language="none"}}flash{{/code}} (note, this intentionally differs from the output of the previous command):
158
159 {{code language="bash"}}
160 source activate flash
161 {{/code}}
162
163 The active environment is shown in parentheses in front of the shell's command prompt.
164
165 To list the Anaconda packages available in your active environment:
166
167 {{code language="bash"}}
168 conda list
169 {{/code}}
170
171 (% class="code" %)
172 (((
173 To permanently install e.g. Pydoocs into your active environment:
174 )))
175
176 {{code language="bash"}}
177 conda install pydoocs
178 {{/code}}
179
180 To deactivate the environment:
181
182 {{code language="bash"}}
183 conda deactivate
184 {{/code}}
185
186 To remove an environment named {{code language="none"}}test{{/code}} permanently:
187
188 {{code language="bash"}}
189 conda env remove --name test
190 {{/code}}
191
192 === Caveat - flashlxuser[1,2] ===
193
194 As no there is no alias for {{code language="none"}}conda{{/code}} on flahlxuser1 & flashlxuser2 - Use:
195
196 {{code language="bash"}}
197 /opt/conda/bin/conda
198 {{/code}}
199
200 === References ===
201
202
203 * [[Conda cheat sheet>>url:https://docs.conda.io/projects/conda/en/latest/user-guide/cheatsheet.html||rel="nofollow" shape="rect" class="external-link"]]
204 * [[How to use Conda environments with JupyterHub in screen shots>>attach:conda_on_jupyterhub.pdf]]
205 * [[doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Online data analysis.Anaconda Python at FLASH.JupyterHub on Maxwell.WebHome]]
206
207 * [[attach:anaconda_and_venv.pdf]]: Christopher Behrens on Benefits of Anaconda and Virtual Envronments, 2019-01-14
208 * [[attach:conda_server.pdf]]: Christopher Behrens on FLASH Anaconda Packages and Repositories, 2019-02-11
209 * [[attach:conda_on_jupyterhub.pdf]]: Christopher Behrens on Conda Packages with Jupyterhub, 2019-04-xx
210
211