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Last modified by makuadm on 2026-01-07 06:21
From version 2.1
edited by cpassow
on 2022-04-04 08:06
Change comment: There is no comment for this version
To version 29.1
edited by cpassow
on 2022-04-06 16:47
Change comment: There is no comment for this version

Summary

Details

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Title
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1 -DEMO - Documentation
1 +DEMO - Working with FLASH data
Content
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1 -(% style="list-style-type: square;" %)
2 -* Short descriptions including Links:
3 -(% style="list-style-type: square;" %)
4 -** GPFS
5 -** JupyterHub
6 -** conda ?
1 +Experimental data is recorded as HDF files[link] on the GPFS file system[link]. The access rights[link to ACLs] are linked to the user's DESY account and can be managed by the PI via the GAMMA portal[link]. The experimental data can be downloaded via the GAMMA portal, but it is advised to use the DESY computing infrastructure. Access point are via ssh[link], Maxwell-Display Server[link] or JuyterHub[link]. We recommmend using the JupyterHub for data exploration and the SLURM resources[link] for high performances computing.
7 7  
8 -(% style="list-style-type: square;" %)
9 -* Links Repository
10 -(% style="list-style-type: square;" %)
11 -** including Method Description
3 +For simplified acccess we provide a conda module flashh5[link] which can be installed in a personal conda environment[link] on the Maxwell Cluster. Example on the usage can be found here [link - repo + binder]
12 12  
13 13  \\
14 14  
15 -(% style="list-style-type: square;" %)
16 -* Links to Binder
7 +{{expand title="TEST - How to login JupyterHub"}}
17 17  
9 +
10 +{{view-file att--filename="tmp.mp4" height="250"/}}
11 +{{/expand}}
12 +
18 18  \\
19 19  
20 20  \\
21 21  
22 -Questions:
17 +----
23 23  
24 -(% style="list-style-type: square;" %)
25 -* for whom
26 -* where Maxwell / local / extern
27 -* distribution
19 +=== TODO ===
20 +
21 +(% class="task-list" %)
22 +(((
23 +{{task reference="/Tasks/Task_18" status="InProgress"}}
24 +Short descriptions including Links:   → as Text\\
25 +
26 +(% class="task-list" %)
27 +(((
28 +
29 +
30 +{{task reference="/Tasks/Task_19" status="InProgress"}}
31 +GPFS
32 +{{/task}}
33 +
34 +{{task reference="/Tasks/Task_40" status="InProgress"}}
35 +Access rights
36 +{{/task}}
37 +
38 +{{task reference="/Tasks/Task_41" status="InProgress"}}
39 +Gamma Portal
40 +{{/task}}
41 +
42 +{{task reference="/Tasks/Task_42" status="InProgress"}}
43 +Maxwell
44 +{{/task}}
45 +
46 +{{task reference="/Tasks/Task_20" status="InProgress"}}
47 +JupyterHub
48 +{{/task}}
49 +
50 +{{task reference="/Tasks/Task_21" status="InProgress"}}
51 +conda ?
52 +{{/task}}
53 +
54 +{{task reference="/Tasks/Task_36" status="InProgress"}}
55 +explain install from channel instead of fixed environment, but can use environment file from example repository
56 +{{/task}}
57 +)))
58 +{{/task}}
59 +)))
60 +
61 +\\
62 +
63 +(% class="task-list" %)
64 +(((
65 +{{task reference="/Tasks/Task_22" status="InProgress"}}
66 +distribution
67 +
68 +(% class="task-list" %)
69 +(((
70 +
71 +
72 +{{task reference="/Tasks/Task_23" status="InProgress"}}
73 +channel  (where to host?)
74 +{{/task}}
75 +
76 +{{task reference="/Tasks/Task_24" status="InProgress"}}
77 +environment file (repository with examples)
78 +{{/task}}
79 +)))
80 +{{/task}}
81 +)))
82 +
83 +\\
84 +
85 +(% class="task-list" %)
86 +(((
87 +{{task reference="/Tasks/Task_25" status="InProgress"}}
88 +Documentation
89 +
90 +(% class="task-list" %)
91 +(((
92 +
93 +
94 +{{task reference="/Tasks/Task_26" status="InProgress"}}
95 +here VS repository VS sphinx
96 +{{/task}}
97 +)))
98 +{{/task}}
99 +)))
100 +
101 +\\
102 +
103 +(% class="task-list" %)
104 +(((
105 +{{task reference="/Tasks/Task_27" status="InProgress"}}
106 +Binder
107 +
108 +(% class="task-list" %)
109 +(((
110 +
111 +
112 +{{task reference="/Tasks/Task_28" status="InProgress"}}
113 +examples with Stefan
114 +{{/task}}
115 +)))
116 +{{/task}}
117 +)))
118 +
119 +\\
120 +
121 +(% class="task-list" %)
122 +(((
123 +{{task reference="/Tasks/Task_29" status="InProgress"}}
124 +Screencast
125 +
126 +(% class="task-list" %)
127 +(((
128 +
129 +
130 +{{task reference="/Tasks/Task_30" status="InProgress"}}
131 +login in jupyter hub
132 +{{/task}}
133 +
134 +{{task reference="/Tasks/Task_31" status="InProgress"}}
135 +login maxwell display
136 +{{/task}}
137 +
138 +{{task reference="/Tasks/Task_32" status="InProgress"}}
139 +use slix
140 +{{/task}}
141 +
142 +{{task reference="/Tasks/Task_33" status="InProgress"}}
143 +use hdfview plugin in jupterLab
144 +{{/task}}
145 +
146 +{{task reference="/Tasks/Task_34" status="InProgress"}}
147 +create conda env with flashh5
148 +{{/task}}
149 +)))
150 +{{/task}}
151 +)))
152 +
153 +\\
154 +
155 +\\
156 +
157 +----
158 +
159 +==== under review ====
160 +
161 +\\
162 +
163 +{{code language="bash"}}
164 +conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
165 +source activate flashh5
166 +conda install ipython numpy pandas #TODO: fix dependcies
167 +conda install -c https://www.desy.de/~cpassow/condarepo/ flashh5
168 +
169 +## on jhub
170 +conda install ipykernel
171 +python -m ipykernel install --user --name flashh5 --display-name "flashh5"
172 +
173 +
174 +## to remove on jhub
175 +## delete from: /home/$USER/.local/share/jupyter/kernels/
176 +{{/code}}
177 +
178 +\\
179 +
180 +{{code language="py" title="moved to repository?"}}
181 +class RunDirectory:
182 +
183 + def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
184 + ...
185 +
186 + def get_run(daq, run_number): # daq is not needed!
187 +
188 + ...
189 +
190 +
191 +class Run: # constructor optional without RunDirectory or use there self.path
192 +
193 + def get_files():
194 + ...
195 +
196 + def get_channels(): # of file #1
197 + ...
198 +
199 + def get_start_time(): # better as attribute?
200 + ...
201 +
202 + def get_stop_time(): # which? | better as attribute?
203 + ...
204 +
205 + def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
206 + ...
207 +
208 + def to_series(channel):
209 + ...
210 +
211 + def to_array(channel):
212 + ...
213 +{{/code}}
214 +
215 +{{code language="py" title="ideas"}}
216 +run.to_df(daq_map)
217 +run.to_series(daq_adr or daq_map) # on channel only?
218 +run.to_array(daq_adr) # on channel only?
219 +
220 +## interesting?
221 +# run.to_dask(daq_map)
222 +# run.to_xarray(daq_map)
223 +{{/code}}
224 +
225 +\\