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Last modified by makuadm on 2026-01-07 06:21
From version 35.1
edited by sndueste
on 2023-09-28 16:54
Change comment: There is no comment for this version
To version 2.1
edited by cpassow
on 2022-04-04 08:06
Change comment: There is no comment for this version

Summary

Details

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Title
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1 -DEMO - Working with FLASH data
1 +DEMO - Documentation
Author
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1 -XWiki.sndueste
1 +XWiki.cpassow
Content
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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.
1 +(% style="list-style-type: square;" %)
2 +* Short descriptions including Links:
3 +(% style="list-style-type: square;" %)
4 +** GPFS
5 +** JupyterHub
6 +** conda ?
2 2  
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]
8 +(% style="list-style-type: square;" %)
9 +* Links Repository
10 +(% style="list-style-type: square;" %)
11 +** including Method Description
4 4  
5 5  \\
6 6  
7 -{{expand title="How to login JupyterHub"}}
15 +(% style="list-style-type: square;" %)
16 +* Links to Binder
8 8  
9 -
10 -{{view-file att--filename="tmp.mp4" height="250"/}}
11 -{{/expand}}
12 -
13 13  \\
14 14  
15 -{{info}}
16 -=== Reference implementation (Python) ===
17 -
18 -(imperative)  (% class="Object" %)[[https:~~/~~/gitlab.desy.de/christopher.passow/flash-daq-hdf>>url:https://gitlab.desy.de/christopher.passow/flash-daq-hdf||shape="rect"]]
19 -
20 -(% class="Object" %)(object oriented) [[https:~~/~~/gitlab.desy.de/christopher.passow/fdh-builder>>url:https://gitlab.desy.de/christopher.passow/fdh-builder.git||shape="rect"]]
21 -
22 22  \\
23 -{{/info}}
24 24  
25 -link to Repos and Fab
22 +Questions:
26 26  
27 -\\
28 -
29 -\\
30 -
31 -\\
32 -
33 -{{expand title="older ideas ..."}}
34 -\\
35 -
36 -----
37 -
38 -=== TODO ===
39 -
40 -(% class="task-list" %)
41 -(((
42 -{{task reference="/Tasks/Task_18" status="InProgress"}}
43 -Short descriptions including Links:   → as Text\\
44 -
45 -(% class="task-list" %)
46 -(((
47 -
48 -
49 -{{task reference="/Tasks/Task_19" status="InProgress"}}
50 -GPFS
51 -{{/task}}
52 -
53 -{{task reference="/Tasks/Task_40" status="InProgress"}}
54 -Access rights
55 -{{/task}}
56 -
57 -{{task reference="/Tasks/Task_41" status="InProgress"}}
58 -Gamma Portal
59 -{{/task}}
60 -
61 -{{task reference="/Tasks/Task_42" status="InProgress"}}
62 -Maxwell
63 -{{/task}}
64 -
65 -{{task reference="/Tasks/Task_20" status="InProgress"}}
66 -JupyterHub
67 -{{/task}}
68 -
69 -{{task reference="/Tasks/Task_21" status="InProgress"}}
70 -conda ?
71 -{{/task}}
72 -
73 -{{task reference="/Tasks/Task_36" status="InProgress"}}
74 -explain install from channel instead of fixed environment, but can use environment file from example repository
75 -{{/task}}
76 -)))
77 -{{/task}}
78 -)))
79 -
80 -\\
81 -
82 -(% class="task-list" %)
83 -(((
84 -{{task reference="/Tasks/Task_22" status="InProgress"}}
85 -distribution
86 -
87 -(% class="task-list" %)
88 -(((
89 -
90 -
91 -{{task reference="/Tasks/Task_23" status="InProgress"}}
92 -channel  (where to host?)
93 -{{/task}}
94 -
95 -{{task reference="/Tasks/Task_24" status="InProgress"}}
96 -environment file (repository with examples)
97 -{{/task}}
98 -)))
99 -{{/task}}
100 -)))
101 -
102 -\\
103 -
104 -(% class="task-list" %)
105 -(((
106 -{{task reference="/Tasks/Task_25" status="InProgress"}}
107 -Documentation
108 -
109 -(% class="task-list" %)
110 -(((
111 -
112 -
113 -{{task reference="/Tasks/Task_26" status="InProgress"}}
114 -here VS repository VS sphinx
115 -{{/task}}
116 -)))
117 -{{/task}}
118 -)))
119 -
120 -\\
121 -
122 -(% class="task-list" %)
123 -(((
124 -{{task reference="/Tasks/Task_27" status="InProgress"}}
125 -Binder
126 -
127 -(% class="task-list" %)
128 -(((
129 -
130 -
131 -{{task reference="/Tasks/Task_28" status="InProgress"}}
132 -examples with Stefan
133 -{{/task}}
134 -)))
135 -{{/task}}
136 -)))
137 -
138 -\\
139 -
140 -(% class="task-list" %)
141 -(((
142 -{{task reference="/Tasks/Task_29" status="InProgress"}}
143 -Screencast
144 -
145 -(% class="task-list" %)
146 -(((
147 -
148 -
149 -{{task reference="/Tasks/Task_30" status="InProgress"}}
150 -login in jupyter hub
151 -{{/task}}
152 -
153 -{{task reference="/Tasks/Task_31" status="InProgress"}}
154 -login maxwell display
155 -{{/task}}
156 -
157 -{{task reference="/Tasks/Task_32" status="InProgress"}}
158 -use slix
159 -{{/task}}
160 -
161 -{{task reference="/Tasks/Task_33" status="InProgress"}}
162 -use hdfview plugin in jupterLab
163 -{{/task}}
164 -
165 -{{task reference="/Tasks/Task_34" status="InProgress"}}
166 -create conda env with flashh5
167 -{{/task}}
168 -)))
169 -{{/task}}
170 -)))
171 -
172 -\\
173 -
174 -\\
175 -
176 -----
177 -
178 -==== under review ====
179 -
180 -\\
181 -
182 -{{code language="bash"}}
183 -conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
184 -source activate flashh5
185 -conda install ipython numpy pandas #TODO: fix dependcies
186 -conda install -c https://www.desy.de/~cpassow/condarepo/ flashh5
187 -
188 -## on jhub
189 -conda install ipykernel
190 -python -m ipykernel install --user --name flashh5 --display-name "flashh5"
191 -
192 -
193 -## to remove on jhub
194 -## delete from: /home/$USER/.local/share/jupyter/kernels/
195 -{{/code}}
196 -
197 -\\
198 -
199 -{{code language="py" title="moved to repository?"}}
200 -class RunDirectory:
201 -
202 - def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
203 - ...
204 -
205 - def get_run(daq, run_number): # daq is not needed!
206 -
207 - ...
208 -
209 -
210 -class Run: # constructor optional without RunDirectory or use there self.path
211 -
212 - def get_files():
213 - ...
214 -
215 - def get_channels(): # of file #1
216 - ...
217 -
218 - def get_start_time(): # better as attribute?
219 - ...
220 -
221 - def get_stop_time(): # which? | better as attribute?
222 - ...
223 -
224 - def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
225 - ...
226 -
227 - def to_series(channel):
228 - ...
229 -
230 - def to_array(channel):
231 - ...
232 -{{/code}}
233 -
234 -{{code language="py" title="ideas"}}
235 -run.to_df(daq_map)
236 -run.to_series(daq_adr or daq_map) # on channel only?
237 -run.to_array(daq_adr) # on channel only?
238 -
239 -## interesting?
240 -# run.to_dask(daq_map)
241 -# run.to_xarray(daq_map)
242 -{{/code}}
243 -
244 -\\
245 -
246 -\\
247 -{{/expand}}
24 +(% style="list-style-type: square;" %)
25 +* for whom
26 +* where Maxwell / local / extern
27 +* distribution