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Last modified by makuadm on 2026-01-07 06:21
From version 33.1
edited by sndueste
on 2023-09-28 16:51
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]
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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 -link to Repos and Fab
16 -
17 17  \\
18 18  
19 -\\
22 +Questions:
20 20  
21 -\\
22 -
23 -{{expand}}
24 -\\
25 -
26 -----
27 -
28 -=== TODO ===
29 -
30 -(% class="task-list" %)
31 -(((
32 -{{task reference="/Tasks/Task_18" status="InProgress"}}
33 -Short descriptions including Links:   → as Text\\
34 -
35 -(% class="task-list" %)
36 -(((
37 -
38 -
39 -{{task reference="/Tasks/Task_19" status="InProgress"}}
40 -GPFS
41 -{{/task}}
42 -
43 -{{task reference="/Tasks/Task_40" status="InProgress"}}
44 -Access rights
45 -{{/task}}
46 -
47 -{{task reference="/Tasks/Task_41" status="InProgress"}}
48 -Gamma Portal
49 -{{/task}}
50 -
51 -{{task reference="/Tasks/Task_42" status="InProgress"}}
52 -Maxwell
53 -{{/task}}
54 -
55 -{{task reference="/Tasks/Task_20" status="InProgress"}}
56 -JupyterHub
57 -{{/task}}
58 -
59 -{{task reference="/Tasks/Task_21" status="InProgress"}}
60 -conda ?
61 -{{/task}}
62 -
63 -{{task reference="/Tasks/Task_36" status="InProgress"}}
64 -explain install from channel instead of fixed environment, but can use environment file from example repository
65 -{{/task}}
66 -)))
67 -{{/task}}
68 -)))
69 -
70 -\\
71 -
72 -(% class="task-list" %)
73 -(((
74 -{{task reference="/Tasks/Task_22" status="InProgress"}}
75 -distribution
76 -
77 -(% class="task-list" %)
78 -(((
79 -
80 -
81 -{{task reference="/Tasks/Task_23" status="InProgress"}}
82 -channel  (where to host?)
83 -{{/task}}
84 -
85 -{{task reference="/Tasks/Task_24" status="InProgress"}}
86 -environment file (repository with examples)
87 -{{/task}}
88 -)))
89 -{{/task}}
90 -)))
91 -
92 -\\
93 -
94 -(% class="task-list" %)
95 -(((
96 -{{task reference="/Tasks/Task_25" status="InProgress"}}
97 -Documentation
98 -
99 -(% class="task-list" %)
100 -(((
101 -
102 -
103 -{{task reference="/Tasks/Task_26" status="InProgress"}}
104 -here VS repository VS sphinx
105 -{{/task}}
106 -)))
107 -{{/task}}
108 -)))
109 -
110 -\\
111 -
112 -(% class="task-list" %)
113 -(((
114 -{{task reference="/Tasks/Task_27" status="InProgress"}}
115 -Binder
116 -
117 -(% class="task-list" %)
118 -(((
119 -
120 -
121 -{{task reference="/Tasks/Task_28" status="InProgress"}}
122 -examples with Stefan
123 -{{/task}}
124 -)))
125 -{{/task}}
126 -)))
127 -
128 -\\
129 -
130 -(% class="task-list" %)
131 -(((
132 -{{task reference="/Tasks/Task_29" status="InProgress"}}
133 -Screencast
134 -
135 -(% class="task-list" %)
136 -(((
137 -
138 -
139 -{{task reference="/Tasks/Task_30" status="InProgress"}}
140 -login in jupyter hub
141 -{{/task}}
142 -
143 -{{task reference="/Tasks/Task_31" status="InProgress"}}
144 -login maxwell display
145 -{{/task}}
146 -
147 -{{task reference="/Tasks/Task_32" status="InProgress"}}
148 -use slix
149 -{{/task}}
150 -
151 -{{task reference="/Tasks/Task_33" status="InProgress"}}
152 -use hdfview plugin in jupterLab
153 -{{/task}}
154 -
155 -{{task reference="/Tasks/Task_34" status="InProgress"}}
156 -create conda env with flashh5
157 -{{/task}}
158 -)))
159 -{{/task}}
160 -)))
161 -
162 -\\
163 -
164 -\\
165 -
166 -----
167 -
168 -==== under review ====
169 -
170 -\\
171 -
172 -{{code language="bash"}}
173 -conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
174 -source activate flashh5
175 -conda install ipython numpy pandas #TODO: fix dependcies
176 -conda install -c https://www.desy.de/~cpassow/condarepo/ flashh5
177 -
178 -## on jhub
179 -conda install ipykernel
180 -python -m ipykernel install --user --name flashh5 --display-name "flashh5"
181 -
182 -
183 -## to remove on jhub
184 -## delete from: /home/$USER/.local/share/jupyter/kernels/
185 -{{/code}}
186 -
187 -\\
188 -
189 -{{code language="py" title="moved to repository?"}}
190 -class RunDirectory:
191 -
192 - def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
193 - ...
194 -
195 - def get_run(daq, run_number): # daq is not needed!
196 -
197 - ...
198 -
199 -
200 -class Run: # constructor optional without RunDirectory or use there self.path
201 -
202 - def get_files():
203 - ...
204 -
205 - def get_channels(): # of file #1
206 - ...
207 -
208 - def get_start_time(): # better as attribute?
209 - ...
210 -
211 - def get_stop_time(): # which? | better as attribute?
212 - ...
213 -
214 - def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
215 - ...
216 -
217 - def to_series(channel):
218 - ...
219 -
220 - def to_array(channel):
221 - ...
222 -{{/code}}
223 -
224 -{{code language="py" title="ideas"}}
225 -run.to_df(daq_map)
226 -run.to_series(daq_adr or daq_map) # on channel only?
227 -run.to_array(daq_adr) # on channel only?
228 -
229 -## interesting?
230 -# run.to_dask(daq_map)
231 -# run.to_xarray(daq_map)
232 -{{/code}}
233 -
234 -\\
235 -
236 -\\
237 -{{/expand}}
238 -
239 -\\
24 +(% style="list-style-type: square;" %)
25 +* for whom
26 +* where Maxwell / local / extern
27 +* distribution