Changes for page Troubleshooting

Last modified by kindler on 2025/05/14 16:54
From version 39.1
edited by kindler
on 2022/03/21 17:22
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To version 26.1
edited by kindler
on 2021/10/21 16:50
Change comment: There is no comment for this version

Summary

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1 1  (% class="wikigeneratedid" %)
2 -This page collects some more commonly encountered problems when using the systems via the Collaboratory.
2 +(Test sentence)
3 3  
4 -(% class="wikigeneratedid" %)
5 -For more information on the Collaboratory, please seee the [[documentation of the EBRAINS Collaboratory environment>>https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/]].
4 +== Problems with the Jupyter notebook environment ("Lab") ==
6 6  
7 -== Jupyter notebook environment ("Lab") related ==
8 -
9 9  === Error message "Error in Authenticator.pre_spawn_start: ... 401: Unauthorized" ===
10 10  
11 11  When a new user accesses the Lab in a new collab for the first time, it is possible, that the JuypterLab is not starting and instead shows a "...401 Unauthorized" message.
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14 14  
15 15  === No example notebooks in the Jupyter notebook environment ("Lab") ===
16 16  
17 -When starting the Jupyter notebook environment for the first time it can take a bit (without visible "in progress" indication) until the example files appear in the file-chooser. Until then the list is just empty. So the fix here is "have a minute patience", then click the "Lab" link again.
14 +When starting the Jupyter notebook environment for the first time it takes about a minute (without visible "in progress" indication) until the example files appear in the file-chooser. Until then the list is just empty. So the fix here is "have a minute patience"
18 18  
19 19  [[image:NoFiles.png]]
20 20  
21 21  === Timeout when starting the Jupyter notebook environment ("Lab") ===
22 22  
23 -It is possible, that accessing the "Lab" link results in a "timeout" message. This can happen, when the lab environment is started for the first time on one of the virtual machines providing the service, as the very first start per machine takes some time (in the order of 2 minutes). Accessing the "Lab" link again after a few minutes usually works.
20 +It is possible, that accessing the "Lab" link results in a "timeout" message. This can happen, when the lab environment is started for the first time on one of the virtual machines providing the service, as the very first start per machine takes quite some time (in the order of 2 minutes). Accessing the "Lab" link again after a few minutes usually works.
24 24  
25 25  === Lab error message "Cannot open - Could not find path..." ===
26 26  
27 -When first opening the Lab it is in rare cases possible, that it can not open the path /shared/name-of-the-collab, even though in the drive the path is already accessible (see the two screenshots below from the Lab and the Drive). This is due to some delay in synchronisation between the file systems. Fix: Wait a few minutes and try again.
24 +When first opening the Lab it is possible, that it can not open the path /shared/name-of-the-collab, even though in the drive the path is already accessible (see the two screenshots below from the Lab and the Drive). This is due to some delay in synchronisation between the file systems. Fix: Wait a few minutes and try again... (If that does not fix the problem, please contact support@ebrains.eu)
28 28  
26 +
29 29  [[image:1623846216460-541.png]]
30 30  
31 31  In the "Drive" the path is visible:
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33 33  [[image:1623846323177-898.png||height="287" width="350"]]
34 34  
35 35  
36 -=== Import error for hbp_service_client ===
34 +=== Test jobs make problems at Jülich ===
37 37  
38 -The hbp_service_client was needed for the now not-existing-any-longer Collaboratory version 1. The import line can be deleted from scripts.
36 +Since August 2021 accessing the "Lab" link in the left hand navigation menu brings up a new site selection menu:
39 39  
38 +[[image:Screenshot 2021-08-30 at 19.00.59.png||height="252" width="300"]]
40 40  
41 -== BrainScaleS-2 specific ==
40 +Via choosing a different lab execution site it is be possible to choose a specific site, if there are specific needs for the created Jupyter virtual machine for a given task (e.g. a large memory requirement). Currently all the examples do not need any site specific features, so you can select in principle any site. BUT (as of end of August 21) there is a sporadic problem with the NMPI communication, if running at Jülich. Thus for now, please use CSCS as the primary execution site.
42 42  
43 -The [[BrainScaleS external user chat>>https://chat.bioai.eu/external-users/channels/town-square]] has service announcements (e.g. when a system is down due to maintenance) and is also a good place to ask general questions.
44 44  
45 -=== BrainScaleS-2 inhibitory synapse weights (October 2021) ===
43 +=== BrainScaleS-2 inhibitory synapse weights ===
46 46  
47 47  21 October 2021: the pyNN version for BrainScaleS has been updated. Since then, inhibitory synapse weights need to negative numbers, otherwise the error message:   
48 48  
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51 51  will be created (visibie in the .out file created by the job. In the notebook interface the error message can be, that the file needed for plotting is missing).
52 52  
53 53  
54 -=== BrainScaleS-2: "Job error" in the Collaboratory (June 2021) ===
55 55  
53 +
54 +
55 +== BrainScaleS specific tips ==
56 +
57 +The [[BrainScaleS external user chat>>https://chat.bioai.eu/external-users/channels/town-square]] has service announcements (e.g. when a system is down due to maintenance) and is also a good place to ask general questions.
58 +
59 +==== BrainScaleS-2: "Job error" in the Collaboratory, though it worked until 21 June 2021 ====
60 +
56 56  On 21 June 2021 we changed the platform selection in the nmpi command client.submit_job(...,platform=nmpi.BRAINSCALES,...). From then on, please specify nmpi.BRAINSCALES**2** as the platform to run networks on the BrainScaleS-2 architecture (i.e. on "wafer">60).
57 57  
58 58  In the JobManager, a job with the now wrong platform=nmpi.BRAINSCALES shown in the "log" part of the detailed job information:
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61 61  
62 62  Also since 21 June 2021 a separate quota setting is used for BrainScaleS-2 (visible on the Quota tab in the JobManager)
63 63  
64 -=== BrainScaleS-2 interactive demo does not work with error message "ModuleNotFoundError: No module named 'pynn_brainscales'" ===
69 +=== BrainScaleS-1 ===
65 65  
66 -The BrainScaleS-2 interactive examples need the BrainScaleS client software. Currently (December 2021) this software is not available from the started-by-default "Python 3" kernel in the Jupyter lab, but requires the "EBRAINS_release_...." kernel. Please choose the kernel by clicking the kernel name in the lower left hand corner of the Lab window ("Python 3" in the screenshot)
71 +Currently (2 July 2021) the default-system ("wafer 33") is under maintenance. Please see the [[BrainScaleS-1 chat>>https://chat.bioai.eu/external-users/channels/brainscales]] for updates.
67 67  
68 -[[image:1639576461861-804.png||height="42" width="456"]]
69 69  
70 -Then select the "EBRAINS_release_..." kernel from the dialog box and run the example again.
71 -
72 -[[image:1639576524483-695.png||height="259" width="420"]]
73 -
74 -It may be necessary to restart the newly chosen kernel via "Kernel > restart Kernel" from the menu.
75 -
76 -[[image:1639576718553-361.png||height="125" width="518"]]
77 -
78 -== BrainScaleS-1 specific ==
79 -
80 -The [[BrainScaleS external user chat>>https://chat.bioai.eu/external-users/channels/town-square]] has service announcements (e.g. when a system is down due to maintenance) and is also a good place to ask general questions.
81 -
82 -=== //PyMarocco.None// needs to be changed to //PyMarocco.Without (Nov 2021)// ===
83 -
84 -November 2021: //marocco.backend = PyMarocco.None// had to be changed to //marocco.backend = PyMarocco.Without// due to the move to Python3, which has None as a reserved keyword. See also [[this FAQ entry in the guidebook>>https://electronicvisions.github.io/hbp-sp9-guidebook/pm/using_pm_newflow.html#rename-pymarocco-none-to-pymarocco-without]].
85 -
86 -Symptom of the problem: In the .out file of the job execution, this error appears:
87 -
88 -{{{ File "run.py", line ...
89 - marocco.backend = PyMarocco.None
90 - ^
91 -SyntaxError: invalid syntax}}}
92 -
93 -There are also some additional Python3 related changes in the brainscales_system_chain_test.py example. Please find a [[working example script>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/shared/NMC%20Collab%20copy%20template/BrainScaleS/BrainScaleS_01_Chain.ipynb]] in our [[copy-template Drive>>https://wiki.ebrains.eu/bin/view/Collabs/nmc-collab-copy-template/Drive]] (for copying into users collabs).
94 -
95 -==== ====
74 +==== ====
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