Wiki source code of Troubleshooting

Version 35.1 by kindler on 2021/12/15 14:58
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kindler 27.1 1 == Jupyter notebook environment ("Lab") related ==
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kindler 3.1 3 === Error message "Error in Authenticator.pre_spawn_start: ... 401: Unauthorized" ===
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kindler 8.1 5 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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kindler 8.1 7 To fix this error, please access the **"Drive"** link in the collab once (the "Drive" is also in the left hand navigation menu of the Collab). After the "Drive" has been accesses once the JupyterLab should start.
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kindler 3.1 9 === No example notebooks in the Jupyter notebook environment ("Lab") ===
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kindler 34.1 11 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", then click the "Lab" link again.
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kindler 7.1 13 [[image:NoFiles.png]]
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kindler 3.1 15 === Timeout when starting the Jupyter notebook environment ("Lab") ===
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17 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.
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kindler 14.1 19 === Lab error message "Cannot open - Could not find path..." ===
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kindler 34.1 21 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.
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23 [[image:1623846216460-541.png]]
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kindler 18.1 25 In the "Drive" the path is visible:
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kindler 17.1 27 [[image:1623846323177-898.png||height="287" width="350"]]
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30 === Test jobs make problems at Jülich ===
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kindler 34.1 32 Since August 2021 accessing the "Lab" link in the left hand navigation menu brings up a site selection menu:
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kindler 25.1 34 [[image:Screenshot 2021-08-30 at 19.00.59.png||height="252" width="300"]]
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kindler 34.1 36 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. The "safe choice" is to use CSCS as the primary execution site.
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kindler 34.1 39 === ===
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kindler 28.1 44 == BrainScaleS-2 specific ==
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kindler 27.1 46 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.
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kindler 31.1 48 === BrainScaleS-2 inhibitory synapse weights (October 2021) ===
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kindler 27.1 50 21 October 2021: the pyNN version for BrainScaleS has been updated. Since then, inhibitory synapse weights need to negative numbers, otherwise the error message:   
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kindler 27.1 52 "pyNN.errors.ConnectionError: Weights must be negative for current-based, inhibitory synapses"
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54 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).
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kindler 31.1 57 === BrainScaleS-2: "Job error" in the Collaboratory (June 2021) ===
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59 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).
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61 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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63 {{{72 is not a valid wafer module for BrainScaleS-1. Since 21 June 2021, please use "nmpi.BRAINSCALES2" as platform specification ...}}}
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kindler 20.1 65 Also since 21 June 2021 a separate quota setting is used for BrainScaleS-2 (visible on the Quota tab in the JobManager)
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kindler 34.1 67 === BrainScaleS-2 interactive demo does not work with error message "ModuleNotFoundError: No module named 'pynn_brainscales'" ===
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69 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)
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71 [[image:1639576461861-804.png]]
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73 Then select the "EBRAINS_release_..." kernel from the dialog box and run the example again.
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75 [[image:1639576524483-695.png]]
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kindler 28.1 77 == BrainScaleS-1 specific ==
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kindler 28.1 79 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.
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kindler 29.1 81 === //PyMarocco.None// needs to be changed to //PyMarocco.Without (Nov 2021)// ===
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kindler 27.1 83 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]].
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kindler 27.1 85 Symptom of the problem: In the .out file of the job execution, this error appears:
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87 {{{ File "run.py", line ...
88 marocco.backend = PyMarocco.None
89 ^
90 SyntaxError: invalid syntax}}}
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kindler 30.1 92 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).
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kindler 34.1 94 ==== ====