Wiki source code of Troubleshooting

Version 50.1 by kindler on 2024/10/08 13:41
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kindler 37.1 1 (% class="wikigeneratedid" %)
2 This page collects some more commonly encountered problems when using the systems via the Collaboratory.
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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/]].
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kindler 40.1 7 == Temporary problems ==
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kindler 44.1 9 Currently none known.
kindler 40.1 10
kindler 27.1 11 == Jupyter notebook environment ("Lab") related ==
kindler 22.1 12
kindler 3.1 13 === Error message "Error in Authenticator.pre_spawn_start: ... 401: Unauthorized" ===
kindler 1.1 14
kindler 8.1 15 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.
kindler 1.1 16
kindler 8.1 17 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 19 === No example notebooks in the Jupyter notebook environment ("Lab") ===
kindler 2.1 20
kindler 38.1 21 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.
kindler 2.1 22
kindler 7.1 23 [[image:NoFiles.png]]
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kindler 3.1 25 === Timeout when starting the Jupyter notebook environment ("Lab") ===
kindler 2.1 26
kindler 38.1 27 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.
kindler 2.1 28
kindler 14.1 29 === Lab error message "Cannot open - Could not find path..." ===
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kindler 34.1 31 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.
kindler 14.1 32
33 [[image:1623846216460-541.png]]
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kindler 18.1 35 In the "Drive" the path is visible:
kindler 14.1 36
kindler 17.1 37 [[image:1623846323177-898.png||height="287" width="350"]]
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kindler 23.1 39
kindler 47.1 40 === Error message: "Could not identify EBRAINS kernel " ===
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42 If your notebook shows "RuntimeError: Could not identify EBRAINS kernel (probably too old version). Please select the appropriate kernel EBRAINS_experimental_release.": Please check, whether an EBRAINS kernel has been selected as kernel for the notebook execution.  In the example screenshot below the "Python 3 (ipykernel)" has been used, as shown in the upper right hand corner of the tab with the notebook.
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44 [[image:1666184857320-440.png]]
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47 Fix: click the current kernel name to get the kernel selection dialog box and select the "EBRAINS_experimental_release" kernel (blue highlight in the screenshot shown below):
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49 [[image:image-20221019150927-1.png]]
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kindler 40.1 51 === Import error for hbp_service_client ===
kindler 23.1 52
kindler 39.1 53 The hbp_service_client was needed for the now not-existing-any-longer Collaboratory version 1. The import line can be deleted from scripts.
kindler 23.1 54
kindler 28.1 55 == BrainScaleS-2 specific ==
kindler 26.1 56
kindler 27.1 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.
kindler 26.1 58
kindler 31.1 59 === BrainScaleS-2 inhibitory synapse weights (October 2021) ===
kindler 23.1 60
kindler 27.1 61 21 October 2021: the pyNN version for BrainScaleS has been updated. Since then, inhibitory synapse weights need to negative numbers, otherwise the error message:   
kindler 19.1 62
kindler 27.1 63 "pyNN.errors.ConnectionError: Weights must be negative for current-based, inhibitory synapses"
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65 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 68 === BrainScaleS-2: "Job error" in the Collaboratory (June 2021) ===
kindler 19.1 69
70 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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72 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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74 {{{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 76 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 78 === BrainScaleS-2 interactive demo does not work with error message "ModuleNotFoundError: No module named 'pynn_brainscales'" ===
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80 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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kindler 36.1 82 [[image:1639576461861-804.png||height="42" width="456"]]
kindler 34.1 83
84 Then select the "EBRAINS_release_..." kernel from the dialog box and run the example again.
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kindler 36.1 86 [[image:1639576524483-695.png||height="259" width="420"]]
kindler 34.1 87
kindler 36.1 88 It may be necessary to restart the newly chosen kernel via "Kernel > restart Kernel" from the menu.
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90 [[image:1639576718553-361.png||height="125" width="518"]]
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kindler 28.1 92 == BrainScaleS-1 specific ==
kindler 21.1 93
kindler 28.1 94 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.
kindler 21.1 95
kindler 48.1 96 === Jobs for wafer 33 fail with "Slurm execution failed with state CANCELLED by 0" ===
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98 Wafer 33 is currently (August 2023) not available for use from the EBRAINS Collaboratory via the NMPI batch system. Please use wafer 30 instead.  The copy template for the example job has been updated to use wafer 30.
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kindler 29.1 100 === //PyMarocco.None// needs to be changed to //PyMarocco.Without (Nov 2021)// ===
kindler 28.1 101
kindler 27.1 102 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]].
kindler 21.1 103
kindler 27.1 104 Symptom of the problem: In the .out file of the job execution, this error appears:
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106 {{{ File "run.py", line ...
107 marocco.backend = PyMarocco.None
108 ^
109 SyntaxError: invalid syntax}}}
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kindler 30.1 111 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).
kindler 27.1 112
kindler 50.1 113 ==== ====
kindler 49.1 114
115 == Spikey ==
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kindler 50.1 117 Support for the use of spikey via the EBRAINS RI has been removed in fall 2024. We recommend to use the much more versatile BrainScaleS-2 interactive instead.