Warning: The Collaboratory Drive will be down Friday 14th June , from 18:00 CET (my timezone) until Monday evening for a migration effort.



This page collects some more commonly encountered problems when using the systems via the Collaboratory.

For more information on the Collaboratory, please seee the documentation of the EBRAINS Collaboratory environment.

Temporary problems

Currently none known.

Jupyter notebook environment ("Lab") related

Error message "Error in Authenticator.pre_spawn_start: ... 401: Unauthorized"

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.

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.

No example notebooks in the Jupyter notebook environment ("Lab")

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.

NoFiles.png

Timeout when starting the Jupyter notebook environment ("Lab")

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.

Lab error message "Cannot open - Could not find path..."

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.

1623846216460-541.png

In the "Drive" the path is visible:

1623846323177-898.png

Error message: "Could not identify EBRAINS kernel "

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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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):

image-20221019150927-1.png

Import error for hbp_service_client

The hbp_service_client was needed for the now not-existing-any-longer Collaboratory version 1. The import line can be deleted from scripts.

BrainScaleS-2 specific

The BrainScaleS external user chat has service announcements (e.g. when a system is down due to maintenance) and is also a good place to ask general questions.

BrainScaleS-2 inhibitory synapse weights (October 2021)

21 October 2021: the pyNN version for BrainScaleS has been updated. Since then, inhibitory synapse weights need to negative numbers, otherwise the error message:    

    "pyNN.errors.ConnectionError: Weights must be negative for current-based, inhibitory synapses"

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).

BrainScaleS-2: "Job error" in the Collaboratory (June 2021)

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.BRAINSCALES2 as the platform to run networks on the BrainScaleS-2 architecture (i.e. on "wafer">60).

In the JobManager, a job with the now wrong platform=nmpi.BRAINSCALES shown in the "log" part of the detailed job information:

72 is not a valid wafer module for BrainScaleS-1. Since 21 June 2021, please use "nmpi.BRAINSCALES2" as platform specification ...

Also since 21 June 2021 a separate quota setting is used for BrainScaleS-2 (visible on the Quota tab in the JobManager)

BrainScaleS-2 interactive demo does not work with error message "ModuleNotFoundError: No module named 'pynn_brainscales'"

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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Then select the "EBRAINS_release_..." kernel from the dialog box and run the example again.

1639576524483-695.png

It may be necessary to restart the newly chosen kernel via "Kernel > restart Kernel" from the menu.

1639576718553-361.png

BrainScaleS-1 specific

The BrainScaleS external user chat has service announcements (e.g. when a system is down due to maintenance) and is also a good place to ask general questions.

Jobs for wafer 33 fail with "Slurm execution failed with state CANCELLED by 0"

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.

PyMarocco.None needs to be changed to PyMarocco.Without (Nov 2021)

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.

Symptom of the problem: In the .out file of the job execution, this error appears:

  File "run.py", line ...
    marocco.backend = PyMarocco.None
                                ^
SyntaxError: invalid syntax

There are also some additional Python3 related changes in the brainscales_system_chain_test.py example. Please find a working example script in our copy-template Drive (for copying into users collabs).

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