WorkerLostError: Worker exited prematurely: signal 6 (SIGABRT).

[AgustinPardo]

Hello,

Problem description

Please explain:

• what you tried to achieve,

Run MEMOTE server (https://memote.io/) with a "json" model.

• how you went about it (referring to the code sample), and

I drag the file model to the drag area of the web

• why the current behaviour is a problem and what output you expected instead.

I received this error output:

"WorkerLostError: Worker exited prematurely: signal 6 (SIGABRT)"

Screenshot:

Regards

[Midnighter]

Thank you for opening the issue. I'll look into it over the next days.

[Linelili]

Hello, I received the same error as AgustinPardo, when I tried to run MEMOTE on the server (https://memote.io/) with a "xml" model: "WorkerLostError: Worker exited prematurely: signal 6 (SIGABRT)"

When running MEMOTE locally using "memote run model.xml", the program doesn't continue at the "test_stoichiometric_consistency" step.

Best regards

[Midnighter]

A bit off-topic: @Linelili test_stoichiometric_consistency contains a mixed-integer problem. If you run memote with the default GLPK solver it will take a very long time (or even get stuck). You can avoid this by either using a different solver such as CPLEX or Gurobi or by setting a time-out option with --solver-timeout 30 on the command line.

[AgustinPardo]

Hi, Thanks for the answer! But my problem was running the memote web application.

Regards

[Linelili]

Hi @Midnighter
thank you very much for the quick reply. I tried both, changing the solver to CPLEX and using the solver-timeout on the command line (alone and in combination). Unfortunately, memote is still not finishing on the command-line.

Nevertheless, I don't want to distract from the MEMOTE web application issue.
I just thought this stoichiometry test might be a hint for the problem in the web application, as I used the same model in the web application and the command line.

[AgustinPardo]

@Linelili

You can avoid that step

Look at this issue: https://github.com/opencobra/memote/issues/680#issuecomment-697191654

[Midnighter]

We are working on improving that test, too, in #701.

[Linelili]

@AgustinPardo and @Midnighter thanks for the hints and comments.

@AgustinPardo for me the MEMOTE web application worked now after adding the SBO-term "SBO:0000629" to the Biomass reaction! Maybe this works for you as well?

[Midnighter]

@AgustinPardo I have just updated the webservice. Please try your model again. Please feel free to re-open the issue if it doesn't work.