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opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
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WorkerLostError: Worker exited prematurely: signal 9 (SIGKILL) #717

Closed niazche closed 3 years ago

niazche commented 3 years ago

Hello:

I was trying to run my SBML file and the memote is giving me an error showing "WorkerLostError: Worker exited prematurely: signal 9 (SIGKILL)". I am attaching my sbml format model here as a text file.

Please let me know the issue and potential solution.

Thank you

New Text Document.txt

niazche commented 3 years ago

Just to be clear, I was using the moemote.io website. Thanks!

Midnighter commented 3 years ago

Thank you for attaching the model. That will make it possible to find the cause for the error. Have you already tried to use memote from the command line on your model? That is, only if you are comfortable working on the command line or with Python, of course.

niazche commented 3 years ago

Thanks for the reply. No, I am not very comfortable with that. Is it an issue withe memote.io website?

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From: Moritz E. Beber @.> Sent: Saturday, April 24, 2021 1:32:51 PM To: opencobra/memote @.> Cc: Niaz Chowdhury @.>; Author @.> Subject: Re: [opencobra/memote] WorkerLostError: Worker exited prematurely: signal 9 (SIGKILL) (#717)

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Thank you for attaching the model. That will make it possible to find the cause for the error. Have you already tried to use memote from the command line on your model? That is, only if you are comfortable working on the command line or with Python, of course.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_opencobra_memote_issues_717-23issuecomment-2D826135176&d=DwMCaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=oOKCGrU77UifYbJaHsP_jg6VG0Gz7Vegdkufkru0EjQ&m=89DVopmpzVxz10-eIKeQ4gLMot3hLp6WyEYVI7aifek&s=hW8lmFvZo26MRKlhv9FekqnqXGW-NYyxHRFzCbaTa4g&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AT2CWFM67MOVW37BCPFBFPDTKMFFHANCNFSM43P2QKAQ&d=DwMCaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=oOKCGrU77UifYbJaHsP_jg6VG0Gz7Vegdkufkru0EjQ&m=89DVopmpzVxz10-eIKeQ4gLMot3hLp6WyEYVI7aifek&s=OO1yYcvdMTNaQmuziHf3tDZFLxaOGwG07X2Alh-ap2A&e=.

Midnighter commented 3 years ago

Your model is quite large with 4460 metabolites and 4042 reactions. Maybe @carrascomj, you could check the logs on the server but I can guess at potential problems:

  1. Due to the size of your model the server may run out of memory.
  2. The size is generally not a problem for memote but on memote.io we can only use the open source GLPK solver due to licensing restrictions. This mathematical solver is a lot slower than commercial solver for some types of problems. Thus your job may have run out of time.

In any case, I ran memote on my laptop and I have attached the report here for you. It took a long time (1 h) and quite a bit of memory (8 GB) indeed. It shows that a lot of the reactions in your model are recognized as biomass reactions. This is a problem with your model. I can see that a large number of exchange and transport reactions have the name "biomass". That doesn't make sense to me and confuses memote. I would change those names to something more specific. Additionally, you could add the SBO term SBO:0000629 to your true Root_Biomass_MB reaction. You also have a compartment named biomass which I have not seen being done before.

@carrascomj maybe we should skip the informative consistency checks by default on memote.io? 🤔

niazche commented 3 years ago

Thank you so much for your help! I will keep your suggestion in mind while building my next model.

Sincerely,

Niaz

From: Moritz E. Beber @.> Sent: April 24, 2021 5:31 PM To: opencobra/memote @.> Cc: Niaz Chowdhury @.>; Author @.> Subject: Re: [opencobra/memote] WorkerLostError: Worker exited prematurely: signal 9 (SIGKILL) (#717)

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Your model is quite large with 4460 metabolites and 4042 reactions. Maybe @carrascomjhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_carrascomj&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=oOKCGrU77UifYbJaHsP_jg6VG0Gz7Vegdkufkru0EjQ&m=_eZDUO-HJKolSrbUrcnQygs1-O1fsCHLBEpfm4GC95o&s=ROLQ2KIbIjV5oPjk4rLOamIeavWyMi4MQFGgTWFVxKA&e=, you could check the logs on the server but I can guess at potential problems:

  1. Due to the size of your model the server may run out of memory.
  2. The size is generally not a problem for memote but on memote.io we can only use the open source GLPK solver due to licensing restrictions. This mathematical solver is a lot slower than commercial solver for some types of problems. Thus your job may have run out of time.

In any case, I ran memote on my laptop and I have attached the report herehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_opencobra_memote_files_6370867_report.zip&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=oOKCGrU77UifYbJaHsP_jg6VG0Gz7Vegdkufkru0EjQ&m=_eZDUO-HJKolSrbUrcnQygs1-O1fsCHLBEpfm4GC95o&s=9robgi4au1LXElNs-jAoHkBeiB7HeKvmyf2ZeTkvuD4&e= for you. It took a long time (1 h) and quite a bit of memory (8 GB) indeed. It shows that a lot of the reactions in your model are recognized as biomass reactions. This is a problem with your model. I can see that a large number of exchange and transport reactions have the name "biomass". That doesn't make sense to me and confuses memote. I would change those names to something more specific. Additionally, you could add the SBO term SBO:0000629https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ebi.ac.uk_sbo_main_SBO-3A0000629&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=oOKCGrU77UifYbJaHsP_jg6VG0Gz7Vegdkufkru0EjQ&m=_eZDUO-HJKolSrbUrcnQygs1-O1fsCHLBEpfm4GC95o&s=WOo8fTeUTbzipdKutsr8T_ZAKafqtGbIS54FlRJQQ2g&e= to your true Root_Biomass_MB reaction. You also have a compartment named biomass which I have not seen being done before.

@carrascomjhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_carrascomj&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=oOKCGrU77UifYbJaHsP_jg6VG0Gz7Vegdkufkru0EjQ&m=_eZDUO-HJKolSrbUrcnQygs1-O1fsCHLBEpfm4GC95o&s=ROLQ2KIbIjV5oPjk4rLOamIeavWyMi4MQFGgTWFVxKA&e= maybe we should skip the informative consistency checks by default on memote.io? 🤔

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_opencobra_memote_issues_717-23issuecomment-2D826161837&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=oOKCGrU77UifYbJaHsP_jg6VG0Gz7Vegdkufkru0EjQ&m=_eZDUO-HJKolSrbUrcnQygs1-O1fsCHLBEpfm4GC95o&s=_Pgud2F0dQqZ9M6wZV2_6mnXT2g1mAXBNk3w_vjWRmA&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AT2CWFNPFXGQ7NPCBDBOV4TTKNBDXANCNFSM43P2QKAQ&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=oOKCGrU77UifYbJaHsP_jg6VG0Gz7Vegdkufkru0EjQ&m=_eZDUO-HJKolSrbUrcnQygs1-O1fsCHLBEpfm4GC95o&s=oRrPr5RQR9KsX4pN3DQlJegPycUlLUrSERbJl147Wz0&e=.

carrascomj commented 3 years ago

If those tests are the problem, maybe we can do it since it doesn't affect the score. Do we have an estimate of the dimensions of the stoichiometry matrix that cannot be run on memote.io (we cannot deterministically measure that for the additional inconsistency tests but maybe for other tests that are memory intensive)? I believe setting a warning on the web app about the size of the model would help the users.

Midnighter commented 3 years ago

Sorry I don't currently have such estimates since resources were downsized quite a bit after the end of the DeCaF project.

I had another idea, since recently the COIN-OR CBC interface became available in optlang, we could use that solver for MIP tests. I haven't run any benchmarks, though, comparing it to GLPK.

Midnighter commented 3 years ago

I'm closing this issue. Let's continue the discussion elsewhere.