Question in Microbiome Modeling Toolbox -- Worker Aborted

[Xinyi Chen]

Hello, 

I am using mgpipe function from the Microbiome Modeling Toolbox in Linux Cluster but change the abundance file to another one. I used AGORA2 Infofile as the reference file, and mgpipe function for species level model (used createPanModels beforehand). The rest inputs are the same as demo example.

I ran the codes multiple times but couldn't figure out the reason why I am getting the error (listed below). My abundance file have 318 species in total and reduce to 177 species by setting cutoff = 0.0001. The abundance data file is also attached here. 

Thanks a lot!

Best regards,

Xinyi

Warning: A worker aborted during execution of the parfor loop. The parfor loop

will now run again on the remaining workers.

> In distcomp/remoteparfor/handleIntervalErrorResult (line 240)

  In distcomp/remoteparfor/getCompleteIntervals (line 387)

  In parallel_function>distributed_execution (line 745)

  In parallel_function (line 577)

  In buildModelStorage (line 134)

  In mgPipe (line 104)

  In initMgPipe (line 202)    25%     [..........         90%     [....................................    ]Error using distcomp.remoteparfor/rebuildParforController (line 194)

All workers aborted during execution of the parfor loop.

 

Error in distcomp.remoteparfor/handleIntervalErrorResult (line 253)

                obj.rebuildParforController();

 

Error in distcomp.remoteparfor/getCompleteIntervals (line 387)

                            [r, err] = obj.handleIntervalErrorResult(r);

 

Error in buildModelStorage (line 134)

parfor i = 1:size(microbeNames, 1)

 

Error in mgPipe (line 104)

    [activeExMets,couplingMatrix]=buildModelStorage(microbeNames, modPath,

    dietFilePath, adaptMedium, includeHumanMets, numWorkers, pruneModels,

    biomasses);

 

Error in initMgPipe (line 202)

[netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary, statistics,

modelsOK] = mgPipe(modPath, abunFilePath, computeProfiles, resPath,

dietFilePath, infoFilePath, biomasses, hostPath, hostBiomassRxn,

hostBiomassRxnFlux, figForm, numWorkers, rDiet, pDiet, lowerBMBound,

upperBMBound, includeHumanMets, adaptMedium, pruneModels);

The client lost connection to worker 2. This might be due to network problems,

or the interactive communicating job might have errored.

[Almut Heinken]

Hello,
it seems like the issue is with the Parallel Computing Toolbox, not with mgPipe uitself. Have a look here:

https://fr.mathworks.com/matlabcentral/answers/1981944-all-workers-aborted-during-execution-of-parfor-loop

Best regards,

Almut

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