Docker: 'Error encountered while requesting the server' on Mac OS

[ohld]

Hi there!

I have a MacBook'15 and I wanted to install and use GROBID via docker.

So in terminal I've done

docker pull lfoppiano/grobid:0.5.4     
docker run -t --rm --init -p 8080:8070 -p 8081:8071 lfoppiano/grobid:0.5.4

After that I went to http://localhost:8080/ --> TEI --> Process Header Document. I've tried to upload several different PDFs and every time I had this bug:

If I tried the same with your demo website http://cloud.science-miner.com/grobid/ - everything worked.

The docker logs I'll attach below

[ohld]

 ~ docker run -t --rm --init -p 8080:8070 -p 8081:8071 lfoppiano/grobid:0.5.4
[WARN  tini (6)] Tini is not running as PID 1 and isn't registered as a child subreaper.
Zombie processes will not be re-parented to Tini, so zombie reaping won't work.
To fix the problem, use the -s option or set the environment variable TINI_SUBREAPER to register Tini as a child subreaper, or run Tini as PID 1.
22:18:31.808 [main] INFO org.grobid.service.main.GrobidServiceApplication - Configuration file: /opt/grobid/grobid-service/config/config.yaml
INFO  [2019-04-03 22:18:36,597] io.dropwizard.server.DefaultServerFactory: Registering jersey handler with root path prefix: /
INFO  [2019-04-03 22:18:36,604] io.dropwizard.server.DefaultServerFactory: Registering admin handler with root path prefix: /
INFO  [2019-04-03 22:18:36,608] io.dropwizard.assets.AssetsBundle: Registering AssetBundle with name: grobidAssets for path /*
INFO  [2019-04-03 22:18:38,228] com.hubspot.dropwizard.guicier.DropwizardModule: Added guice injected health check: org.grobid.service.resources.HealthResource
INFO  [2019-04-03 22:18:38,308] org.grobid.service.GrobidRestService: Initiating Servlet GrobidRestService
INFO  [2019-04-03 22:18:38,324] org.grobid.core.main.LibraryLoader: Loading external native sequence labelling library
INFO  [2019-04-03 22:18:38,345] org.grobid.core.main.LibraryLoader: Loading Wapiti native library...
INFO  [2019-04-03 22:18:38,368] org.grobid.core.main.LibraryLoader: Native library for sequence labelling loaded
INFO  [2019-04-03 22:18:38,388] org.grobid.core.lexicon.Lexicon: Initiating dictionary
INFO  [2019-04-03 22:18:38,404] org.grobid.core.lexicon.Lexicon: End of Initialization of dictionary
INFO  [2019-04-03 22:18:38,406] org.grobid.core.lexicon.Lexicon: Initiating names
INFO  [2019-04-03 22:18:38,409] org.grobid.core.lexicon.Lexicon: End of initialization of names
INFO  [2019-04-03 22:18:40,340] org.grobid.core.lexicon.Lexicon: Initiating country codes
INFO  [2019-04-03 22:18:40,343] org.grobid.core.lexicon.Lexicon: End of initialization of country codes
INFO  [2019-04-03 22:18:40,597] org.grobid.core.factory.GrobidPoolingFactory: Number of Engines in pool active/max: 1/10
INFO  [2019-04-03 22:18:40,597] org.grobid.service.GrobidRestService: Initiating of Servlet GrobidRestService finished.
INFO  [2019-04-03 22:18:40,619] com.hubspot.dropwizard.guicier.DropwizardModule: Registering org.grobid.service.resources.HealthResource as a root resource class
INFO  [2019-04-03 22:18:40,621] com.hubspot.dropwizard.guicier.DropwizardModule: Registering org.grobid.service.GrobidRestService as a root resource class
INFO  [2019-04-03 22:18:40,624] com.hubspot.dropwizard.guicier.DropwizardModule: Registering org.grobid.service.exceptions.mapper.GrobidServiceExceptionMapper as a provider class
INFO  [2019-04-03 22:18:40,626] com.hubspot.dropwizard.guicier.DropwizardModule: Registering org.grobid.service.exceptions.mapper.GrobidExceptionsTranslationUtility as a provider class
INFO  [2019-04-03 22:18:40,627] com.hubspot.dropwizard.guicier.DropwizardModule: Registering org.grobid.service.exceptions.mapper.GrobidExceptionMapper as a provider class
INFO  [2019-04-03 22:18:40,628] com.hubspot.dropwizard.guicier.DropwizardModule: Registering org.grobid.service.exceptions.mapper.WebApplicationExceptionMapper as a provider class
INFO  [2019-04-03 22:18:40,635] org.grobid.service.main.GrobidServiceApplication: Service config=GrobidServiceConfiguration{server=DefaultServerFactory{applicationConnectors=[io.dropwizard.jetty.HttpConnectorFactory@4159e81b], adminConnectors=[io.dropwizard.jetty.HttpConnectorFactory@236ab296], adminMaxThreads=64, adminMinThreads=1, applicationContextPath=/, adminContextPath=/}, logging=DefaultLoggingFactory{level=INFO, loggers={org.apache.pdfbox.pdmodel.font.PDSimpleFont="OFF"}, appenders=[io.dropwizard.logging.ConsoleAppenderFactory@49293b43, io.dropwizard.logging.FileAppenderFactory@5a82ebf8]}, metrics=MetricsFactory{frequency=1 minute, reporters=[]}}
INFO  [2019-04-03 22:18:40,669] io.dropwizard.server.ServerFactory: Starting grobid-service

 _______  _______  _______  ______  _________ ______     _______  _______  _______          _________ _______  _______
(  ____ \(  ____ )(  ___  )(  ___ \ \__   __/(  __  \   (  ____ \(  ____ \(  ____ )|\     /|\__   __/(  ____ \(  ____ \
| (    \/| (    )|| (   ) || (   ) )   ) (   | (  \  )  | (    \/| (    \/| (    )|| )   ( |   ) (   | (    \/| (    \/
| |      | (____)|| |   | || (__/ /    | |   | |   ) |  | (_____ | (__    | (____)|| |   | |   | |   | |      | (__
| | ____ |     __)| |   | ||  __ (     | |   | |   | |  (_____  )|  __)   |     __)( (   ) )   | |   | |      |  __)
| | \_  )| (\ (   | |   | || (  \ \    | |   | |   ) |        ) || (      | (\ (    \ \_/ /    | |   | |      | (
| (___) || ) \ \__| (___) || )___) )___) (___| (__/  )  /\____) || (____/\| ) \ \__  \   /  ___) (___| (____/\| (____/\
(_______)|/   \__/(_______)|/ \___/ \_______/(______/   \_______)(_______/|/   \__/   \_/   \_______/(_______/(_______/


INFO  [2019-04-03 22:18:40,956] org.eclipse.jetty.setuid.SetUIDListener: Opened application@474179fa{HTTP/1.1,[http/1.1]}{0.0.0.0:8070}
INFO  [2019-04-03 22:18:40,958] org.eclipse.jetty.setuid.SetUIDListener: Opened admin@420cd102{HTTP/1.1,[http/1.1]}{0.0.0.0:8071}
INFO  [2019-04-03 22:18:40,965] org.eclipse.jetty.server.Server: jetty-9.4.11.v20180605; built: 2018-06-05T18:24:03.829Z; git: d5fc0523cfa96bfebfbda19606cad384d772f04c; jvm 1.8.0_181-8u181-b13-1~deb9u1-b13
WARN  [2019-04-03 22:18:41,623] org.glassfish.jersey.internal.inject.Providers: A provider org.grobid.service.exceptions.mapper.GrobidExceptionsTranslationUtility registered in SERVER runtime does not implement any provider interfaces applicable in the SERVER runtime. Due to constraint configuration problems the provider org.grobid.service.exceptions.mapper.GrobidExceptionsTranslationUtility will be ignored. 
INFO  [2019-04-03 22:18:42,555] io.dropwizard.jersey.DropwizardResourceConfig: The following paths were found for the configured resources:

    POST    /api/annotatePDF (org.grobid.service.GrobidRestService)
    POST    /api/citationPatentAnnotations (org.grobid.service.GrobidRestService)
    GET     /api/grobid (org.grobid.service.GrobidRestService)
    GET     /api/health (org.grobid.service.resources.HealthResource)
    GET     /api/isalive (org.grobid.service.GrobidRestService)
    POST    /api/processAffiliations (org.grobid.service.GrobidRestService)
    PUT     /api/processAffiliations (org.grobid.service.GrobidRestService)
    POST    /api/processCitation (org.grobid.service.GrobidRestService)
    PUT     /api/processCitation (org.grobid.service.GrobidRestService)
    POST    /api/processCitationNames (org.grobid.service.GrobidRestService)
    PUT     /api/processCitationNames (org.grobid.service.GrobidRestService)
    POST    /api/processCitationPatentPDF (org.grobid.service.GrobidRestService)
    POST    /api/processCitationPatentST36 (org.grobid.service.GrobidRestService)
    POST    /api/processCitationPatentTXT (org.grobid.service.GrobidRestService)
    POST    /api/processDate (org.grobid.service.GrobidRestService)
    PUT     /api/processDate (org.grobid.service.GrobidRestService)
    POST    /api/processFulltextAssetDocument (org.grobid.service.GrobidRestService)
    PUT     /api/processFulltextAssetDocument (org.grobid.service.GrobidRestService)
    POST    /api/processFulltextDocument (org.grobid.service.GrobidRestService)
    PUT     /api/processFulltextDocument (org.grobid.service.GrobidRestService)
    POST    /api/processHeaderDocument (org.grobid.service.GrobidRestService)
    PUT     /api/processHeaderDocument (org.grobid.service.GrobidRestService)
    POST    /api/processHeaderNames (org.grobid.service.GrobidRestService)
    PUT     /api/processHeaderNames (org.grobid.service.GrobidRestService)
    POST    /api/processReferences (org.grobid.service.GrobidRestService)
    PUT     /api/processReferences (org.grobid.service.GrobidRestService)
    POST    /api/referenceAnnotations (org.grobid.service.GrobidRestService)
    GET     /api/version (org.grobid.service.GrobidRestService)

INFO  [2019-04-03 22:18:42,561] org.eclipse.jetty.server.handler.ContextHandler: Started i.d.j.MutableServletContextHandler@74697863{/,null,AVAILABLE}
INFO  [2019-04-03 22:18:42,573] io.dropwizard.setup.AdminEnvironment: tasks = 

    POST    /tasks/log-level (io.dropwizard.servlets.tasks.LogConfigurationTask)
    POST    /tasks/gc (io.dropwizard.servlets.tasks.GarbageCollectionTask)

INFO  [2019-04-03 22:18:42,584] org.eclipse.jetty.server.handler.ContextHandler: Started i.d.j.MutableServletContextHandler@7d25913{/,null,AVAILABLE}
INFO  [2019-04-03 22:18:42,624] org.eclipse.jetty.server.AbstractConnector: Started application@474179fa{HTTP/1.1,[http/1.1]}{0.0.0.0:8070}
INFO  [2019-04-03 22:18:42,626] org.eclipse.jetty.server.AbstractConnector: Started admin@420cd102{HTTP/1.1,[http/1.1]}{0.0.0.0:8071}
INFO  [2019-04-03 22:18:42,627] org.eclipse.jetty.server.Server: Started @12639ms
INFO  [2019-04-03 22:18:54,301] org.grobid.core.jni.WapitiModel: Loading model: /opt/grobid/grobid-home/models/affiliation-address/model.wapiti (size: 2700194)
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/affiliation-address/model.wapiti"
Model path: /opt/grobid/grobid-home/models/affiliation-address/model.wapiti
INFO  [2019-04-03 22:18:54,760] org.grobid.core.jni.WapitiModel: Loading model: /opt/grobid/grobid-home/models/name/header/model.wapiti (size: 2225578)
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/name/header/model.wapiti"
Model path: /opt/grobid/grobid-home/models/name/header/model.wapiti
INFO  [2019-04-03 22:18:55,047] org.grobid.core.jni.WapitiModel: Loading model: /opt/grobid/grobid-home/models/name/citation/model.wapiti (size: 436519)
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/name/citation/model.wapiti"
Model path: /opt/grobid/grobid-home/models/name/citation/model.wapiti
INFO  [2019-04-03 22:18:55,117] org.grobid.core.jni.WapitiModel: Loading model: /opt/grobid/grobid-home/models/header/model.wapiti (size: 36094028)
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/header/model.wapiti"
Model path: /opt/grobid/grobid-home/models/header/model.wapiti
INFO  [2019-04-03 22:19:01,747] org.grobid.core.jni.WapitiModel: Loading model: /opt/grobid/grobid-home/models/date/model.wapiti (size: 102435)
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/date/model.wapiti"
Model path: /opt/grobid/grobid-home/models/date/model.wapiti
INFO  [2019-04-03 22:19:01,766] org.grobid.core.jni.WapitiModel: Loading model: /opt/grobid/grobid-home/models/citation/model.wapiti (size: 16235248)
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/citation/model.wapiti"
Model path: /opt/grobid/grobid-home/models/citation/model.wapiti
INFO  [2019-04-03 22:19:04,233] org.grobid.core.jni.WapitiModel: Loading model: /opt/grobid/grobid-home/models/fulltext/model.wapiti (size: 21734019)
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/fulltext/model.wapiti"
Model path: /opt/grobid/grobid-home/models/fulltext/model.wapiti
INFO  [2019-04-03 22:19:07,531] org.grobid.core.jni.WapitiModel: Loading model: /opt/grobid/grobid-home/models/segmentation/model.wapiti (size: 16788068)
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/segmentation/model.wapiti"
Model path: /opt/grobid/grobid-home/models/segmentation/model.wapiti
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/reference-segmenter/model.wapiti"
INFO  [2019-04-03 22:19:17,656] org.grobid.core.jni.WapitiModel: Loading model: /opt/grobid/grobid-home/models/reference-segmenter/model.wapiti (size: 4921245)
Model path: /opt/grobid/grobid-home/models/reference-segmenter/model.wapiti
INFO  [2019-04-03 22:19:18,530] org.grobid.core.jni.WapitiModel: Loading model: /opt/grobid/grobid-home/models/figure/model.wapiti (size: 695735)
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/figure/model.wapiti"
Model path: /opt/grobid/grobid-home/models/figure/model.wapiti
INFO  [2019-04-03 22:19:18,641] org.grobid.core.jni.WapitiModel: Loading model: /opt/grobid/grobid-home/models/table/model.wapiti (size: 1364953)
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/table/model.wapiti"
Model path: /opt/grobid/grobid-home/models/table/model.wapiti
INFO  [2019-04-03 22:19:18,812] org.grobid.core.factory.GrobidPoolingFactory: Number of Engines in pool active/max: 1/10

and after that a docker died...............

How can I make this works in docker? Thanks!

[lfoppiano]

Dear @ohld thank you for reporting this issue.

Could you give me more details about your docker machine? how many CPU and memory?
I have understand correctly you didn't manage to successfully process any file?

Regards
Luca

[lfoppiano]

dear @ohld I've made some tests, and what I have understood is that if there isn't enough memory, the container will die. Unfortunately docker is not explaining much about.

I've made a test with 1Gb memory and I could not process any file, on the other hand if you high it to 4Gb (I don't recall the minimum amount to be honest), it should be fine. Would be good to test if this theory works.

In the meantime I'm pushing a new image with a fix for the tiny (which is not PID 1) warnings.

[ohld]

I have understand correctly you didn't manage to successfully process any file?
Yessir

My docker settings are on a screenshot. Maybe the 2Gb is not enough too. That is sad because it means that I can not run this docker on small machines in the future. Maybe we can minify it somehow? Maybe some alpine docker images can save the memory? (I'm not a docker specialist so maybe my advice can save only the disk space, not RAM).

[ohld]

I just tried to change from Memory: 2.0 GiB to Memory: 4.0 GiB and everything worked fine. I think you should add somewhere that 4.0 GiB RAM is minimum for docker image.

[kermitt2]

Hello! Memory requirements are actually documented in the readme and documentation introduction:

Lazy loading of models and resources. Depending on the selected process, only the required data are loaded in memory. For instance, extracting only metadata header from a PDF requires less than 2 GB memory in a multithreading usage, extracting citations uses around 3GB and extracting all the PDF structure around 4GB. 

So we should make that more visible and link it to the docker documentation, thanks !

[ohld]

Thanks

[lfoppiano]

I'll close when the documentation is updated 👍 and I need to fix the tiny issue (#416 (comment)) and push a new image.