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From Olga Patterson <olga.patter...@utah.edu>
Subject Re: Synchonizing Batches AE and StatusCallbackListener
Date Fri, 21 Apr 2017 18:12:07 GMT
Erik,

My team at the VA have developed an easy way of implementing UIMA AS pipelines and scaling
them to a large number of nodes - using Leo framework that extends UIMA AS 2.8.1. We have
run pipelines on over 200M documents scaled across multiple nodes with dozens of service instances
and it performs great.

Here is some info:
http://department-of-veterans-affairs.github.io/Leo/

The documentation for Leo reflects an earlier version of Leo, but if you are interested in
using it with Java 8 and UIMA 2.8.1, we have not released the latest version in on the VA
github yet but we can share it with you so that you can test it out and possibly provide your
comments back to us.

Leo has simple-to-use functionality for flexible batch read and write and it can work with
any UIMA AEs and existing descriptor files and type system descriptions, so if you already
have a pipeline, wrapping it with Leo would take just a few lines of code.

Let me know if you are interested and I can help you to get started.

Olga Patterson 







-----Original Message-----
From: Jaroslaw Cwiklik <uimaee@gmail.com>
Reply-To: "user@uima.apache.org" <user@uima.apache.org>
Date: Friday, April 21, 2017 at 8:08 AM
To: "user@uima.apache.org" <user@uima.apache.org>
Subject: Re: Synchonizing Batches AE and StatusCallbackListener

    Erik, thanks. This is more clear what you are trying to accomplish. First,
    there are no plans to retire the CPE. It is supported and I don't know of
    any plans to retire it. The only issue is ongoing development. My efforts
    are focused on extending and improving UIMA-AS.
    
    I don't have an answer yet how to handle the CPE crash scenario with
    respect to batching and subsequent restart from the last known good batch.
    Seems like some coordination would be needed to avoid redoing the whole
    collection after a crash. Its been awhile since I've looked at the CPE.
    Will take a look and see what is possible if anything.
    
    There is another Apache UIMA project called DUCC which stands for
    Distributed Uima Cluster Computing. From your email it looks like you have
    a cluster of machines available. Here is a quick description of DUCC:
    
    DUCC is a Linux cluster controller designed to scale out any UIMA pipeline
    for high throughput collection processing jobs as well as for low latency
    real-tme applications. Building on UIMA-AS, DUCC is particularly well
    suited to run large memory Java analytics in multiple threads in order to
    fully utilize multicore machines. DUCC manages the life cycle of all
    processes deployed across the cluster, including non-UIMA processes such as
    tomcat servers or VNC sessions.
    
     You can find more info on this here:
    https://uima.apache.org/doc-uimaducc-whatitam.html
    
    In UIMA-AS batching is an application concern. I am a bit fuzzy on
    implementation so perhaps someone else can comment how to implement
    batching and how to handle errors. You can use a CasMultipler and a custom
    FlowController to manage CASes and react to errors.The UIMA-AS service can
    take an input CAS representing your batch, pass it on to the CasMultiplier,
    generate CASes for each piece of work and deliver results to the
    CasConsumer with a FlowController in the middle orchestrating the flow. I
    defer to application deployment experts to provide you with more detail.
    
    Jerry
    
    
    
    
    
    
    
    On Fri, Apr 21, 2017 at 2:21 AM, Erik Fäßler <erik.faessler@uni-jena.de>
    wrote:
    
    > Hi Jerry,
    >
    > thanks a lot for your answer! I’m sorry that I didn’t make myself clearer.
    > I will try again! :-)
    > Here comes a lot of text, sorry for that. The post actually has two parts:
    > The first explaining my issue, the second responding to the pointer to
    > UIMA-AS.
    >
    > First: Yes, I use a CPE. I process text documents. Tens of millions of
    > them.
    > So, I have the following components to my issue, running with the CPE.
    >
    > 1. A CAS-Consumer (just an AnalysisEngine internally, of course). This
    > consumer is responsible to serialise the document CAS into XMI and send the
    > XMI to a database. It is a XMI-to-database consumer. For performance
    > reasons, the XMI of multiple CASes is buffered and then sent as a batch,
    > lets say, 50 CAS XMIs at a time.
    > 2. A CPE StatusCallbackListener which also writes to the same database,
    > but in another table. It logs into the database which documents have been
    > successfully processed by the CPE. It also works on a batch basis.
    >
    > The goal: The CallbackListener should only mark those documents as
    > successfully processed (i.e. as “finished”) where the CAS-Consumer actually
    > has sent the XMI data to the database.
    >
    > Reason: I don’t want documents marked as “finished” where the XMI data is
    > not in the database but still in the CAS buffer. Because when now the
    > pipeline crashes, the XMI data never gets sent to the database. Then, the
    > processing state is inconsistent: Documents that have not been written into
    > the database are marked as successfully processed. But their data is
    > missing.
    >
    > Also, not each XMI data is stored. There is a condition in the consumer to
    > decide whether the XMI is to be stored or not. Thus, I cannot “create
    > consistency” by checking which XMI made it into the database.
    >
    > Is this better understandable?
    >
    >
    >
    > Regarding UIMA-AS:
    >
    > I tried it out a few years back when it was rather new, UIMA 2.3.1 or
    > something. Back then, it was like the following:
    > 1. Install a broker (or something - ActiveMQ was it called?)
    > 2. Configure it.
    > 3. Start it.
    > 4. For each AE you want to use, deploy the AE on some server in your
    > cluster (multiple AEs can be bundled into an AAE).
    > 5. Start a reader process that will then fill the broker queue.
    > 6. Wait until processing is finished.
    > 7. Stop all the AE services deployed to the cluster, if you want to save
    > the resources.
    > 8. Stop the broker.
    >
    > This was quite a while back so perhaps this is not exactly how it was. But
    > it seemed overly complex to me. I had to login into each server where I
    > wanted work to be done. We have like 20 nodes or something. Perhaps I could
    > write a script for that, but then I would have to keep track of the servers
    > that are free to use at a current time. Because I am not the only one using
    > the cluster.
    > And then I have to stop all AE “services”. Until then, they will use
    > memory because they just idle when there is nothing more to do.
    >
    > In contrast, CPEs are self-contained projects in my case which I can
    > distribute easily through our job system (SLURM).
    >
    > I thought all the setup for UIMA-AS would pay out in better performance.
    > But in my - admittedly limited - tests there was not much of a performance
    > difference. CPEs seemed to be a bit faster due to the lack of CAS
    > serialization between reader and AEs.
    >
    > Of course, this was years in the past. Is the process a bit simpler today?
    > Or perhaps I got it wrong to begin with, that’s possible. But I read the
    > documentation back then and couldn’t see how to do things much simpler.
    >
    > BUT if CPEs can’t solve my issue and UIMA-AS can, then perhaps I will try
    > it again.
    >
    > Another question: You said “CPE was replaced by UIMA-AS”. Does that mean
    > that CPEs will eventually be removed from UIMA? Are they still a part of
    > UIMA 3?
    >
    > Sorry for all the text!
    >
    > Best regards and thanks!
    >
    > Erik
    >
    > > On 20 Apr 2017, at 20:31, Jaroslaw Cwiklik <uimaee@gmail.com> wrote:
    > >
    > > Hi Erik, sorry for a delay responding to your question. This seems like a
    > > CPE question is this right? I am not quite following what is the issue
    > you
    > > are running into. Could you explain this better? With a clearer problem
    > > description perhaps others will jump in with an answer  :)
    > >
    > > Just FYI, the CPE was replaced by the UIMA-AS quite a long time ago.
    > > Perhaps UIMA-AS can work better for you. You can read about it here:
    > > https://uima.apache.org/d/uima-as-2.9.0/uima_async_scaleout.html
    > >
    > > Jerry
    > > UIMA Team
    > >
    > > On Tue, Apr 18, 2017 at 5:56 AM, Erik Fäßler <erik.faessler@uni-jena.de>
    > > wrote:
    > >
    > >> Hi all,
    > >>
    > >> I have a use case where a consumer of mine sends CAS XMI data into a
    > >> database in batchProcessComplete(). I also use a StatusCallbackListener
    > >> that logs into the database whether a document has been completed
    > >> processing, this is also done batch wise.
    > >> Now the issue is, if the pipeline crashes for any reason, I must start
    > >> over because the “completion” flag from the CallbackListener and the
    > data
    > >> actually sent by the XMI consumer is not synchronised, i.e. I don’t
    > know if
    > >> the data has actually been sent for a document that has completed
    > >> processing because everything is done batch-wise and not immediately for
    > >> performance reasons. I also cannot just look into the database which XMI
    > >> data is there because it only gets sent on a met condition.
    > >>
    > >> I would like to somehow communicate between the consumer and the
    > >> CallbackListener to send their data for the same documents in
    > agreement. Is
    > >> there anything I can do to achieve this?
    > >>
    > >> Best,
    > >>
    > >> Erik
    >
    >
    

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