I haven't made our code available, Sorry. Not sure if I can. But from my description, you should find it pretty easy. I started by extending a GenericObjectPool and going from there. As each instance is instantiated, I re-read the piper file - creating a new engine which is assigned to a Pool member.
Peter On Sat, Mar 9, 2019 at 9:20 AM Jeffrey Miller <jeff...@gmail.com> wrote: > Thanks for your response Sean- we are still working on this (and have some > things to look into given your last response), but I will share details > when we have it working. We are still deciding on whether to use Spark or > Apache Beam. > > Just to clarify my previous confusion, I assumed the TS wrappers were so > you could avoid creating multiple pipelines and just run one instance of > the pipeline with a separate JCAS per thread. I thought the main motivation > behind that would be to avoid loading >1 dictionaries into memory, for > example. But it sounds like I was mistaken. With respect to sharing > resources, are static variables the main concern? Do you know if this is a > problem for any of the annotators in the default clinical pipeline (the > regular components, not the thread safe ones)? From Peter's response (I am > not sure if that split off into another forum thread because the subject > changed), it sounds like it may not be a problem? I'd like to really > understand thread-safe with respect to core cTAKES components (with the > caveat that community-created annotators could be implemented in any number > of ways, making it hard to declare cTAKES is "thread-safe"). I'd be happy > to contribute documentation back to the wiki once I feel I have a solid > grasp on it. > > Peter- have you made your pipeline pool code available anywhere? > > On Fri, Mar 8, 2019 at 12:49 PM Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > > Hi all, > > > > >Is there any known reason that you can't create a pipeline pool, but > keep > > everything in the same process? > > -- No, but ... > > > Is it safe to load multiple pipelines in > > the same process as long as only one thread can access each one at a time > > (we plan to use this in a Spark pipeline). > > -- If you are talking about oob ctakes being the process, only a single > > pipeline will run on multiple threads. The threads will share resources, > > static variables, etc. and the pipeline will give you terrible results > and > > very quickly crash. That is why I wrote the thread-safe wrappers. > > -- That being said, supposedly you can configure spark to handle this by > > keeping everything contained in a unique copy per thread. Sort of like > > ThreadLocal (I think), but more effective on a full-pipeline level. > > > > > it must have reduced the DefaultJCasTermAnnotator to a singleton object > > in memory. > > -- Yes. The thread-safe pipeline is not meant to have siblings in the > > same process - the wrappers can only do so much. That being said, I am > > pretty sure that the Default... is thread-safe so it doesn't actually > need > > the wrapper. Regardless, the rest of the pipeline would crash. > > > > Jeff, can you share information about your efforts on spark? If we could > > get that working and in standard ctakes it would be fantastic. > > > > I hope that this information is useful. > > > > Sean > > > > > > > > ________________________________________ > > From: Jeffrey Miller <jeff...@gmail.com> > > Sent: Friday, March 8, 2019 11:23 AM > > To: dev@ctakes.apache.org > > Subject: Re: ctake web service [EXTERNAL] > > > > Is there any known reason that you can't create a pipeline pool, but keep > > everything in the same process? Is it safe to load multiple pipelines in > > the same process as long as only one thread can access each one at a time > > (we plan to use this in a Spark pipeline). One caveat I have noticed- it > > seems like if I use the thread safe components to build a pipeline pool, > > only one dictionary for the DefaultJCasTermAnnotator can be loaded per > > process. For example, I was trying to take advantage of the ability to > > switch pipelines via a query parameter that is suggested at in the code > for > > the rest service. The two pipelines used different ontology dictionaries, > > but it seemed like with the thread safe components it must have reduced > > the DefaultJCasTermAnnotator to a singleton object in memory, because it > > only used the first dictionary instantiated. Either way, given how Sean > > described how the thread safe components worked above, you probably > > wouldn't want to use them in a pipeline pool, assuming that the problems > > with threading was limited to multiple threads access the same pipeline > at > > the same time, and not having multiple pipelines loaded into memory each > > accessed by only a single thread. > > > > On Fri, Mar 8, 2019 at 11:06 AM Kathy Ferro <healthcare1...@gmail.com> > > wrote: > > > > > I thought about creating a queue that acts as traffic cop. Only the > > > traffic cop calls the WS. I also want to test multiple WS running on > > > different port. Traffic cop calls which every WS is available and keep > > > track of WS statuses. With all this processing going, it might kill > the > > > power for blocks. > > > > > > On Fri, Mar 8, 2019 at 10:34 AM Finan, Sean < > > > sean.fi...@childrens.harvard.edu> wrote: > > > > > > > Hi all, > > > > > > > > I guess that a quick test could be run with a multi-threaded > pipeline. > > > > Tim, for some reason I recall you checking in one with a dockerfile. > > > Maybe > > > > not, and it might not be the default in the service. Anyway, you > could > > > set > > > > the procs to something like 50 and throw 50 users at it. It > definitely > > > > does not scale anything close to linearly. ctakes aes aren't build > for > > > > thread-safety, so they are all wrapped with locks and there is a lot > of > > > > thread contention. However, running such a test might indicate the > > > source > > > > of the problem. > > > > > > > > The other option is to create a queue that collects post calls and > > doles > > > > them out serially to a single pipeline. User #50 would probably not > > > > appreciate it though ... > > > > ________________________________________ > > > > From: gandhi rajan <gandhiraja...@gmail.com> > > > > Sent: Friday, March 8, 2019 10:02 AM > > > > To: dev@ctakes.apache.org > > > > Subject: Re: ctake web service [EXTERNAL] > > > > > > > > Hi Kathy, > > > > > > > > I guess the initializations happens in post construct method. So if > we > > > > could synchronize that I feel we can get away from the problem. > > > > Unfortunately I m not able to tet this as my setup is gone with my > old > > > job. > > > > Try it out. > > > > > > > > Regards, > > > > Gandhi. > > > > > > > > On Friday, March 8, 2019, Kathy Ferro <healthcare1...@gmail.com> > > wrote: > > > > > > > > > Tim, > > > > > > > > > > Thanks for reply. I'm continuing the research. With all the > layers > > > that > > > > > wrap around this, you would think we can handle this suggestion. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy < > > > > > timothy.mil...@childrens.harvard.edu> wrote: > > > > > > > > > > > That's a good question that I've also heard from others, and > > > > > unfortunately > > > > > > I don't know the answer. My use cases are typically a single job > > at a > > > > > time > > > > > > making sequential calls, so I wasn't stressing it with multiple > > > > > > asynchronous calls. I would've thought that the Tomcat container > > > would > > > > > have > > > > > > some ability to manage that though! > > > > > > Tim > > > > > > > > > > > > ________________________________________ > > > > > > From: Kathy Ferro <healthcare1...@gmail.com> > > > > > > Sent: Thursday, March 7, 2019 6:10 PM > > > > > > To: dev@ctakes.apache.org > > > > > > Subject: Re: ctake web service [EXTERNAL] > > > > > > > > > > > > Tim, > > > > > > > > > > > > Does docker solution handle multiple instances? I tested the > Rest > > > Web > > > > > > Service with 2 requests at the same time, it errors out. I > removed > > > the > > > > > > part that write the result xml file to the disc; it still error > > out. > > > > > > > > > > > > Best, > > > > > > Kathy > > > > > > > > > > > > On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy < > > > > > > timothy.mil...@childrens.harvard.edu> wrote: > > > > > > > > > > > > > I don't know what the solution was, but I leave my ctakes REST > > > server > > > > > > > running basically full time and haven't seen time outs yet. > > > > > > > Tim > > > > > > > > > > > > > > ________________________________________ > > > > > > > From: gandhi rajan <gandhiraja...@gmail.com> > > > > > > > Sent: Monday, March 4, 2019 10:43 AM > > > > > > > To: dev@ctakes.apache.org > > > > > > > Subject: Re: ctake web service [EXTERNAL] > > > > > > > > > > > > > > Hi Kathy, Sean did respond that there is no timeout happening > > from > > > > > cTAKES > > > > > > > end. You might probably have to look at database settings for > > this > > > > > closed > > > > > > > connection issue. > > > > > > > > > > > > > > Does someone have any clue on this? > > > > > > > > > > > > > > On Monday, March 4, 2019, Kathy Ferro < > healthcare1...@gmail.com> > > > > > wrote: > > > > > > > > > > > > > > > Gandhi, > > > > > > > > > > > > > > > > Do you get any response to this issue? Does it try to keep > the > > > > > > > connection > > > > > > > > open while WS is up? Or does it open and close after it's > done? > > > > > > > > > > > > > > > > We are still getting this error. > > > > > > > > "ERROR JdbcRareWordDictionary - No operations allowed after > > > > statement > > > > > > > > closed." > > > > > > > > > > > > > > > > Thanks > > > > > > > > Kathy > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Fri, Aug 17, 2018 at 9:43 AM Gandhi Rajan Natarajan < > > > > > > > > gandhi.natara...@arisglobal.com> wrote: > > > > > > > > > > > > > > > > > Hi Kathy, > > > > > > > > > > > > > > > > > > Sometime back we encountered this issue and the problem > seems > > > to > > > > be > > > > > > DB > > > > > > > > > connections getting timed out. > > > > > > > > > > > > > > > > > > Currently we are using the following implementations: > > > > > > > > > > > > > > > > "org.apache.ctakes.dictionary.lookup2.dictionary. > > > > > JdbcRareWordDictionary" > > > > > > > > > and "org.apache.ctakes.dictionary.lookup2.concept. > > > > > JdbcConceptFactory" > > > > > > > > > > > > > > > > > > Does anybody aware of any timeout settings that needs to be > > > done > > > > in > > > > > > > these > > > > > > > > > implementations to avoid DB connection timeout issue? > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > > > From: Kathy Ferro <healthcare1...@gmail.com> > > > > > > > > > Sent: Thursday, August 16, 2018 11:07 PM > > > > > > > > > To: dev@ctakes.apache.org > > > > > > > > > Subject: ctake web service > > > > > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > > > > > Just want to see if anybody has experience this issue. > > > > > > > > > > > > > > > > > > If the web service had been up for a day or two, it will > drop > > > the > > > > > > > > > dictionary lookup. The only result it returns are > > > > > > ConllDependencyNode > > > > > > > > tag > > > > > > > > > in the xmi file; no mention, no concept, etc... > > > > > > > > > > > > > > > > > > I haven't have a chance to investigate it, yet. > > > > > > > > > > > > > > > > > > Kathy > > > > > > > > > This email and any files transmitted with it are > confidential > > > and > > > > > > > > intended > > > > > > > > > solely for the use of the individual or entity to whom they > > are > > > > > > > > addressed. > > > > > > > > > If you are not the named addressee you should not > > disseminate, > > > > > > > distribute > > > > > > > > > or copy this e-mail. Please notify the sender or system > > manager > > > > by > > > > > > > email > > > > > > > > > immediately if you have received this e-mail by mistake and > > > > delete > > > > > > this > > > > > > > > > e-mail from your system. If you are not the intended > > recipient > > > > you > > > > > > are > > > > > > > > > notified that disclosing, copying, distributing or taking > any > > > > > action > > > > > > in > > > > > > > > > reliance on the contents of this information is strictly > > > > prohibited > > > > > > and > > > > > > > > > against the law. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > Regards, > > > > > > > Gandhi > > > > > > > > > > > > > > "The best way to find urself is to lose urself in the service > of > > > > others > > > > > > > !!!" > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > Regards, > > > > Gandhi > > > > > > > > "The best way to find urself is to lose urself in the service of > others > > > > !!!" > > > > > > > > > >
