Re: Running cTakes in parallel

[Kim Ebert]

Hi Michelle,

If you bring in the patch to LVG you can certainly run multiple
instances of cTAKES in the same JVM instance; however, you cannot run
multiple thread using the same instance. I know in UIMA there are some
methods for running multiple threads using a single instance, and this I
believe will cause issues with LVG, and perhaps other code in cTAKES.

It isn't too hard to grab the LVG source and recompile it to include the
patch.

Thanks,

IMAT Solutions 
Kim Ebert
Software Engineer
Office: 801.669.7342
kim.eb...@imatsolutions.com 
On 02/25/2015 11:57 AM, Michelle Chen wrote:
> Quick question, is it possible to run multiple instances of cTakes in
> parallel?
>
> I'm currently using ctakes-clinical-pipeline's fastPipeline() and wanted to
> run it over multiple documents. Would it be okay to create multiple
> AnalysisEngine? How has other people done this process?
>
> I wasn't sure if this would work because of this Issue
> .
> ---
> Michelle Chen
>
> Massachusetts Institute of Technology
> Electrical Engineering and Computer Science
> B.S. '14, M.Eng. '15
>

Re: Running cTakes in parallel

[Jay Vyas]

We also have a spark implementation in the ctakes sandbox you can use (for up 
to date see jayunit100/SparkStreamingApps on gh).

Sent from my iPhone

> On Feb 25, 2015, at 2:17 PM, Finan, Sean  
> wrote:
> 
> Hi Michelle,
> 
> When it comes to 
>> multiple instances of cTakes in parallel
> You can certainly start as many pipelines as you want as separate JVM 
> processes, just make sure that you divide your notes among separate batches, 
> one batch per process.  Also keep in mind that you don't want to clobber your 
> disk or reserve more ram than you've actually got available.
> 
> We have an UIMA-AS ( http://uima.apache.org/doc-uimaas-what.html ) solution 
> that we have used with cTAKES.  It is a small collection of bash scripts that 
> set up an environment and control processes.  There are also a couple .xml 
> descriptors and configuration files that UIMA-AS needs  At some point it 
> should be cleaned up a bit and checked in to sandbox, but it has been a very 
> low (subgrade) priority for me.  Since you are local you could check out our 
> setup in person if you like.
> 
> Sean
> 
> -Original Message-
> From: michelle1919c...@gmail.com [mailto:michelle1919c...@gmail.com] On 
> Behalf Of Michelle Chen
> Sent: Wednesday, February 25, 2015 2:07 PM
> To: dev@ctakes.apache.org
> Subject: Running cTakes in parallel
> 
> Quick question, is it possible to run multiple instances of cTakes in 
> parallel?
> 
> I'm currently using ctakes-clinical-pipeline's fastPipeline() and wanted to 
> run it over multiple documents. Would it be okay to create multiple 
> AnalysisEngine? How has other people done this process?
> 
> I wasn't sure if this would work because of this Issue 
>   >.
> ---
> Michelle Chen
> 
> Massachusetts Institute of Technology
> Electrical Engineering and Computer Science B.S. '14, M.Eng. '15

RE: Running cTakes in parallel

[Finan, Sean]

Hi Michelle,

When it comes to 
> multiple instances of cTakes in parallel
You can certainly start as many pipelines as you want as separate JVM 
processes, just make sure that you divide your notes among separate batches, 
one batch per process.  Also keep in mind that you don't want to clobber your 
disk or reserve more ram than you've actually got available.

We have an UIMA-AS ( http://uima.apache.org/doc-uimaas-what.html ) solution 
that we have used with cTAKES.  It is a small collection of bash scripts that 
set up an environment and control processes.  There are also a couple .xml 
descriptors and configuration files that UIMA-AS needs  At some point it should 
be cleaned up a bit and checked in to sandbox, but it has been a very low 
(subgrade) priority for me.  Since you are local you could check out our setup 
in person if you like.

Sean

-Original Message-
From: michelle1919c...@gmail.com [mailto:michelle1919c...@gmail.com] On Behalf 
Of Michelle Chen
Sent: Wednesday, February 25, 2015 2:07 PM
To: dev@ctakes.apache.org
Subject: Running cTakes in parallel

Quick question, is it possible to run multiple instances of cTakes in parallel?

I'm currently using ctakes-clinical-pipeline's fastPipeline() and wanted to run 
it over multiple documents. Would it be okay to create multiple AnalysisEngine? 
How has other people done this process?

I wasn't sure if this would work because of this Issue 
.
---
Michelle Chen

Massachusetts Institute of Technology
Electrical Engineering and Computer Science B.S. '14, M.Eng. '15

Running cTakes in parallel

[Michelle Chen]

Quick question, is it possible to run multiple instances of cTakes in
parallel?

I'm currently using ctakes-clinical-pipeline's fastPipeline() and wanted to
run it over multiple documents. Would it be okay to create multiple
AnalysisEngine? How has other people done this process?

I wasn't sure if this would work because of this Issue
.
---
Michelle Chen

Massachusetts Institute of Technology
Electrical Engineering and Computer Science
B.S. '14, M.Eng. '15

URGENT! RE: New Website

[Finan, Sean]

Hi all,

It looks like a few people (myself included) are interested in having 
information on people, projects, papers, and applications that use cTAKES on 
the web page.  I have created a form on google that might help us collect this 
and other information.  Please visit 
https://docs.google.com/forms/d/10ryw42aqkIf2ygjNTa_To1OgGDZzDqHizVg__Jxyuws/viewform?usp=send_form
Most of the form is multiple choice, so it only takes a minute or two to 
complete it.  The more information we have the better we can develop and 
promote cTAKES, so this is very important.

Thank you,
Sean

-Original Message-
From: Mohammad Alodadi [mailto:mso1...@gmail.com] 
Sent: Wednesday, February 25, 2015 2:09 AM
To: dev@ctakes.apache.org
Subject: Re: New Website

I like the look of the new website. 
I was thinking, if someone could collect references of all the research papers, 
that use cTakes in their methodology, in a page and include the link in the use 
cases page, that would be a very great idea to see the different uses of cTakes.

Sincerely,

Mohammad Alodadi


> On Feb 24, 2015, at 8:46 PM, taposh.d@kp.org wrote:
> 
> Hi Michelle -
> 
> The site looks nice. 
> Would it be possible to add link to source via svn or github. 
> Also, case studies would help potential people. 
> 
> Regards,
> 
> Taposh D. Roy
> Health Data Lead
> Decision Support Team
> 
> Kaiser Permanente
> Program Office
> 1950 Franklin Street, 17th Floor
> Oakland, California 94588
> 510-987-4121 (Office)
> 510-206-1633 (cell)
> 
> 
> 
> NOTICE TO RECIPIENT:  If you are not the intended recipient of this 
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> or disclosing its contents.  If you have received this e-mail in 
> error, please notify the sender immediately by reply e-mail and 
> permanently delete this e-mail and any attachments without reading, 
> forwarding or saving them.  Thank you.
> 
> 
> 
> 
> 
> From:   Michelle Chen 
> To: dev@ctakes.apache.org
> Date:   02/24/2015 04:30 PM
> Subject:New Website
> 
> 
> 
> Hello everyone,
> 
> We are planning on publishing the new website on March 2, 2015. Here 
> is the link to the proposed site:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_repos_asf_ctakes_site_new_index.html&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SFiBdOhfH5CdMkKcR10nLGTTP4hqatPnp7nAnpr_ZFw&s=t5Zx2haIAOy9nVTKfqs7L7uRwblbLJ7imHALjP2iMqI&e=
>  .
> (Note: Not all of the pages are fully functional yet, but we figured 
> that this new look is exciting news and wanted feedback.)
> 
> Some ideas for feedback:
> 1. Succinct quotations from users and devs about "How has cTakes 
> helped you?" so that we can populate the "Why cTAKES?" page. (with 
> permission to use information of your name, position, employer, and/or 
> product/project) 2. Use cases (with potential screenshots) of cTAKES 
> to populate the "Examples" page of GUI or other use cases. The 
> "examples" page is in the process of being revamped.
> 3. Mobile feedback: This has not been tested on devices, but what 
> would be needed/useful?
> 4. What is missing from the web page? E.g. FAQs, useful tips. Where 
> are there broken links?
> 6. Anything!
> 
> We welcome any suggestions or code contributions directly the website 
> itself. Look forward to hearing from everyone. Have a great day.
> 
> 
> Sincerely,
> Michelle Chen
> 

Re: New Website

[Murali Nagendranath]

+1

On Wed, Feb 25, 2015 at 7:35 AM, Pei Chen  wrote:

> Looks great...
> +1 to replace the old site!
> I'll take a quick double check on any ASF branding requirements at the same
> time.
>
> On Tue, Feb 24, 2015 at 7:29 PM, Michelle Chen 
> wrote:
>
> > Hello everyone,
> >
> > We are planning on publishing the new website on March 2, 2015. Here is
> the
> > link to the proposed site:
> > http://svn.apache.org/repos/asf/ctakes/site/new/index.html.
> > (Note: Not all of the pages are fully functional yet, but we figured that
> > this new look is exciting news and wanted feedback.)
> >
> > Some ideas for feedback:
> > 1. Succinct quotations from users and devs about "How has cTakes helped
> > you?" so that we can populate the "Why cTAKES?" page. (with permission to
> > use information of your name, position, employer, and/or product/project)
> > 2. Use cases (with potential screenshots) of cTAKES to populate the
> > "Examples" page of GUI or other use cases. The "examples" page is in the
> > process of being revamped.
> > 3. Mobile feedback: This has not been tested on devices, but what would
> be
> > needed/useful?
> > 4. What is missing from the web page? E.g. FAQs, useful tips. Where are
> > there broken links?
> > 6. Anything!
> >
> > We welcome any suggestions or code contributions directly the website
> > itself. Look forward to hearing from everyone. Have a great day.
> >
> >
> > Sincerely,
> > Michelle Chen
> >
>

Re: New Website

[Pei Chen]

Looks great...
+1 to replace the old site!
I'll take a quick double check on any ASF branding requirements at the same
time.

On Tue, Feb 24, 2015 at 7:29 PM, Michelle Chen  wrote:

> Hello everyone,
>
> We are planning on publishing the new website on March 2, 2015. Here is the
> link to the proposed site:
> http://svn.apache.org/repos/asf/ctakes/site/new/index.html.
> (Note: Not all of the pages are fully functional yet, but we figured that
> this new look is exciting news and wanted feedback.)
>
> Some ideas for feedback:
> 1. Succinct quotations from users and devs about "How has cTakes helped
> you?" so that we can populate the "Why cTAKES?" page. (with permission to
> use information of your name, position, employer, and/or product/project)
> 2. Use cases (with potential screenshots) of cTAKES to populate the
> "Examples" page of GUI or other use cases. The "examples" page is in the
> process of being revamped.
> 3. Mobile feedback: This has not been tested on devices, but what would be
> needed/useful?
> 4. What is missing from the web page? E.g. FAQs, useful tips. Where are
> there broken links?
> 6. Anything!
>
> We welcome any suggestions or code contributions directly the website
> itself. Look forward to hearing from everyone. Have a great day.
>
>
> Sincerely,
> Michelle Chen
>