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From Supun Nakandala <supun.nakand...@gmail.com>
Subject Re: Airavata Registry Considerations
Date Sun, 07 Jun 2015 17:49:08 GMT
Hi All,

I did the initial POC on the subject and would like to summarize the
findings here.

I used the same Registry CPI and RegistryImpl class tried to use a mongo db
back end  instead of the JPA one. The architecture of the module is as
follows
[image: Inline image 1]
MongoDB stores its internal data in JSON format and we can simply insert
JSON data directly. Therefore I have used a Thrift to JSON conversion layer
and get rid of the additional DB models. The conversion layer is based on a
generic serializer/ deserializer and therefore it is easy to make data
model changes without changing registry. But if we make changes to ID
fields and Indexed -fields those changes has to be updated in the MongoDB
indexes. I see getting rid of the additional DB model classes layer as a
-plus point. This also reduces the developer effort required when
incorporating changes.

One major difference between the current registry data modelling and this
approach is the Experiment model. In the MongoDB based model all related
data to an experiment is stored in the same experiment document. A sample
JSON which gets stored in the database would be similar to this
https://gist.github.com/scnakandala/19fe3c6edf3be3354439. It is possible to
change sub document contents and retrieve sub documents only. eg.
retrieving a specific task. But in this POC I have not used that function.
When updating I have retrieved the entire document update the required
fields in the application logic and update the entire document. The reason
for this is to keep the Dao objects simple as possible and to do the
quickly do the implementation. However it is said the first approach has
slight performance advantages compared to the current approach.

I have push the changes to Airavata git repository under the branch name
"mongo-registry". The implementation is not 100% complete yet but captures
most of the idea.

Things I have not investigated yet

1. Read/Write performance
2. Cluster deployment of MongoDB and Consistency of data

Thanks
Supun




On Fri, May 22, 2015 at 10:33 PM, Suresh Marru <smarru@apache.org> wrote:

> Hi Supun & Supun :)
>
> This is good discussion. I think we need to balance both aspects here. I
> am not at all favoring shoehorning into mongodb and again spend few months
> addressing the unknowns. On the other hand, GSoC is the right time to
> explore alternatives.
>
> My expectation from this document was not so much of criticizing the
> current JPA based implementation. Back then the focus was to adopt thrift
> for the data models (thanks Supun K for the recommendation). Among other
> things, thrift helped us to keep the focus on airavata’s core capabilities
> and quickly unify all the legacy interfaces. The currently JPA registry was
> developed from scratch in a hurry to help with thrift adoption. I think it
> did well and exceeded initial expectations.
>
> We now slowly circled through all the components and made tremendous
> progress. We reduced the internal footprint significantly (rabbitmq in
> favor of WS Messenger, work queues in place of custom co-ordination in
> workflow interpreter and so forth). I think its time to step back and
> re-look at the metadata management needs.
>
> How about we not worry on the implementation costs and focus on what
> criteria we should look into potential solutions and how to profile them?
> We should also include the full JPA based implementation as one of the
> candidates. As both of you said, its important to identify the profiling
> criteria. Chathuri has early work on this, in both the survey paper and
> performance measurements, we probably should revisit them and build from
> there.
>
> Thanks,
> Suresh
>
> On May 22, 2015, at 12:28 PM, Supun Nakandala <supun.nakandala@gmail.com>
> wrote:
>
> Hi Supun,
>
> On Fri, May 22, 2015 at 9:42 PM, Supun Kamburugamuve <supun06@gmail.com>
> wrote:
>
>> Hi Supun,
>>
>> In normal software developments, it is normal to have these kind of
>> slowness. We cannot foresee all the things when we develop. The solution is
>> to improve the performance of important operations rather than re-writing
>> everything from the beginning. For example for this particular select
>> operations you can directly use SQL rather than going through JPA.
>>
>> I'm pretty sure you'll encounter more problems, if you implement this in
>> MongoDB than in the current MySQL. If that happens, do you think abandoning
>> that technology and going for a new database will be a good solution? Now
>> you have more experience with MySQL than MongoDB as well.
>>
>> Rather than going to abandon everything you have because of one problem,
>> trying to fix it may be better for you in the long run.
>>
>> Thanks,
>> Supun..
>>
>> I completely agree with you. Writing things from scratch will need more
> development effort and proper testing. And has the potential of
> incorporating new unknown issues. It is completely possible to fix these
> issues in current registry and I have mentioned that in the doc also.
>
> In addition to that I also checked several other alternatives and found
> MongoDB interesting. I am not saying that we should completely rewrite
> registry using MongoDB. But I think it is worth exploring it at a POC level.
>
>
>> On Fri, May 22, 2015 at 11:49 AM, Supun Nakandala <
>> supun.nakandala@gmail.com> wrote:
>>
>>> Hi Supun,
>>>
>>> I haven't done done profiling of registry based operations. Here what I
>>> mean by slow performance is mainly the slowness of the SELECT operations in
>>> PHP Reference Gateway. e.g fetching Projects, fetching experiments. Even a
>>> simple query to fetch the 20 most recent experiments is embarrassingly slow
>>> in PGA.
>>>
>>> Even though I didn't do a proper profiling of operations I did a query
>>> log analysis for a SELECT experiment query. This was a simple query to
>>> fetch 20 most recent experiments. I found that JPA layer is generating
>>> enormous amount of queries for this task rather than one single query (due
>>> to the select N+1 isssue). This issue is same for fetching a single
>>> experiment by specifying the id.
>>>
>>> I think it is ok to say that current registry has become bottleneck for
>>> most of the PGA specific operations. But I don't have evidence to show how
>>> it has become a bottleneck for the Orchestrator or GFac specific
>>> operations. For that as you have mentioned we need to profile the
>>> operations. But I think the argument is still valid even for GFac and
>>> Orchestrator based operations.
>>>
>>> I have attached the query log for the above mentioned select operation
>>> here with. If you observe the query log you can see that every associated
>>> entity is fetched separately using complex join operations.
>>>
>>>
>>>
>>> On Fri, May 22, 2015 at 8:05 PM, Supun Kamburugamuve <supun06@gmail.com>
>>>  wrote:
>>>
>>>> Hi Supun,
>>>>
>>>> In your report it says Slow performance. Do you have any data about
>>>> this slow performance? For a typical request in what percent the registry
>>>> slow down the processing compared to overall time it takes to execute that
>>>> request?
>>>>
>>>> Do you have a use case where registry is the bottleneck?
>>>>
>>>> Thanks,
>>>> Supun..
>>>>
>>>> On Fri, May 22, 2015 at 9:45 AM, Suresh Marru <smarru@apache.org>
>>>> wrote:
>>>>
>>>>> Hi Supun,
>>>>>
>>>>> This is very good analysis, you have nicely embraced the problem.
>>>>> Before we jump into the solution, we may want to do small POC’s to
validate
>>>>> your claims.
>>>>>
>>>>> Thank you for getting a headstart, this also cuts into GSoC goals of
>>>>> Douglas’s project. So lets work on this collaboratively.
>>>>>
>>>>> Hi Madhu,
>>>>>
>>>>> Can you please provide guidance on this effort on how to academically
>>>>> approach the data management challenges of Airavata. The students might
>>>>> appreciate insights on how to profile and benchmark any possible solutions.
>>>>>
>>>>> Cheers,
>>>>> Suresh
>>>>>
>>>>> On May 22, 2015, at 9:18 AM, Supun Nakandala <
>>>>> supun.nakandala@gmail.com> wrote:
>>>>>
>>>>> Hi Devs,
>>>>>
>>>>> I have compiled a document based on the analysis I did on current
>>>>> registry architecture/technology and possible modification and
>>>>> alternatives. You can find the document at
>>>>> https://docs.google.com/document/d/1XWAQLtdtCf9nTigAz6r5JINHR99bP0oeYaTgeEIVr4w/edit#
>>>>>
>>>>> Thanks
>>>>> Supun
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Supun Kamburugamuva
>>>> Member, Apache Software Foundation; http://www.apache.org
>>>> E-mail: supun06@gmail.com;  Mobile: +1 812 369 6762
>>>> Blog: http://supunk.blogspot.com
>>>>
>>>>
>>>
>>>
>>> --
>>> Thank you
>>> Supun Nakandala
>>> Dept. Computer Science and Engineering
>>> University of Moratuwa
>>>
>>
>>
>>
>> --
>> Supun Kamburugamuva
>> Member, Apache Software Foundation; http://www.apache.org
>> E-mail: supun06@gmail.com;  Mobile: +1 812 369 6762
>> Blog: http://supunk.blogspot.com
>>
>>
>
>
> --
> Thank you
> Supun Nakandala
> Dept. Computer Science and Engineering
> University of Moratuwa
>
>
>


-- 
Thank you
Supun Nakandala
Dept. Computer Science and Engineering
University of Moratuwa

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