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RE: How to best decide mapper output/reducer input for a huge string?
You might try creating a "stub" MR job in which the mappers produce no output; that would isolate the time spent reading from HBase without the trouble of instrumenting your code.
From: Pavan Sudheendra [mailto:[EMAIL PROTECTED]]
Sent: Monday, September 23, 2013 3:31 AM
Subject: Re: How to best decide mapper output/reducer input for a huge string?

@John, to be really frank i don't know what the limiting factor is.. It might be all of them or a subset of them.. Cannot tell..

On Mon, Sep 23, 2013 at 2:58 PM, Pavan Sudheendra <[EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>> wrote:
@Rahul, Yes you are right. 21 mappers are spawned where all the 21 mappers are functional at the same time.. Although, @Pradeep, i should do the compression like you say.. I'll give it a shot.. As far as i can see, i think i'll need to implement Writable and write out the key of the mapper using the specific data types instead of writing it out as a string which might slow the operation down..

On Mon, Sep 23, 2013 at 9:29 AM, Pradeep Gollakota <[EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>> wrote:

It's hard to tell whether there's anything wrong with your design or not since you haven't given us specific enough details. The best thing you can do is instrument your code and see what is taking a long time. Rahul mentioned a problem that I myself have seen before, with only one region (or a couple) having any data. So even if you have 21 regions, only mapper might be doing the heavy lifting.

A combiner is hugely helpful in terms of reducing the data output of mappers. Writing a combiner is a best practice and you should almost always have one. Compression can be turned on by setting the following properties in your job config.
    <name> mapreduce.map.output.compress </name>
    <value> true</value>
You can also try other compression codes such as Lzo, Snappy, Bzip2, etc. depending on your use cases. Gzip is really slow but gets the best compression ratios. Snappy/Lzo are a lot faster but don't have as good of a compression ratio. If your computations are CPU bound, then you'd probably want to use Snappy/Lzo. If your computations are I/O bound, and your CPUs are idle, you can use Gzip. You'll have to experiment and find the best settings for you. There are a lot of other tweaks that you can try to get the best performance out of your cluster.

One of the best things you can do is to install Ganglia (or some other similar tool) on your cluster and monitor usage of resources while your job is running. This will tell you if your job is I/O bound or CPU bound.

Take a look at this paper by Intel about optimizing your Hadoop cluster and see if that fits your deployment. http://software.intel.com/sites/default/files/m/f/4/3/2/f/31124-Optimizing_Hadoop_2010_final.pdf

If your cluster is already optimized and your job is not I/O bound, then there might be a problem with your algorithm and might warrant a redesign.

Hope this helps!
- Pradeep

On Sun, Sep 22, 2013 at 8:14 PM, Rahul Bhattacharjee <[EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>> wrote:
One mapper is spawned per hbase table region. You can use the admin ui of hbase to find the number of regions per table. It might happen that all the data is sitting in a single region , so a single mapper is spawned and you are not getting enough parallel work getting done.
If that is the case then you can recreate the tables with predefined splits to create more regions.

On Sun, Sep 22, 2013 at 4:38 AM, John Lilley <[EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>> wrote:
How large are the rows in HBase?  22 million rows is not very much but you mentioned "huge strings".  Can you tell which part of the processing is the limiting factor (read from HBase, mapper output, reducers)?
From: Pavan Sudheendra [mailto:[EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>]
Sent: Saturday, September 21, 2013 2:17 AM
Subject: Re: How to best decide mapper output/reducer input for a huge string?

No, I don't have a combiner in place. Is it necessary? How do I make my map output compressed? Yes, the Tables in HBase are compressed.
Although, there's no real bottleneck, the time it takes to process the entire table is huge. I have to constantly check if i can optimize it somehow..
Oh okay.. I'll implement a Custom Writable.. Apart from that, do you see any thing wrong with my design? Does it require any kind of re-work? Thank you so much for helping..

On Sat, Sep 21, 2013 at 1:06 PM, Pradeep Gollakota <[EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>> wrote:
One thing that comes to mind is that your keys are Strings which are highly inefficient. You might get a lot better performance if you write a custom writable for your Key object using the appropriate data types. For example, use a long (LongWritable) for timestamps. This should make (de)serialization a lot faster. If HouseHoldId is an integer, your speed of comparisons for sorting will also go up.

Ensure that your map output's are being compressed. Are your tables in HBase compressed? Do you have a combiner?

Have you been able to profile your code to see where the bottlenecks are?

On Sat, Sep 21, 2013 at 12:04 AM, Pavan Sudheendra <[EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>> wrote:
Hi Pradeep,
Yes.. Basically i'm only writing the key part as the map output.. The V of <K,V> is not of much use to me.. But i'm hoping to change that if it leads to faster execution.. I'm kind of a newbie so looking to make the map/reduce job run a lot faster..
Also, yes. It gets sorted by the HouseHoldID which is what i needed.. But seems if i write a map output for each and every row of a 19 m row HBase table, its taking nearly a day to complete