[Swift-user] sort on large data

[Gagan Munisiddha Gowda]

Hi Yadu,

I am in the same direction where I am trying to use a shared file system
(S3 bucket / S3FS).

I have setup : *WORKER_INIT_SCRIPT=/path/to/mounts3fs.sh in
cloud-tutorials/ec2/configs** (as mentioned in the tutorials)*

Though i am able to setup the passwd-s3fs file in the desired location
(using mounts3fs.sh script), i see that the S3 bucket is not getting
mounted.

I have verified the passwd-s3fs file and mount point and all seems to be
created as expected. But, one observation was the owner of these files were
'root' user as it was getting created through the setup.sh.

So, i added more commands to change the permissions and made 'ubuntu' as
the owner for all related files.

Even after all these changes, i see that the S3 bucket is still not mounted.

*PS: If i connect to the workers and run the s3fs command manually, it does
mount !*

sudo s3fs -o allow_other,gid=1000,use_cache=/home/ubuntu/cache <my-bucket>
<mount-point>;

(tried with and without sudo)

Thanks for your help.


On Sun, Oct 19, 2014 at 4:43 AM, Yadu Nand Babuji <yadunand at uchicago.edu>
wrote:

>  Hi Jiada Tu,
>
> 1) Here's an example for returning an array of files :
>
> type file;
> app (file outs[]) make_outputs (file script)
> {
>     bash @script;
> }
>
> file outputs[] <filesys_mapper; prefix="outputs">;
> file script       <"make_outputs.sh">; # This script creates a few files
> with outputs as prefix
> (outputs) = make_outputs(script);
>
> 2) The products of a successful task execution, must be visible to the
> headnode (where swift runs) either through a
> - shared filesystem (NFS, S3 mounted over s3fs etc)  or
> - must be brought back over the network.
> But, we can reduce the overhead in moving the results to the headnode and
> then to the workers for the reduce stage.
>
> I understand that this is part of your assignment, so I will try to answer
> without getting too specific, at the same time,
> concepts from hadoop do not necessarily work directly in this context. So
> here are some things to consider to get
> the best performance possible:
>
> - Assuming that the texts contain 10K unique words, your sort program will
> generate a file containing atmost 10K lines
>  (which would be definitely under an MB). Is there any advantage into
> splitting this into smaller files ?
>
> - Since the final merge involves tiny files, you could very well do the
> reduce stage on the headnode and be quite efficient
>   (you can define the reduce app only for site:local)
>
>   sites : [local, cloud-static]
>   site.local {
>                 ....
>                 app.reduce {
>                         executable : ${env.PWD}/reduce.py
>                 }
>   }
>
>   site.cloud-static {
>                 ....
>                 app.python {
>                         executable : /usr/bin/python
>                 }
>
>  }
>
>  This assumes that you are going to define your sorting app like this :
>
>   app (file freqs) sort (file sorting_script, file input ) {
>        python @sorting_script @input;
>  }
>
>
> - The real cost is in having the original text reach the workers, this can
> be made faster by :
>     - A better headnode with better network/disk IO (I've measured
> 140Mbit/s between m1.medium nodes, c3.8xlarge comes with 975Mbits/s)
>     - Use S3 with S3fs and have swift-workers pull data from S3 which is
> pretty scalable, and remove the IO load from the headnode.
>
> - Identify the optimal size for data chunks for your specific problem.
> Each chunk of data in this case comes with the overhead of starting
>   a new remote task, sending the data and bringing results back. Note that
> the result of a wordcount on a file whether it is 1Mb or 10Gb
>   is still the atmost 1Mb (with earlier assumptions)
>
> - Ensure that the data with the same datacenter, for cost as well as
> performance. By limiting the cluster to US-Oregon we already do this.
>
> If you would like to attempt this using S3FS, let me know, I'll be happy
> to explain that in detail.
>
> Thanks,
> Yadu
>
>
>
> On 10/18/2014 04:18 PM, Jiada Tu wrote:
>
> I am doing an assignment with swift to sort large data. The data contains
> one record (string) each line. We need to sort the records base on ascii
> code. The data is too large to fit in the memory.
>
>  The large data file is in head node, and I run the swift script directly
> on head node.
>
>  Here's what I plan to do:
>
>  1) split the big file into 64MB files
> 2) let each worker task sort one 64MB files. Say, each task will call a
> "sort.py" (written by me). sort.py will output a list of files,
> say:"sorted-worker1-001; sorted-worker1-002; ......". The first file
> contains the records started with 'a', the second started with 'b', etc.
> 3) now we will have all records started with 'a' in
> (sorted-worker1-001;sorted-worker2-001;...); 'b' in
>  (sorted-worker1-002;sorted-worker2-002; ......); ...... Then I send all
> the files contains records 'a' to a "reduce" worker task and let it merge
> these files into one single file. Same to 'b', 'c', etc.
> 4) now we get 26 files (a-z) with each sorted inside.
>
>  Basically what I am doing is simulate Map-reduce. step 2 is map and step
> 3 is reduce
>
>  Here comes some problems:
> 1) for step 2, sort.py need to output a list of files. How can swift app
> function handles list of outputs?
>
>     app (file[] outfiles) sort (file[] infiles) {
>           sort.py // how to put out files here?
>     }
>
>  2) As I know (may be wrong), swift will stage all the output file back
> to the local disk (here is the head node since I run the swift script
> directly on headnode). So the output files in step 2 will be staged back to
> head node first, then stage from head node to the worker nodes to do the
> step 3, then stage the 26 files in step 4 back to head node. I don't want
> it because the network will be a huge bottleneck. Is there any way to tell
> the "reduce" worker to get data directly from "map" worker? Maybe a shared
> file system will help, but is there any way that user can control the data
> staging between workers without using the shared file system?
>
>  Since I am new to the swift, I may be totally wrong and misunderstanding
> what swift do. If so, please correct me.
>
>
>
>
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-- 
Regards,
Gagan
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