[BioC] Bioconductor Cloud AMI

[Martin Morgan]

On 01/01/2013 02:59 AM, Rohmatul Fajriyah wrote:
>
>
> Dear All,
>
> I have a simulation program in R, which I run it in my laptop.
> To produce 1 result, it took about 7 hours and I need about 50, 100, and 500 results.

It's worth asking whether the amount of time to do a simulation seems reasonable 
for the processing power of a modern computer -- maybe there are some 
inefficiencies in your R code that could result in speed-ups of 100-fold or 
more? Probably at a high level you can step through your code and see where the 
obvious bottlenecks are. If that fails, then ?Rprof might be helpful. Also for 
that kind of computing investment it's worth asking whether you are implementing 
your simulation with an appropriate algorithm; perhaps there are ways to 
re-formulate the problem in a more insightful way, leading to both greater 
throughput and perhaps analytic or conceptual insight.

Martin

> (I use Mac OS, Macbook Pro. Hardware specs are 2.9 GHz Dual-Core Intel Core i7 Processor and RAM: 8GB.)
>
> Then I tried to learn and use Cloud Computing, which was ended up with the Bioconductor Cloud AMI.
>
> I took the High-Memory Quadruple Extra Large Instance, API name: m2.4xlarge.
> With the hope that it will make it faster in producing the results.
>
> What happened was the amazon cloud computing produced the result longer than my laptop.
> It took about 8 hours for 1 result.
>
> I am really new to the cloud computing.
> Could you help me to find out, what my mistake was in using/setting the cloud computing, therefore, the result was produce longer than my laptop?
> What should I do to make it faster, please?
>
> For your attention and kindness, thank you very much in advance.
> Happy New Year 2013.
>
> With kind regards,
> R Fajriyah
> 	[[alternative HTML version deleted]]
>
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793