Parallel Join Excessively Slow
1
1
Entering edit mode
@schifferl
Last seen 15 days ago
New York, NY

Within the curatedMetagenomicData package parallelization was used to increase performance. However, after some profiling, it was found that parallelization actually slowed processes down, as compared to similar tasks done in serial. The result is difficult to make sense of and a small example has been constructed here to reproduce the scenario. Any helpful comments would be welcomed.

biocparallel curatedmetagenomicdata parallel dplyr • 866 views
ADD COMMENT
3
Entering edit mode
@martin-morgan-1513
Last seen 18 days ago
United States

Here are several examples that illustrate the cost of parallel evaluation

> library(BiocParallel)
> v = integer(1e8)
> system.time(lapply(1:8, function(i, v) i, v))
   user  system elapsed 
  0.004   0.000   0.001 

Cost of starting up the nodes

> system.time(bplapply(1:8, function(i, v) i))
   user  system elapsed 
  0.148   0.012   0.481 

Cost of transferring data to the workers

> system.time(bplapply(1:8, function(i, v) i, v))
   user  system elapsed 
  0.092   0.476   1.727 

Cost of retrieving data from the workers

> system.time(bplapply(1:8, function(i, v) v, v))
   user  system elapsed 
  0.600   1.704   3.378 

and of course the dominant cost, iteration instead of vectorization

> system.time(1:8)
   user  system elapsed 
      0       0       0 

It seems likely that you've replaced a vectorized calculation with an interation, and are moving large amounts of data to and from the workers.

bpvec() might be a better fit to your needs. And generally, the iteration over n assays implies potentially polynomial scaling, where the first assay is copied in the first iteration, then the first and second assays in the second iteration, then the first, second, and third assays in the third iteration, etc; one would rather develop a more efficient algorithm.

 

ADD COMMENT

Login before adding your answer.

Traffic: 276 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6