[R-sig-hpc] Parallel linear model

[Dirk Eddelbuettel]

The difference between user and elapsed is an old hat. Here is a great
example (and IIRC first shown here by Simon) with no compute time:

   R> system.time(mclapply(1:8, function(x) Sys.sleep(1)))   ## 2 cores by default
      user  system elapsed 
     0.000   0.012   4.014 
   R> system.time(mclapply(1:8, function(x) Sys.sleep(1), mc.cores=8))
      user  system elapsed 
     0.012   0.020   1.039 
   R> 

so elapsed time is effectively the one second a Sys.sleep(1) takes, plus
overhead, if we allow for all eight (hyperthreaded) cores here.  By Brian
Ripley's choice a default of two is baked-in, so clueless users only get a
small gain.  "user time" is roughly the actual system load _summed over all
processes / threads_.

With that, could I ask any of the participants in the thread to re-try with a
proper benchmarking package such as rbenchmark or microbenchmark?  Either one
beats to the socks of system.time:

   R> library(rbenchmark)
   R> benchmark( mclapply(1:8, function(x) Sys.sleep(1)), mclapply(1:8, function(x) Sys.sleep(1), mc.cores=8), replications=1)
                                                      test replications elapsed relative user.self sys.self user.child sys.child
   1               mclapply(1:8, function(x) Sys.sleep(1))            1   4.013  3.89612     0.000    0.008      0.000     0.004
   2 mclapply(1:8, function(x) Sys.sleep(1), mc.cores = 8)            1   1.030  1.00000     0.004    0.008      0.004     0.000
   R> 

and

   R> library(microbenchmark)
   R> microbenchmark( mclapply(1:8, function(x) Sys.sleep(1)), mclapply(1:8, function(x) Sys.sleep(1), mc.cores=8), times=1)
   Unit: seconds
                                                      expr     min      lq  median      uq     max
   1               mclapply(1:8, function(x) Sys.sleep(1)) 4.01377 4.01377 4.01377 4.01377 4.01377
   2 mclapply(1:8, function(x) Sys.sleep(1), mc.cores = 8) 1.03457 1.03457 1.03457 1.03457 1.03457
   R> 

(and you normally want to run either with 10 or 100 or ... replications /
times).

Dirk

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com