We publish R tutorials from scientists at academic and scientific institutions with a goal to give everyone in the world access to a free knowledge. Our tutorials cover different topics including statistics, data manipulation and visualization!

Data Management

After using R for a few years people come to realize how inefficient loops are (in all languages), even after pre-allocating memory. Then you begin to use the apply functions and revel at their speed. However, once you have datasets > 10-15 million the apply family can begin to creep along (relative to the amount of logic in your function). Luckily, most datasets I work with are between 1 – 5 million records and do not encounter performance issues too often. However, when we do run into large datasets we have our parallel packages.

While writing this demo from my home laptop I was not seeing performance gains in parallel, because I was running out of RAM to maximize the efficiency of parallel processing. Therefore, I decided to checkout Google’s Cloud and was quite happy with the aesthetics and performance of their platform. Now, I do not work for Google, but it is worth checking out their trial.

custom (8 vCPUs, 32 GB memory)

Most programmers know to try and avoid loops whenever possible because of they are extremely resource intensive. However, with languages such as R, the majority of the time spent is manipulating the dataset. Oftentimes this includes cleaning and feature engineering which requires user-defined functions. If you have less than 10,000 observations and the function is not overly complex then for loops are fine. The example below processes 150 observations in three hundredth of a second.

IrisClassifier <- function(df,i){ if(df[1][i,] >= 5.8 & df[4][i,] >= 1.8){ return('virginica') }else if(df[1][i,] <= 5.7 & df[4][i,] <= 1){ return('setosa') }else{ return('versicolor') } } iris$Check <- '' system.time( for(i in 1:nrow(iris)){ iris$Check[i] <- IrisClassifier(iris,i) } )

User Time | System Time | Elapsed Time |
---|---|---|

0.03 | 0.00 | 0.03 |

How does the apply family speed up our functions? It converts a scalar (single item) process to a vector (array) process. Think of a mill having to cut lumber piece-by-piece or having one large saw and applying it to all of the lumber at once.

IrisClassifier <- function(col1,col2){ if(col1 >= 5.8 & col2 >= 1.8){ return('virginica') }else if(col1 <= 5.7 & col2 <= 1){ return('setosa') }else{ return('versicolor') } } system.time(iris$Check <- mapply(psuedoClassifier,iris[,1],iris[,4]))

User Time | System Time | Elapsed Time |
---|---|---|

0.00 | 0.00 | 0.00 |

Required Libraries:

library(doSNOW) library(foreach) library(data.table) library(sqldf) library(ggplot2)

For this example we will be using a simple dataset starting with 1,000,000 million observations and increment by 1,000,000 to 30,000,000 million observations. The entire script is located at the end of this example.

df <- df <- data.frame(a = round(rnorm(values[i],mean = 18,sd = 10),0), b = round(rnorm(values[i],mean = 10,sd = 11),0), c = round(rnorm(values[i],mean = 400,sd = 44),0), d = round(rnorm(values[i],mean = 100,sd = 33),0), e = round(rnorm(values[i],mean = 11,sd = 3),0), f = round(rnorm(values[i],mean = 223,sd = 1000),0) )

For this example we will use the `mapply`

to show how to apply a function with multiple parameters. I find most articles online only demonstrating how to apply with one parameter so I used this as an excuse to demonstrate applying a function with multiple parameters.

unspirited.func <- function(a,b,c,d,e,f){ if(a > 20 & b 300 & c 30 & log(c)> 6) { return('Fail - A') }else if(b > 38 & log(c)> 6) { return('Fail- B') }else if(d > 175 & log(c)> 6) { return('Fail - D') }else if(e > 18 & log(c)> 6) { return('Fail - E') }else if(f > 1989 & log(c)> 6) { return('Fail - F') }else{ return('Unsure') } }

Type | Number of Observations | Elapsed Time |
---|---|---|

Loop | 50000 | 24.593 |

mapply | 50000 | 0.536 |

Loop | 100000 | 59.314 |

mapply | 100000 | 1.228 |

Loop | 150000 | 117.658 |

mapply | 150000 | 1.865 |

Loop | 200000 | 209.694 |

mapply | 200000 | 2.658 |

Loop | 250000 | 317.212 |

mapply | 250000 | 3.283 |

Loop | 300000 | 521.578 |

mapply | 300000 | 3.816 |

Loop | 350000 | 615.212 |

mapply | 350000 | 4.625 |

Loop | 400000 | 854.06 |

mapply | 400000 | 5.571 |

Loop | 450000 | 928.809 |

mapply | 450000 | 6.437 |

Loop | 500000 | 1210.446 |

mapply | 500000 | 7.179 |

**Parallel Operations**

Luckily most current laptops, pcs, and cloud machines all offer multiple cores of processing power. Therefore, how does parallel processing work? Essentially, R starts up **n** number of instances and sends subsets of the original data to be processed in those instances using its own processing core, and then finally returning the results back together.

Type | Number of Observations | Elapsed Time |
---|---|---|

mapply | 1000000 | 14.851 |

Parallel-2 | 1000000 | 13.641 |

Parallel-3 | 1000000 | 9.407 |

Parallel-4 | 1000000 | 8.741 |

Parallel-5 | 1000000 | 8.326 |

Parallel-6 | 1000000 | 8.977 |

mapply | 5000000 | 95.012 |

Parallel-2 | 5000000 | 64.179 |

Parallel-3 | 5000000 | 49.724 |

Parallel-4 | 5000000 | 42.357 |

Parallel-5 | 5000000 | 40.959 |

Parallel-6 | 5000000 | 40.204 |

mapply | 10000000 | 198.36 |

Parallel-2 | 10000000 | 137.413 |

Parallel-3 | 10000000 | 108.221 |

Parallel-4 | 10000000 | 91.929 |

Parallel-5 | 10000000 | 87.314 |

Parallel-6 | 10000000 | 87.57 |

mapply | 15000000 | 304.673 |

Parallel-2 | 15000000 | 209.789 |

Parallel-3 | 15000000 | 162.592 |

Parallel-4 | 15000000 | 138.99 |

Parallel-5 | 15000000 | 135.785 |

Parallel-6 | 15000000 | 132.459 |

mapply | 20000000 | 411.984 |

Parallel-2 | 20000000 | 292.82 |

Parallel-3 | 20000000 | 224.262 |

Parallel-4 | 20000000 | 186.6 |

Parallel-5 | 20000000 | 184.216 |

Parallel-6 | 20000000 | 179.269 |

mapply | 25000000 | 529.586 |

Parallel-2 | 25000000 | 373.688 |

Parallel-3 | 25000000 | 282.885 |

Parallel-4 | 25000000 | 238.923 |

Parallel-5 | 25000000 | 229.101 |

Parallel-6 | 25000000 | 227.555 |

Parallel-2 | 30000000 | 451.788 |

Parallel-3 | 30000000 | 349.257 |

Parallel-4 | 30000000 | 286.526 |

Parallel-5 | 30000000 | 277.594 |

Parallel-6 | 30000000 | 274.735 |

**Considerations**

- Required Setup time
- Parallel will end up using more RAM
- Shared server resources

After hearing Max Kuhn speak a few years ago he said always check to see if someone has already written the function you are coding. After, writing this post I did stumble upon some builtin in parallel apply functions. However, I have not researched exactly how these operate.

**The Entire Script**

############################################################################################################################### # Name : Parallel Process Example # Date : 2016-09-03 # Author : Christopher M # Dept : Business Analytics # Purpose : ~ ############################################################################################################################### # ver user date(YYYYMMDD) change # 1.0 ~ 20160903 initial ############################################################################################################################### library(parallel) library(ggplot2) ## Display number of CPU cores on host detectCores(all.tests = FALSE, logical = TRUE) ## Example function for processing unspirited.func <- function(a,b,c,d,e,f){ if(a > 20 & b 300 & c 30 & log(c)> 6) { return('Fail - A') }else if(b > 38 & log(c)> 6) { return('Fail- B') }else if(d > 175 & log(c)> 6) { return('Fail - D') }else if(e > 18 & log(c)> 6) { return('Fail - E') }else if(f > 1989 & log(c)> 6) { return('Fail - F') }else{ return('Unsure') } } ## kfold function to split data for parallel processing kfold <- function(df,k){ require(sqldf) if( length(which(colnames(df)=='folds'))>0){ stop(print('Rename column(s) named folds')) break } #randomize the data df<-sqldf("SELECT * FROM df order by random()") #Create equally size folds df$folds <- cut(seq(1,nrow(df)),breaks=k,labels=FALSE) return(df) } ## function for parallel processing parallelApply <- function(df,cols,func,cores){ require(doSNOW) require(foreach) require(data.table) cl <- makeCluster(cores, type="SOCK") registerDoSNOW(cl) ## Create ID to compute in parallel df <- kfold(df,cores) ## Process data in parallel system.time(NewDataFrame <- foreach(i = 1:cores) %dopar% { tmpdata <- subset(df, folds == i) mapply(func,tmpdata[,cols[1]],tmpdata[,cols[2]],tmpdata[,cols[3]],tmpdata[,cols[4]],tmpdata[,cols[5]],tmpdata[,cols[6]]) }) ## Bind data back into dataframe NewDataFrame <- rbindlist(Map(as.data.frame, NewDataFrame)) colnames(NewDataFrame) <- c('ParRow') df <- cbind(df,NewDataFrame) stopCluster(cl) return(df) } ## values for dataframe length values <- seq(1e6,30e6,1e6) capture <- data.frame() for(i in 1:length(values)){ print(paste("processing:",values[i],"rows. There are",length(values)-i,"iterations left to complete")) df <- data.frame(a = round(rnorm(values[i],mean = 18,sd = 10),0), b = round(rnorm(values[i],mean = 10,sd = 11),0), c = round(rnorm(values[i],mean = 400,sd = 44),0), d = round(rnorm(values[i],mean = 100,sd = 33),0), e = round(rnorm(values[i],mean = 11,sd = 3),0), f = round(rnorm(values[i],mean = 223,sd = 1000),0) ) ##______________________________________________________________________________ ## Apply performance <- system.time(df$Check <- mapply(unspirited.func,df[,1],df[,2],df[,3],df[,4],df[,5],df[,6])) capture <- rbind(capture,data.frame(Type = 'mapply',Rows = values[i],elapsed = performance[3],PercentDifference = 1)) df$Check <- NULL print('finished') print(capture) ##______________________________________________________________________________ ## Parallel Apply base <- as.numeric(subset(capture,Rows == values[i] & Type == 'mapply')[3]) for(x in 2:6){ print(paste('running on',x,'cores')) performance <- system.time(df <- parallelApply(df,c(1,2,3,4,5,6),unspirited.func,x)) capture <- rbind(capture,data.frame(Type = paste('Parallel-',x,sep=''),Rows = values[i],elapsed = performance[3], PercentDifference = abs(1-(performance[3]/base)))) df$ParRow <- NULL df$folds <- NULL } gc() print(capture) } options(scipen=999) ## Example plots ggplot(subset(capture,Type != 'Loop'),aes(Rows,elapsed,color = Type))+ geom_line( aes(linetype=Type))+ geom_point(size=3 )+ ylab("elapsed (seconds)") + geom_text(data=subset(capture,Rows ==max(capture$Rows)), aes(label=Type))+ ggtitle("Mapply ~ Parallel") tmp <- subset(capture,Type != 'mapply') tmp$PercentDifference <- tmp$PercentDifference + 1 mapply <- subset(capture,Type == 'mapply') capture_ <- rbind(tmp,mapply) ggplot(subset(capture_,Type != 'Loop'),aes(Rows,PercentDifference,color = Type))+ geom_line( aes(linetype=Type))+ geom_point(size=3 )+ ylab("Performance Increase") + ggtitle("Mapply ~ Parallel") + scale_x_continuous(breaks = seq(5e6,30e6,5e6))+ scale_y_continuous(breaks = seq(0,3,.1))