Introduction

To compare the speed of saving and loading R objects to and from MongoDB with or without serialization.

Environment

• OpenVZ with Ubuntu 12.04, i7-2600 CPU @ 3.4GHz, 2 processors, 4G RAM
• Local MongoDB
• Local PostgreSQL
• R 1.14.1
• rmongodb 1.0.3
• RPostgreSQL 0.3-2

Initialize

sudo apt-get install mongodb

Benchmark

```r Test saving object serialized or not { # loading package library(rmongodb) mongo <- mongo.create() if (!mongo.is.connected(mongo)) { stop(“disconnected”) } }

save1 <- function(a) { for(i in 1:repeat.time) { b <- mongo.bson.from.list(list(Rdata = a))
mongo.insert(mongo, “test.save1”, b) } }

load1 <- function() { result <- list() length(result) <- repeat.time cursor <- mongo.find(mongo, “test.save1”) index <- 1 while(mongo.cursor.next(cursor)) { result[[index]] <- mongo.bson.to.list(mongo.cursor.value(cursor)) index <- index + 1 } result }

save2 <- function(a) { for(i in 1:repeat.time) { buf <- mongo.bson.buffer.create() mongo.bson.buffer.append(buf, “Rdata”, serialize(a, NULL, FALSE)) mongo.insert(mongo, “test.save2”, mongo.bson.from.buffer(buf)) } }

load2 <- function() { result <- list() length(result) <- repeat.time cursor <- mongo.find(mongo, “test.save2”) index <- 1 while(mongo.cursor.next(cursor)) { result[[index]] <- unserialize(mongo.bson.value(mongo.cursor.value(cursor), “Rdata”)) index <- index + 1 } result }

repeat.time <- 1000 mongo.drop.database(mongo, “test”) a <- matrix(rnorm(100^2), 100, 100) system.time({ #direct way print(“directly save and load”) save1(a) a.result <- load1() }) system.time({ #serialized way print(“serialized before save and load”) save2(a) a.result2 <- load2() })

I tested many times and notice that the results are very unstable, and
I guess that the serialized way is faster a little bit.

I paste some results here:

rmongodb package (mongo-r-driver) loaded Use ‘help(“mongo”)’ to get started.

[1] TRUE [1] “directly save and load” user system elapsed 1.226 0.083 4.221 [1] “serialized before save and load” user system elapsed 0.746 0.095 3.578 rmongodb package (mongo-r-driver) loaded Use ‘help(“mongo”)’ to get started.

[1] TRUE [1] “directly save and load” user system elapsed 1.227 0.090 3.981 [1] “serialized before save and load” user system elapsed 0.771 0.106 3.327 rmongodb package (mongo-r-driver) loaded Use ‘help(“mongo”)’ to get started.

[1] TRUE [1] “directly save and load” user system elapsed 1.232 0.104 3.808 [1] “serialized before save and load” user system elapsed 0.760 0.110 3.289 rmongodb package (mongo-r-driver) loaded Use ‘help(“mongo”)’ to get started.

[1] TRUE [1] “directly save and load” user system elapsed 1.303 0.078 3.827 [1] “serialized before save and load” user system elapsed 0.763 0.109 3.413 rmongodb package (mongo-r-driver) loaded Use ‘help(“mongo”)’ to get started.

[1] TRUE [1] “directly save and load” user system elapsed 1.237 0.089 3.834 [1] “serialized before save and load” user system elapsed 0.773 0.091 3.458 rmongodb package (mongo-r-driver) loaded Use ‘help(“mongo”)’ to get started.

[1] TRUE [1] “directly save and load” user system elapsed 1.247 0.114 3.970 [1] “serialized before save and load” user system elapsed 0.781 0.110 3.738 rmongodb package (mongo-r-driver) loaded Use ‘help(“mongo”)’ to get started.

[1] TRUE [1] “directly save and load” user system elapsed 1.331 0.142 4.329 [1] “serialized before save and load” user system elapsed 0.753 0.098 3.202 rmongodb package (mongo-r-driver) loaded Use ‘help(“mongo”)’ to get started.

[1] TRUE [1] “directly save and load” user system elapsed 1.217 0.090 3.766 [1] “serialized before save and load” user system elapsed 0.737 0.097 5.339 rmongodb package (mongo-r-driver) loaded Use ‘help(“mongo”)’ to get started.

[1] TRUE [1] “directly save and load” user system elapsed 1.231 0.103 3.875 [1] “serialized before save and load” user system elapsed 0.751 0.105 3.377 rmongodb package (mongo-r-driver) loaded Use ‘help(“mongo”)’ to get started.

[1] TRUE [1] “directly save and load” user system elapsed 1.202 0.085 6.935 [1] “serialized before save and load” user system elapsed 0.752 0.082 3.996 ```