Type:	Package
Title:	Parallel Random Number Generation on GPU
Description:	Builds on 'gpuR' and utilizes the 'clRNG' ('OpenCL') library to provide efficient tools to generate independent random numbers in parallel on a GPU and save the results as 'R' objects, ensuring high-quality random numbers even when 'R' is used interactively or in an ad-hoc manner. Includes Fisher's simulation method adapted from Patefield, William M (1981) <doi:10.2307/2346669> and 'MRG31k3p' Random Number Generator from 'clRNG' library by Advanced Micro Devices, Inc. (2015) https://github.com/clMathLibraries/clRNG.
Version:	0.0.5
Date:	2024-07-11
Maintainer:	Ruoyong Xu <ruoyong.xu@mail.utoronto.ca>
License:	GPL-3
Encoding:	UTF-8
NeedsCompilation:	yes
Depends:	R (≥ 3.5.0), gpuR
Suggests:	knitr
LinkingTo:	RViennaCL, Rcpp, gpuR, RcppEigen
OS_type:	unix
VignetteBuilder:	knitr
RoxygenNote:	7.3.2
Packaged:	2024-07-12 15:56:59 UTC; ruoyong
Author:	Ruoyong Xu [cre, aut, ctb], Patrick Brown [aut, ctb], Advanced Micro Devices, Inc. [cph] (Copyright holder of clRNG library code)
Repository:	CRAN
Date/Publication:	2024-07-16 09:00:02 UTC

createStreamsCpu

Description

Create streams stored on the CPU.

Usage

createStreamsCpu(n = prod(getOption("clrng.Nglobal")))

Arguments

Value

an R matrix of streams on CPU.

Examples

library(clrng)
if (detectGPUs() >= 1) {
  t(createStreamsCpu(n=5))
  ## GPU streams
  myStreamsGpu = vclMatrix(createStreamsCpu(n=4)) }else {
  message("No GPU context available")
}

createStreamsGpu

Description

Generate streams on a GPU device

Usage

createStreamsGpu(n = prod(getOption("clrng.Nglobal")))

Arguments

Value

a stream object of class 'vclMatrix' on GPU

Examples

library(clrng)
if (detectGPUs() >= 1) {
 setBaseCreator(rep(12345,6))
 setContext(grep("gpu", listContexts()$device_type)[1])
 myStreamsGpu = createStreamsGpu(4)
 t(as.matrix(myStreamsGpu))

 myStreamsGpu2 = createStreamsGpu(6)
 t(as.matrix(myStreamsGpu2)) }else {
  message("No GPU context available")
}

fisher.sim

Description

Performs Monte carlo's simulation for Fisher's exact test on GPU.

Usage

fisher.sim(
  x,
  N,
  streams,
  Nglobal = getOption("clrng.Nglobal"),
  type = getOption("clrng.type"),
  returnStatistics = FALSE,
  verbose = FALSE
)

Arguments

Value

a ‘htest’ object of p-value and actual number of replicates and a list of test statistics, streams used, threshold.

Examples

library('clrng')
if (detectGPUs() >= 1) {
  setContext(grep("gpu", listContexts()$device_type)[1])
  
  Job <- matrix(c(1,2,1,0, 3,3,6,1, 10,10,14,9, 6,7,12,11), 4, 4)
  Job <- gpuR::vclMatrix(Job, type="integer")
  
  getOption('clrng.type')
  options(clrng.Nglobal = c(64,16))
  streams <- createStreamsGpu()
  result <- fisher.sim(Job, 1e5, streams = streams)
  print(result)
  result$streams
  result$threshold
} else {
  message("No GPU context available")
}

get_system_info

Description

This function prints operating system, CPU, GPU, and OpenCL version information.

Usage

get_system_info()

Value

List of system information.

logfactSum

Description

Computes the log-factorial of a table on a GPU.

Usage

logfactSum(x, Nglobal = getOption("clrng.Nglobal"))

Arguments

Value

sum of log-factorials of elements of the input matrix ‘x’.

Examples

library(clrng)
if (detectGPUs() >= 1) {
setContext(grep("gpu", listContexts()$device_type)[1])

x <- matrix(c(1:36), 6,6)
logfactSum(x, c(2,2))
# note if matrix is not of integers, a warning will be displayed, eg.
x2 <- matrix(c(1.1,2.1,3.1,4.1,5.1,6.1,7.1,8.1,9.1), 3,3)
is.integer(x2)
logfactSum(x2, c(16,16))} else {
  message("No GPU context available")
}

Sample dataset: month.RData

Description

Counts of birth anomalies by birth month and 12 congenital anomalies categories in 2018 within the United States.

Usage

data(month)

Format

A data frame with 12 rows and 12 columns:

Ane

anencephaly

Men

meningomyelocele/spina bifida

Cya

cyanotic congenital heart disease

Her

congenital diaphragmatic hernia

Omp

omphalocele

Gas

gastrochisis

Lim

limb reduction defect

Cle

cleft lip with or without cleft palate

Pal

cleft palate alone

Dow

Down syndrome

Chr

suspected chromosomal disorder

Hyp

hypospadias.

Source

Centers for Disease Control and Prevention (CDC)

References

https://www.cdc.gov/nchs/data_access/VitalStatsOnline.htm

Examples

data(month)
head(month)

qqnormGpu

Description

Calculate quantiles on a GPU and produce a Q-Q plot in R.

Usage

qqnormGpu(
  y,
  ylim,
  mu = 0,
  sigma = 1,
  lower.tail = 1,
  main = "Normal Q-Q Plot",
  xlab = "Theoretical Quantiles",
  ylab = "Sample Quantiles",
  Nglobal = getOption("clrng.Nglobal"),
  Nlocal = c(2, 2),
  type = getOption("clrng.type"),
  verbose = FALSE,
  ...
)

Arguments

Value

a Normal Q-Q plot.

Examples

library(clrng)
if (detectGPUs() >= 1) {
setContext(grep("gpu", listContexts()$device_type)[1])
y <- stats::rt(256, df = 5)  # generates 256 random numbers from a Student's t-distribution
clrng::qqnormGpu(y, ylim=c(-4,5), mu=0, sigma=1, Nglobal=c(16,4))
x<-stats::rnorm(256)
clrng::qqnormGpu(x, Nglobal=c(8,6)) } else {
  message("No GPU context available")
}

rexpGpu

Description

Generate exponential random numbers parallely on a GPU.

Usage

rexpGpu(
  n,
  rate = 1,
  streams,
  Nglobal = getOption("clrng.Nglobal"),
  type = getOption("clrng.type"),
  verbose = FALSE
)

Arguments

Details

type specifies the precision type of random numbers. If GPU supports "double", 'clrng.Nglobal' is "double", otherwise, ‘clrng.Nglobal’ is "single".

Value

a 'vclVector' or 'vclMatrix' of exponential random numbers.

Examples

library('clrng')
if (detectGPUs() >= 1) {
  setContext(grep("gpu", listContexts()$device_type)[1])
  streams <- createStreamsGpu()
  as.vector(rexpGpu(7, streams=streams))

  # produce float precision random numbers
  options(clrng.type='float')
  as.matrix(rexpGpu(c(2,3), rate=0.5, streams))} else {
  message("No GPU context available")
}

rnormGpu

Description

Generate standard Normal random numbers parallely on a GPU.

Usage

rnormGpu(
  n,
  streams,
  Nglobal = getOption("clrng.Nglobal"),
  type = getOption("clrng.type"),
  verbose = FALSE
)

Arguments

Details

type specifies the precision type of random numbers. If GPU supports "double", 'clrng.Nglobal' is "double", otherwise, ‘clrng.Nglobal’ is "single".

Value

a 'vclVector' or 'vclMatrix' of standard Normal random numbers.

Examples

library(clrng)
if (detectGPUs() >= 1) {
  setContext(grep("gpu", listContexts()$device_type)[1])
  currentPlatform()
  streams <- createStreamsGpu()
  as.vector(rnormGpu(7, streams=streams))

  getOption('clrng.Nglobal')
  # use float precision and global size
  as.matrix(rnormGpu(c(2,3), streams=streams))} else {
  message("No GPU context available")
}

runifGpu

Description

Generate uniform random numbers parallely on a GPU.

Usage

runifGpu(
  n,
  streams,
  Nglobal = getOption("clrng.Nglobal"),
  type = getOption("clrng.type"),
  verbose = FALSE
)

Arguments

Details

type specifies the precision type of random numbers. If GPU supports "double", 'clrng.Nglobal' is "double", otherwise, ‘clrng.Nglobal’ is "single".

Value

a 'vclVector' or 'vclMatrix' of uniform random numbers.

Examples

 
library('clrng')
if (detectGPUs() >= 1) {
  setContext(grep("gpu", listContexts()$device_type)[1])
  currentDevice()
  getOption('clrng.Nglobal')
  streams <- createStreamsGpu()
  as.vector(runifGpu(5, streams))

  # Change global options 
  options(clrng.type="float")
  # produce a matrix of random numbers
  as.matrix(runifGpu(c(2,2), streams))} else {
  message("No GPU context available")
}

setBaseCreator

Description

Set the initial seed of the first stream.

Usage

setBaseCreator(initial = rep(12345, 6))

Arguments

Details

initial is of length 6, recycled if shorter.

Value

a stream object of class 'vclMatrix'.

Examples

library('clrng')
setBaseCreator(c(111,222,333,444,555,666))

Sample dataset: week.RData

Description

Frequencies for birth anomalies by birth day of week and 12 congenital anomalies categories in 2018 within the United States.

Usage

data(week)

Format

A data frame with 7 rows and 12 columns:

Ane

anencephaly

Men

meningomyelocele/spina bifida

Cya

cyanotic congenital heart disease

Her

congenital diaphragmatic hernia

Omp

omphalocele

Gas

gastrochisis

Lim

limb reduction defect

Cle

cleft lip with or without cleft palate

Pal

cleft palate alone

Dow

Down syndrome

Chr

suspected chromosomal disorder

Hyp

hypospadias.

Source

Centers for Disease Control and Prevention (CDC)

References

https://www.cdc.gov/nchs/data_access/VitalStatsOnline.htm