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greeNsort.R

The greeNsort R package (testbed with C-algorithms and R-data generators and C/R powercap RAPL performance measurement)

Installation under Linux (is described for Ubuntu 22.04

update your package system

sudo apt-get update
sudo apt-get upgrade

check available powercap measures

Note that reading the names should work, but reading the counters requires permissions.

first socket package-0 should be available

cat /sys/class/powercap/intel-rapl/intel-rapl:0/name

core should be available under Intel and AMD

cat /sys/class/powercap/intel-rapl/intel-rapl:0/intel-rapl:0:0/name

dram should be available under Intel

cat /sys/class/powercap/intel-rapl/intel-rapl:0/intel-rapl:0:1/name

if you have a graphic card it should be available under Intel (but not AMD)

cat /sys/class/powercap/intel-rapl/intel-rapl:0/intel-rapl:0:2/name

prepare R installation

see https://cran.r-project.org/bin/linux/ubuntu/

sudo apt install --no-install-recommends software-properties-common dirmngr

add the signing key (by Michael Rutter) for these repos

wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

To verify key, run

gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

and check the Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9

check whether lsb_release matches Ubuntu version,

echo $(lsb_release -cs)

otherwise replace $(lsb_release -cs) with the correct one in the following code and add the R 4.0 repo from CRAN

sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

install R

sudo apt-get install r-base

install required Linux libs

sudo apt-get install libxml2-dev
sudo apt-get install libssl-dev
sudo apt-get install libfontconfig1-dev
sudo apt-get install libharfbuzz-dev
sudo apt-get install libfribidi-dev
sudo apt-get install libtiff5-dev

install required R packages

open R

R

and install the required packages

install.packages("curl")
install.packages("httr2")
install.packages("systemfonts")

... takes a while ...

install.packages("devtools")
install.packages(c("abind","gplots","tibble","roxygen2","microbenchmark"))

For function prunif and package greeNsort.Rcpp, takes a while ...

install.packages(c("Rcpp","RhpcBLASctl"))
install.packages("rTRNG")

Quit R without saving data

q("no")

configure our R package compilation

Create local R config folder

mkdir ~/.R

Create makevars file

touch ~/.R/makevars

Put the following line into the makevars file

CFLAGS = -g -ftree-loop-if-convert -ftree-loop-if-convert-stores -fif-conversion -fif-conversion2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g $(LTO)

temporary installation

Go to some directory where you unpack greeNsort.R and greeNsort.Rcpp, such that you have

./greeNsort.R 
./greeNsort.Rcpp

Install them in this sequence

R CMD INSTALL greeNsort.Rcpp
R CMD INSTALL greeNsort.R

configure for your machine

open R

R

load greeNsort

require(greeNsort)

switch to greeNsort directory

setwd("greeNsort.R")

update the powercap RAPL config in src/powercap_config.h by calling

perfconfig()

quit R without saving data

q("no")

replace the greeNsort.Rcpp/src/powercap_config.h by the new one just created in greeNsort.R/src/powercap_config.h

final installation

Now install with the powercap RAPL config for your machine

R CMD INSTALL greeNsort.Rcpp
R CMD INSTALL greeNsort.R

Now the package is installed. Do not try to R CMD check the package before you read on

set permissions

After each reboot, make sure there are read permissions on RAPL counters. If you have the root password, a convenient way is using perfgrants() in R (otherwise talk to your sysadmin).

assuming you are in R

require(greeNsort)
perfgrants()

run a Frogsort0 example

example(Frogsort0)

run the testsuite

testsort(out="", verbose=TRUE)

see help for the testsuite

?testsort

vignettes and package checking

Note that we so far installed from the package source, not as usual from a package build.

Vignettes are available in source /vignettes and compiled under /doc but not as usual copied to the R lib.

You don't need a proper vignette installation.

read, apply, certify

read the greeNsort-1-quickstart vignette to make yourself familiar with using the package.

read the greeNsort-2-measurement vignette to understand the measurement technology.

building vignettes and package checking

For a proper vignette installation and for a successful R CMD check you can rebuild and install but you need first

  • a working LaTeX installation
  • a working pandoc installation

Once you have that the following should work but takes a while

R CMD build greeNsort.R
R CMD INSTALL greeNsort_1.0.0.tar.gz
R CMD check greeNsort_1.0.0.tar.gz

R CMD build greeNsort.Rcpp
R CMD INSTALL greeNsort.Rcpp_1.0.0.tar.gz
R CMD check greeNsort.Rcpp_1.0.0.tar.gz

package development

The packages greeNsort and greeNsort.Rcpp were developed using RStudio. If you want to modify the packages we recommend installing RStudio. Then read the greeNsort-3-development vignette to understand the measurement technology.

Installation under Windows

Installation under Windows is possible, but currently requires some tricks

  • deactivate RAPL-measurement
  • deactivate some C++ algorithms in greeNsort.Rcpp and greeNsort.R algodb