R

Jupyter Notebook with R kernel Container


singularity pull shub://tin6150/DIOS_demonstration
singularity exec DIOS_demonstration_latest.sif /opt/conda/bin/jupyter lab --allow-root

-or-

docker
podman run  -it --entrypoint=/opt/conda/bin/jupyter  tin6150/r4envids lab --allow-root


Jupyter Notebook IR Kernel Setup

conda install -c conda-forge jupyterlab IRkernel is R kernel for Jupyther Notebook. Need to install as R package, then add kernel spec to Jupyter Notebook: Rscript -e "install.packages('IRkernel')" # system wide IRkernel::installspec(user = FALSE) # per user Rscript --no-readline --slave -e "IRkernel::installspec(user = TRUE)" /home/tin/anaconda3/bin/jupyter lab # expect to have browser launched with URL http://localhost:8888/lab # then click icon to create new R notebook

Environment


setenv R_LIBS /path/to/user/R-libraries

# setting R_LIBS will change both where R looks for lib to load and when installing libs 

library( rJava );	# see if it can load the R library named rJava (case sensitive)


listing all installed libraries:
Rscript -e 'library()' 




sI <- sessionInfo()
sI


system('env')	# this is running the env command via the shell and display that info
system('id -a; hostname')

# in jupyter notebook, the system() command output to console 
# use combination of intern=TRUE and wrap with print() just to be sure
print(system( 'uptime', intern=TRUE ))  


library(data.table)
fread( "cat /proc/loadavg", check.names=TRUE ) ## run system command and read result into data frame


Setting dir for user package install


setting user's own library install dir.
for installing CRAN libraries...

You can have a R_LIBS under your home dir.  
If you setup R_LIBS to be a shared folder, then your student can use the same library that you (or I, not as root) install.  



mkdir -p  ~/rlibs36
export R_LIBS=~/rlibs36    (or R_LIBS=/global/home/groups/ac_seasonal/rlibs36 )
I am assuming this for a new R 3.6, are libraries compatible with old version? For Perl I keep them in separate directories; python is a different beast)

# setting R_LIBS will change both where R looks for lib to load and when installing libs 

Running this as user should install a package called diagram:
    Rscript --quiet -e 'install.packages("diagram",    repos = "http://cran.us.r-project.org")'    

after install, you should see files added to ~/rlibs36

If the above don't work,
start interactive R as user
install.packages('diagram',lib='~/rlibs36')

this page has a good write up about this issue:
https://statistics.berkeley.edu/computing/R-packages

Installing packages


installing packages from cran:
(see r4eta or metabolics container)


scripted to run from shell:

Rscript --quiet -e 'install.packages("ggplot2",  repos = "http://cran.us.r-project.org")'    
Rscript --quiet -e 'install.packages(c("aCRM", "akima", "broom", "cluster", "clusterCrit"), repos = "http://cran.us.r-project.org")'

# do NOT have TAB(s) inside the arg list for packages(...), as Rscript can't tolerate it when invoked from a bash script.


Rscript --quiet --no-readline --slave ...
	# --quiet is same as --silent 
	# --slave was to make R run as quietly as possible 
	# --no-readline hopefully do less drawing on screen and make install log more readable...
	# there isn't a --no-verbose or --no-interactive


install many packages in single command:
https://stackoverflow.com/questions/29041423/how-to-install-multiple-packages

install.packages(c("EIAdata", "gdata", "ggmap", "ggplot2")) # rest omitted

have not tried yet:
install.r EIAdata gdata ggmap ggplot2    # rest omitted again

Misc

capabilities() 		# see if support X11, etc
system("id;pwd")	# run OS commands

setwd("dirname")	# cd to dirname, most useful in interactive R session.
source("myFuncList.R")	# import function list from file

.libPaths()		# list path used to scan for R libs 

.libPaths(  c( ./libPaths(), '/home/tin/R/x86_64-pc-linux-gnu-library/3.4' ) )   # add path to library 



rm(list=ls())  		# remove all var in memory

Oracle connection

Sys.setenv(TNS_ADMIN="/site/conf/TNS_ADMIN",ORACLE_HOME="/usr/prog/oracle-client/11.1.0.6",ORACLE_SID='')
# The TNS_ADMIN may not matter if ORACLE_HOME has a network/admin with working conf for tns name resolution.
# ORACLE_SID is very important!  if set, the instance specifier in the dbConnect will be ignored, and db always connect to instance specified by ORACLE_SID !!

library( 'ROracle' )

ora=Oracle()
con=dbConnect(ora,user='user/pass@instance')
summary(con)
# verify connected to desired db)

result=dbGetQuery(con, "select * from tab")
# perform SQL query

result
# see result of query (display content of variable)


result2=dbListTables( con )
# see list of tables for the connected schema

GC: Garbage Collection

gc(verbose=TRUE) 	# explicitly call garbage collection
ls() 			# list all vars
object.size( get("myData") )	
rm()
rm(list=ls())  		# remove all var in memory # probably useful in rstudio when playing, but not in actual program!
sort( sapply( ls(), function(x) { object.size(get(x))} ),decreasing=TRUE )	# list all vars and their sizes

vars are out of scope at the end of function, and gc can happen to them automatically

bigmemory leave data on file.  some packages are build using bigmemory

file-backed big matrix -- https://ljdursi.github.io/beyond-single-core-R/#/132 
data = read.big.matrix(...)

csv is slow.
HDF5 and netCDF recommended. 

ref: https://ljdursi.github.io/beyond-single-core-R/#/111

R Programming

101
R short primer (pdf) (page 12)

• function(arglist){expr}: 
function definition: do expr with list of arguments arglist

• if(cond){expr1}else{expr2}: if-statement:
if cond is true, then expr1, else expr2

• for(var in vec) {expr}: 
for-loop: the counter var runs through the vector vec 
and does expr each run

• while(cond){expr}: while-loop: while cond is
true, do expr each run


• x[n]: the n-th element   # R index starts at 1
• x[m:n]: the m-th to n-th element
• x[c(k,m,n)]: specific elements
• x[x>m & x<n]: elements between m and n

• x$n: element of list or data frame named n

• x[["n"]]: idem		# [[ ]] in R ... 

• [i,j]: element at i-th row and jth column
• [i, ]: row i


• return: show variable on the screen (used in functions)


• as.numeric or as.character: change class to
number or character string

• strptime: change class from character to
date-time (POSIX)


?"%*%"  # get help on topic, quote it if it has "funny" symbols

%*% # matrix multiply
%/% # ?? partitioning data into partition for shipping to different nodes 

%:% # compose or nest foreach objects - https://ljdursi.github.io/beyond-single-core-R/#/84

$>% # like unix pipe, used a lot by dplyr 

%%  # modulus, ie reminder.  eg 7%%3 is 1
2^4 and 2**4 both seems to be power, get 16.  2^4 notation maybe preferred.

R stuff - NA : Not available data

NA is the token to indicate a value that is not availabe.  Kinda like UNDEF.  
It is not a string, and it is not NULL.
It is spelled exactly as NA , both caps.

> foo=NA
> foo
[1] NA
> bar=na
Error: object 'na' not found

• is.na: test if variable is NA

R by default will not compute on dataset that contain NA.
If you don’t mind about the missing data and
want to compute the statistics anyway, you can
add the argument na.rm=TRUE 
(Should I remove the NAs? Yes!).

> max(j, na.rm=TRUE)
[1] 2


R stuff - stat stuff

• lm(v1∼v2): linear fit (regression line) between 
vector v1 on the y-axis and v2 on the x-axis

• nls(v1∼a+b*v2, start=ls(a=1,b=0)): nonlinear fit. 
Should contain equation with variables
(here v1 and v2 and parameters (here a and b)
with starting values

• coef: returns coefficients from a fit
• summary: returns all results from a fit

• sum: sum of a vector
• mean: mean of a vector
• sd: standard deviation of a vector


• aggregate(x,by=ls(y),FUN="mean"): split
data set x into subsets (defined by y) and computes means of the subsets.
Result: a new vector.

• approx: interpolate. Argument: vector with NAs. 
Result: vector without NAs.

stat functions
Ref:
- "UNM Stat 5101"
- CDF and PPF in Excel, R and Python (good graphical guide covering what the p, q, d, r functions cover.)
- SciPy stats function


prefix: p, q, d, r ::

p for "probability", the cumulative distribution function (c.d.f.)
	F(x) = P(X <= x)
   	Answer What is  P(X < 27.4) when X has Normal distribution with mean 50 and standard deviation of 20 aka N(50,20).  N often styled as cursive cap N.
   	if variance (σ) is given, use the relation s.d. = sqrt(sigma) 
   	pnorm( 27.4, mean=50, sd=20, lower.tail=TRUE )
	pnorm( 27.4, 50, 20 )
   	In R, optional param default to mean=0, sd=1, lower.tail=TRUE.
   	Python: scipy.stats.norm.cdf( 27.4, loc=50, scale=20 )
   	Excel:  norm.dist( 27.4, 50, 20, TRUE ) 

	For calculation of the p-value in a right tailed test for a given z-score:
   	1 - pnorm( 27.4, 50, 20 )
   	pnorm(27.4, 50, 20, lower.tail=FALSE )  # lower.tail=FALSE -> upper/right tail
	Python: 
	1 - scipy.stats.norm.cdf( 27.4, 50, 20 )
	scipy.stats.norm.sf( 27.4, 50, 20 )     # sf = 1 - cdf


q for "quantile", the inverse c.d.f. - aka PPF(q) for probability ( 1 - α )
   	p = F(x)
	x = F-inv(p)
   	F-inv is styled as F^-1.
   	So given a number p between zero and one, qnorm looks up the p-th quantile of the normal distribution.
   	Answer What is F-inv(0.95) when X has the N(100, 15^2) distribution?
   	qnorm(0.95, 100, 15)
   	qnorm(0.95, mean=100, sd=15, lower.tail=TRUE)
   	qnorm(0.05, mean=100, sd=15, lower.tail=FALSE)   # from the relation (1-alpha) + alpha = 1, here alpha=0.95
   	Python: scipy.stats.norm.ppf( 0.95, loc=100, scale=15 )
   	Excel: norm.inv( 0.95, 100, 15 ) .  Excel has a norm.s.inv(0.05), but only take mean=0 sd=1.

   	
d for "density", the density function (p.f. or p.d.f.)
   		

r for "random", a random variable having the specified distribution
	Generating random numbers from a standard normal distribution
	N(miu=0,sigma=1)  # N cursive, miu=mean of 0, sigma=standard deviation of 1
	rnorm(n=1, mean=0, sd=1 )
	Python: scipy.stats.norm.rvs( loc=0, scale=1, size=1, random_state=123 ) # random_state is optional, use seed for repeatable/determinsistic result
	If n or size > 1 get a vector.
	Excel:  norm.s.inv( rand() )

pnorm,  qnorm,  dnorm,  and rnorm.  are the p-, q-, d-, r- fn for Normal Distribution

pbinom  qbinom  dbinom  rbinom - for binomial distribution
pchisq	qchisq	dchisq	rchisq - for Chi-Square   scipy.stats.chi2.cdf() etc
pexp	qexp	dexp	rexp   - for Exponential
plogis	qlogis	dlogis	rlogis - for Logistic
plnorm	qlnorm	dlnorm	rlnorm - for Log Normal
ppois	qpois	dpois	rpois  - for Poisson
pt	qt	dt	rt     - for Student t    scipy.stats.t.cdf() etc
punif	qunif	dunif	runif  - for Uniform

Note that for continuous distribution, some of these fn are defined using integrals, and R doesn't do integrations!


All function take option mean and standard deviation.  If omitted, default mean=0, sd=1.  

pnorm(27.4, mean=50, sd=20)
pnorm(27.4, 50, 20)



assignment
a =  5
a <- 5

# both = and <- can be used for assignment
# But <- is prefered by the R crowd.  it also screw with my html code here, so maybe R should go to .rst 

# there are some subtle differences, side effect, formula, etc.
# see https://renkun.me/2014/01/28/difference-between-assignment-operators-in-r/
# overall, for better readability of R code, 
# it was suggested to only use <- for assignment and = for specifying named parameters.
# But I was not convinced and will likely continue to use = 

Data Structures

Adv R

1D:
vector: homegenoeus elements.  c()
list:   heterogeneous elements.  list()

2D:
matrix:     homegenoeus elements.  matrix()
dataframe:  heterogeneous elements, named columns. think table of data/spreadsheet :-D.  data.frame(), tidyverse

3D, multi-dimention:
array:     homogeneous elements.  1-indexed.  array(), dim()


attribute()
structure()

factor() to store categorical data -- ie predefined values

vector, matrix
R short primer (pdf)

vec1 = c( 1, 3, 5, 7)	# c = concatenate, paste together.  
vec2 = c( 2, 4, 6, 8)
vec3 = seq(10,25,5)     # aka: vec3 = seq(from=10,to=25,by=5)  # result: [1] 10 15 20 25

sum(vec2)


> mat1=matrix( data = c(1,2,3,4,5,6), ncol=3 )   # ncol define how many column the matrix has
> mat1
     [,1] [,2] [,3]
[1,]    1    3    5
[2,]    2    4    6

> mat[2,2]
[1] 4

matlb/octave matrix syntax is A LOT nicer :-D
pay special attention to the sequence of the numbers.

cbind	# column bind to create matrix
rbind 	# row    bind


array
R is 1-indexed, so first entry of df is 1
A 1D array is a vector.
A 2D array is a matrix.
3D and higher dim structure is rarer in stats.

dim()
length()
names()
rownames()
colnames()
dimnames()
t() - transpose

c() generalizes to cbind() and rbind() for matrix
abind() for arrays

as.matrix()
as.array()  -- for conversions

dataframe
R is 1-indexed, so first entry of df is 1

coord = data.frame(x = runif(n.total), y = runif(n.total), sampled = 0) 
coord.sampled = coord[coord$sampled == 1,]   # initial sites

data.frame (coord) is like a table
and $ separate the table name and the column name.
Thus, the above eg has 
coord$x
coord$y
coord$sampled
each of them is an array (representing the cell values across many rows of the table).
coord$x[1]  # table coord, column x, row 1  # R is 1-indexed.  (unlike python 0-indexed)
coord$x[2]  # table coord, column x, row 2


> t = data.frame(x = c(11,12,14), y = c(19,20,21), z = c(10,9,7))
> t
   x  y  z
1 11 19 10
2 12 20  9
3 14 21  7

> mean(t$x)
[1] 12.33333


typeof( t )
calss( t )
is.data.frame( t )

cbind(t, data.frame( z = 3:1 )
rbind(t, data.frame(...) )




It’s a common mistake to try and create a data frame by cbind()ing vectors together. This doesn’t work because cbind() will create a matrix unless one of the arguments is already a data frame. Instead use data.frame() directly
Since a data frame is a list of vectors, it is possible for a data frame to have a column that is a list
List
List in a simple form is a vector.
but it can be arbitrary number of object, each having different length.

syntax looks like it has some nested structure, pay close attention.

> L2=list(vec1,vec2)
> L2
[[1]]
[1] 1 3 5 7

[[2]]
[1] 2 4 6 8


> L = list(one=1, two=c(1,2),five=seq(1, 4, length=5))
> L
$one
[1] 1

$two
[1] 1 2

$five
[1] 1.00 1.75 2.50 3.25 4.00


[ ]   returns a list
[[ ]] returns the object which is stored in list
If it is a named list, then
    List$name or List[["name"]] will return same as List[[ ]]
While List["name"] returns a list

ref: https://stackoverflow.com/questions/32819539/proper-way-to-access-list-elements-in-r

for list returned by ans = mccollect( list(jobs...) )
typically ans[[1]], ans[[2]] etc will contain the original answer desired.

Strange R stuff

Formula and tilde (~) operator

Coming from a programming world, R's definition of formula and its use of the tilde (~) operator is one of the weirest sh-IT of R!! =)

R has this concept of formula, and, at least from a user perspective, is different than function. (Actually, a formula can be called 'f' and another function 'f' and they can coexist and be called correctly by the right context!)

For python programmer, forget about programming for a bit. Put on the stat thinking cap :)
Remember the flower classification example in data science class? stack overflow describes this construct:
Species ~ Sepal.Length + Sepal.Width + Petal.Length + Petal.Width
as "Model Species depends on Sepal Length, Sepal Width, Petal Length and Petal Width"

The tilde (~) operator is often used for regression model.
The LHS of the ~ operator is the name of the model (Species).
The RHS are the variables that is fed into the model, with the + operator being overloaded (don't literary means add them, but to treat each as "columns" to find covariance). Most models use data frames, and each "variable" is a column vector of data.

formula has delayed evaluation

Ref: Cran Lazy Eval, scroll down to the Formulas section.

A formula capture delays the evaluation of an expression so that you can later evaluate it with f_eval(). ie
f <- ~ 1 + 2 + 3
The formula 'f' will be defined, but the RHS expression will not be calculated yet.
Only when
f_eval(f)
is executed is the expression calculated.
Above was a one-sided formula.
Below is a two-sided formula:
	g <- y ~ x + z
lazyeval provides abstraction like:
f_rhs(g)   # x + z
f_lhs(g)   # y         

Common formula

R Doc

lm and glm are logistic regresion models. the form y ~ model is interpreted as a specification that the response y is modelled by a linear predictor specified symbolically by model. Such a model consists of a series of terms separated by + operators.

Model operators:
+ 		separate a series of terms that affect the model.
: 		??
* 		factor crossing: a*b interpreted as a+b+a:b
^ 		crossing to specific degree.  eg (a+b)^2 for crossing twice
^in%    terms on the left are  nested within those on the right.
-      	remove dependence on the specified series

I() - To avoid this confusion, the function I() can be used to bracket those portions of a model formula where the operators are used in their arithmetic sense


  1. The lattice package uses them to specify the variables to plot.
  2. The ggplot2 package uses them to specify panels for plotting.
  3. The dplyr package uses them for non-standard evaulation.

Tilde operator

Try to understand this:
x <- c(1:100)
y <- seq(0.1,10,0.1)
	
	
# all these 3 are the same:
plot(y ~ I(x^3)) 
plot(I(x^3), y) 
plot(x^3, y)         # no need to use I() function as ~ operator never used.

# note how ~ syntatically swapped the order of the independent and dependent variables x and y

# but this below is very different:
# ^ is interpreted as model operator for cross reference.  ( due to presence of ~ operator)
ploy(y ~ x^3) 

	
StackOverflow more extensive discussion on formula Regression in Python usinr R-style formula seems to discuss use of ~ and regression formula in R.
import pandas as pd
from statsmodels.formula.api import ols
	
model = ols("MPG ~ Year", data=df)
results = model.fit()

Pipe

stack overflow


%>% is defined by magrittr, which is used by dplyr.
It is the equivalent of unix shell pipe.

iris %>% head() %>% summary() is equiv to summary(head(iris))
which one to use is a matter of preference.

apply family of function

see R-bloggers
apply(t(beaver1),1,max) ## apply function max to data, 1=row-wise)
lapply() returns a list
sapply() returns a vector instead of a list
tapply() does grouping before running summary function on them
by() ... think of GROUP_BY in SQL


Libraries

lifkit

tbd

ModeSim

geoR::lifkit

## likfit - Likelihood Based Parameter Estimation For Gaussian Random Fields
## https://www.rdocumentation.org/packages/geoR/versions/1.8-1/topics/likfit

SimAnneal()
kridge

~

raster::extract()


makCluster
registerDoParallel
%dopar%

Python using R

  1. https://towardsdatascience.com/from-r-vs-python-to-r-and-python-aa25db33ce17
  2. PypeR - R within Python
  3. pyRserve - connect to a remote R server
  4. rpy2 - runs embedded R in a Python process

R using python

  1. rPython
  2. SnakeCharmR - fork, more modern ver of rPython
  3. PythonInR
  4. reticulate

Parallelization in R

6 main types of parallization:
  • same host, FORK based, parent/child memory model with copy-on-write: mclapply, mcparallel, mccollect.
  • Rdsm - shared memory within a single computer, so multiple PSOCK same-node processes can read/write to 1 single memory region.
  • PSOCK based multi-node parallelization, without needing MPI (cluster): SNOW: parLapply, clusterApplyLB
  • MPI based -- SNOW cluster implement on this as well.
  • pbdR, hiding some of the complexity of MPI
  • Hardoop/SparkR but that's a platforms of its own.
  • Packages that does parallelism under the hood. eg BLAS, caret, many others
  • future_map(), purrr -- https://byuistats.github.io/M335/parallel_furrr.html


    Tutorials

    Chris Paciorek (UC Berkeley Stats Dept) Parallel Processing for Distributed Computing Cover R, Python, Matlab and C, as well as how to use them in a Slurm cluster.

    Jonathan Dursi Beyond Single-Core R a slide deck on Parallelization in R. Summary slides:
  • Packages that does parallelism under the hood -- https://ljdursi.github.io/beyond-single-core-R/#/22
  • paralle/multicore with mc* -- https://ljdursi.github.io/beyond-single-core-R/#/51
  • cluster* parLapply snow -- https://ljdursi.github.io/beyond-single-core-R/#/73
  • foreach doParallel isplit %:% -- https://ljdursi.github.io/beyond-single-core-R/#/98
  • Best Practices -- https://ljdursi.github.io/beyond-single-core-R/#/106
  • bigmemory morder mpermute mwhich sub.big.matrix -- https://ljdursi.github.io/beyond-single-core-R/#/133
  • Rdsm -- shared memory within node by multiple process -- https://ljdursi.github.io/beyond-single-core-R/#/142

    Dursi's github repo has data for running his example, and I wrapped that with a Jupyter Notebook container so everyone can try using this Docker Container with Jupyter notebook server:
    Start jupyter notebook web server (on specific port, eg 6997):
    
    docker run -p 6997:6997 -v "$PWD":/mnt -it --entrypoint=/opt/conda/bin/jupyter  tin6150/beyond-single-core-r  lab --allow-root  --no-browser --port=6997 --ip=0.0.0.0
    
    Point web browser to something like
      http://127.0.0.1:6997/
    and paste the token URL link shown on the terminal console
    
    /mnt is a mount of the current dir (PWD) where you started the docker process, and files written there will persist after the container is terminated.  (Other files inside the container are ephemeral!)
    

    Parallelization in R using mc* functions

    mclapply
    mcparallel (likely just called parallel in early days)
    mccollect
    mc.core

    Ref: Beyond single core R
    mc*        are multi-core routines
    mcparallel is good for parallel tasks
    mclapply   is good for data parallelism - easily replace lapply()
    mc.cores   really should represent number of tasks, core can be oversubscribed often with little perf degradation
    
    parallel::mclapply - multi-core lapply - https://nceas.github.io/oss-lessons/parallel-computing-in-r/parallel-computing-in-r.html
    
    instead of 
    	result = lapply(starts, fx)
    use
    	result = mclapply(starts, fx, cores=4)
    mclapply gathers up the responses from each of these function calls, and returns a list of responses that is the same length as the list or vector of input data (one return per input item).
    
    starts is a variable holding data, eg rep(100, 40)
    fx is a custom function that lapply() runs
    
    pvec - for simple use case of applying func to each element of vector and return vector, pvec is easier to use
    # https://ljdursi.github.io/beyond-single-core-R/#/48
    
    
    
    https://ljdursi.github.io/beyond-single-core-R/#/30
    mcparallel  # fork a task , run in background
    mccollect   # wait and collect result.  so kinda like MPI scatter/gather
    
    
    library(multicore)                    ## functionality replaced by library('parallel') 
    fun1 = function() {Sys.sleep(10); 1}
    fun2 = function() {Sys.sleep(5);  2}
    f1 = parallel(fun1())                 ## new fn name is mcparallel()
    f2 = parallel(fun2())
    result = collect(list(f1, f2))
    
    result[[1]]  # would contain result of f1
    
    
    Linear Regression Model fitting, in series vs parallel
    https://ljdursi.github.io/beyond-single-core-R/#/32 and slide 33
    
    fit1 =  lm(DISTANCE  ~ AIR_TIME,  data=jan2010))
    fit2 =  lm(ARR_DELAY ~ DEP_DELAY, data=jan2010))
    
    -vs-
    
    parfits = function() {
         pfit1 = mcparallel(lm(DISTANCE  ~ AIR_TIME,  data=jan2010))
         pfit2 = mcparallel(lm(ARR_DELAY ~ DEP_DELAY, data=jan2010))
         mccollect( list(pfit1, pfit2) )
    }
    parfits()
    
    Note that mcollect asked for the tasks output to be combined into a list.
    Some data structure maybe needed to extract more complex model result??
    
    
    domino data lab on caret/doMC
    
    library(doMC)
    library(caret) # popular ML using foreach to parallelize CV-folds, etc.
    	fit.lda.ser vs
    	fit.lda.par
    
    

    Parallelization in R using cluster functions

    makeCluster()
    stopCluster()
    doParallel()
    registerDoSEQ()
    snow
    foreach
    %do%
    %dopar%
    
    for is run for its side effect
    foreach returns result, side effects maybe gone (when using parallel backend).
    foreach should be tought of lapply, not for loop
    
    
    %do% is serial
    Parallel libs: doParallel, doMC, doMPI
      cl = parallel::makeCluster(4)
      cl = parallel::makeCluster(4, type = "FORK")   # unix fork(), default?
      cl = parallel::makeCluster(4, type = "PSOCK")  # Posix Sockets creates a brand new session in R, nothing inherited from parent.  if do this, may as well use MPI cluster and really scale it.
      cl = parallel::makeForkCluster(4)
    
    use registerDoSEQ() if want to force foreach to run in serial 
    
    much of the parallelization is done using fork() in unix (may not work in windows).
    Also, fork() allow access to vars/memory from parent, but result not returned at the end.
    Need to do some special collection/return if need to save those data.
    Thus, "side-effects" such as those produced by `for` vanishes in parallelization.
    
    SNOW - like PSOCK, entirely new process, so ned to explicitly copy data.  but process can be on remote machine.
    
    
    https://ljdursi.github.io/beyond-single-core-R/#/55
    clusterCall()
    clusterEvalQ() # easier to use for tasks
    
    

    doParallel

    One way to do parallel processing in R
    NumThread=15
    library(doParallel)
    cl = makeCluster( NumThread, outfile="mkcluster.out" )   ## create a cluster object
    registerDoParallel(cl)
    foreach(i=1:3) %dopar% sqrt(i)
    # the %dopar% says to run the foreach loop in parallel for each item
    # all console output inside cluster object will go to outfile 
    # there are eg combine=rbind to merge result
    stopCluster(cl)
    
    .combine=rbind # row-bind, ie, each result becomes a row
    .combine=cbind # col-bind, ie, each result becomes a col
    .combine=c     # c() ?
    
    
    detectCores() ## return number of cores on machine
    
    
    Ref:

    Rdsm

    https://ljdursi.github.io/beyond-single-core-R/#/139
    library(parallel)
    library(Rdsm)
    
    nrows = 7
    cl = makePSOCKcluster(3)       # form 3-process PSOCK (share-nothing) cluster
    init = mgrinit(cl)             # initialize Rdsm
    mgrmakevar(cl,"m",nrows,nrows)  # make a 7x7 shared matrix
    bar = makebarr(cl)
    
    clusterEvalQ(cl,myid = myinfo$id)
    
    clusterExport(cl,c("nrows"))
    dmy = clusterEvalQ(cl,myidxs = getidxs(nrows))
    dmy = clusterEvalQ(cl, m[myidxs,1:nrows] = myid)
    dmy = clusterEvalQ(cl,"barr()")
    
    print(m[,])
    
    
    

    Clustering on Clusters

    https://ljdursi.github.io/beyond-single-core-R/#/57
    ship data to other nodes of the cluster:
    cl = makeCluster(8)
    clusterExport(cl, "jan2010")
    cares = clusterApply(cl, rep(5,4), do.n.kmeans)
    stopCluster(cl)
    mcres = mclapply(rep(5,4), do.n.kmeans, mc.cores=4)
    
    
    https://ljdursi.github.io/beyond-single-core-R/#/59
    # Running across machines:
    # 2 machine, each with 8 core of process?
    
    hosts = c( rep("localhost",8), rep("192.168.0.10", 8) )
    cl = makePSOCKcluster(names=hosts)
    clusterCall(cl, rnorm, 5)
    clusterCall(cl, system, "hostname")
    stopCluster(cl)
    
    

    Snow

    https://ljdursi.github.io/beyond-single-core-R/#/61
    scheduling
    viz of run
    
    library(snow,quiet=TRUE)
    
    do.kmeans.nclusters <- function(n) { kmeans(jan2010, centers=n, nstart=10) }
    
    cl = makeCluster(2)
    clusterExport(cl,"jan2010")
    
    tm = snow.time( clusterApply(cl, 1:6, do.kmeans.nclusters) )
    plot(tm)
    
    # load balance, below is more like mc.preschedule=FALSE, kicking off task to worker only when needed
    tm.lb = snow.time(clusterApplyLB(cl, 1:6, do.kmeans.nclusters))
    plot(tm.lb)
    
    
    https://ljdursi.github.io/beyond-single-core-R/#/73 - Summary for parallel/snow
  • clusterExport good for for SIMD
  • clusterApplyLB good for MIMD
  • mcparallel is best for MIMD?
  • parLapply
  • makePSOCKcluster for small cluster
  • makeMPIcluster for larger cluster -- but read up on pbdR first
  • pdbR -- https://ljdursi.github.io/beyond-single-core-R/#/143
  • pdb*apply -- https://ljdursi.github.io/beyond-single-core-R/#/152
  • using pdbR -- bring hpc distributed memory processing (SPMD) to R, see section 3.1.2 of CPaciorek's Parallel Processing for Distributed Computing
  • https://ljdursi.github.io/beyond-single-core-R/#/83
    foreach parallel
    .multicombine=TRUE
    
    %:% nest foreach object # slide 84
    
    
    
    MPI cluster
    https://ljdursi.github.io/beyond-single-core-R/#/149
    
    init()
    rank = comm.rank()
    ...
    allreduce(length(dta), op="sum")
    comm.print(data.min)
    
    finalize()
    

    nestedParallel

    https://stackoverflow.com/questions/21306027/nesting-parallel-functions-in-r
    
    cl = makeCluster(2, type = "SOCK")
    clusterCall(cl, function() {
      library(doSNOW)
      registerDoSNOW(makeCluster(2, type = "SOCK"))
      NULL
    })
    registerDoSNOW(cl)
    
    




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