README

TIPS AND REMINDERS FOR THE FORGETFUL DEVELOPER :)


* NOTES on where everything lives:

Am testing on PADS

   ~/SwiftR is my "project" main working dir

R is under ~/R and ~/R/pads (compiled for PADS; the ~/R/bin/R
executable gets a library error on pads)

To build R:
  http://cran.r-project.org/src/base/R-2/R-2.11.1.tar.gz (or desired release)
  tar zxf *gz
  cd ddd
  ./configure --prefix=/home/wilde/R/R-2.11.0
  make
  make install

Need to put the right R in the PATH for building and testing.
Using R 2.11 as of 2010.0903

OpenMx source tree checked out under: ~/OpenMx
working in .../trunk
~/SwiftR/OpenMx is a fossil and should be moved and then removed (when certain)

test under: trunk/demo
source("ParallelBootrapDemo")
...  FIXME ^^^

Repo is: https://svn.ci.uchicago.edu/svn/vdl2/SwiftApps/SwiftR

R packages are installed under: ~/RPackages
(These are the release-independent packages?
FIXME: how does this relate to packages under the current R relesae?

#-----
bri$ pwd
/home/wilde/R/R-2.11.0
bri$ cd library/
bri$ pwd
/home/wilde/R/R-2.11.0/library
bri$ ls 
KernSmooth/  OpenMx/  base/   cluster/    foreign/    grid/     mgcv/  rpart/    stats/     tcltk/
MASS/        R.css    boot/   codetools/  grDevices/  lattice/  nlme/  spatial/  stats4/    tools/
Matrix/      Swift/   class/  datasets/   graphics/   methods/  nnet/  splines/  survival/  utils/
bri$ 
#-----

* Note: dont yet know if we do or do not need separate compiles between
communicado, bridled, pads. teraport, and other systems on the CI
net. Hopefully not; if we do, weill need to create a tree to R
releases each with a separate subtree for user-installed packages)
Seems that we do, at least for PADS, we get this error:

login1$ ~/R/bin/R
/home/wilde/R/lib64/R/bin/exec/R:
  error while loading shared libraries: libreadline.so.4:
    cannot open shared object file: No such file or directory
login1$ 

*--

-- Swift package *source* (tbd) is under:

   ~/SwiftR/Swift (the "Swift" package)

-- Swift package is installed under: ????????

* Setup

Get latest R in path for installs etc.

   PATH=/home/wilde/R/R-2.11.0/bin:$PATH

* Fetch, Build, Install OpenMx

* Make Swift Package
  

FIXME: document R CMD BUILD and R CMD INSTALL here


  cd ~/SwiftR/Swift?

* How to build swift package into a source archive:

  R CMD build Swift

* package can also be fetched from svn abd built/installed from source I think?  Isnt this how OpenMx itself works?

* How to build swift package right into source code

* How to test the package

  R CMD check Swift

* Install Swift Package

  R CMD INSTALL Swift # Puts package under current R release:

  $ R CMD INSTALL Swift | tee INSTALL.out

#--- Example:

login1$ R CMD INSTALL Swift
* installing to library '/home/wilde/R/R-2.11.0/library'
* installing *source* package 'Swift' ...
...etc

#---

  R CMD INSTALL -l ~/RLibrary Swift # Puts package under user lib; then need to add this to R search path?
  R CMD INSTALL Swift_0.1.tar.gz  # Installs from a pre-built source archive instead of from Swift/ source dir

* Run tests Swift package tests manually

$ cd ~/SwiftR/Swift
$ R
> require(Swift)
> source("tests/TestSwift.R")

##################  INTERNAL DESIGN LOGIC

the core R function is switapply()

Its a bit more general then the lApply/sApply/etc functions:

For each call it specfies a full set of arguments

lApply calls swiftapply

in swiftapply the remote calls are batched

option processing:
# describe here: func kw args; def vals mostly NULL; options() values override if kw not specified.

Processing mode selects a set of  sites, a cf, and a tc.

Site selects a site within a tc for a secific exec.

rserver.swift runs an app() whose name encodes the site (eg: bashservice, bashlocal)

Provider staging is a problem: its all or none. How to do provider staging for local? I think thats OK: hopefully its fast.

Probem: would like to do multiple sites fomr the internal coaster service rather than an external coaster service

---

cd ~/SwiftR
R CMD INSTALL Swift
R CMD check Swift
R CMD build Swift # produces ./Swift_0.1.tar.gz

wget http://www.ci.uchicago.edu/~wilde/Swift_0.1.tar.hz
R CMD INSTALL -l ~/RLibrary Swift_0.1.tar.gz
export R_LIBS=~/RLibrary
R
require(Swift)