cboettig

#!/bin/bash
for f in *.JPG; do mv "$f" "`basename "$f" .JPG`.jpg"; done;

cboettig

## Credit: Taken from:  http://stackoverflow.com/questions/1358003/tricks-to-manage-the-available-memory-in-an-r-session
# improved list of objects
.ls.objects <- function (pos = 1, pattern, order.by,
                        decreasing=FALSE, head=FALSE, n=5) {
    napply <- function(names, fn) sapply(names, function(x)
                                         fn(get(x, pos = pos)))
    names <- ls(pos = pos, pattern = pattern)
    obj.class <- napply(names, function(x) as.character(class(x))[1])
    obj.mode <- napply(names, mode)
    obj.type <- ifelse(is.na(obj.class), obj.mode, obj.class)

cboettig

#!/bin/sh
echo $(date +"%y-%m-%d-%H:%M:%S") $(free -m | sed -n '2p' | awk '{print $3}') MB  >> mem.log

cboettig

# Commands to flush swap.
# Don't try this if swap in use exceeds memory available.
sudo swapoff -a
sudo swapon -a

# sync writes things in memory to hard disk (kernel) for stability.
sync

cboettig

library(Rmpi)
 
## load the packages we'll need
RLIBS="~/R/x86_64-redhat-linux-gnu-library/2.13"
.libPaths(c(RLIBS, .libPaths()))
 
### Direct RMPI way:
mpi.spawn.Rslaves(nslaves=15)
slavefn <- function() { print(paste("Hello from", foldNumber)) }
mpi.bcast.cmd(foldNumber <- mpi.comm.rank())

cboettig

#!/bin/bash
## Use the current working directory
#$ -cwd
## use bash commands
#$ -S /bin/bash
## combine error and output files
#$ -j y
## Parallel for openmp:
#$ -pe threaded 16
## Launch parallel mpi threads

cboettig

\documentclass{elsarticle}

%% Redefines the elsarticle footer
\makeatletter
\def\ps@pprintTitle{%
 \let\@oddhead\@empty
 \let\@evenhead\@empty
 \def\@oddfoot{\it \hfill\today}%
 \let\@evenfoot\@oddfoot}
\makeatother

cboettig

RSCRIPT = Rscript

pdfclean:
	rm -f *.pdf

clean:
	rm -f index.html
	rm -f *.tex *.bbl *.blg *.aux *.out *.log *.spl

cboettig

## Makefile to use knitr in the vignette
RSCRIPT = Rscript

all: rfishbase.pdf

rfishbase.pdf: rfishbase/rfishbase.Rnw
	cp -f rfishbase/rfishbase.Rnw .
	$(RSCRIPT) --vanilla -e "require(knitr); knit( 'rfishbase.Rnw');"
	#Compile in latex, but keep aux file till we make bibliography
	$(RSCRIPT) -e "tools::texi2dvi( 'rfishbase.tex', pdf = TRUE, clean = FALSE )" 

cboettig

module swap pgi intel
module swap openmpi openmpi-intel
module load gsl
module load R/2.12.1
rm wrightscape/config*
cp wrightscape/src/nersc_makevars wrightscape/src/Makevars
R CMD INSTALL wrightscape