two updated posts, one with updated credits

Author: eddelbuettel

_posts/2013-01-31-using-boost-with-bh.md

@@ -13,7 +13,7 @@ and I had numerous discussions about a basic [Boost](http://www.boost.org) infra
 for other CRAN packages. JJ and Romain chipped in as well, and Jay finally took the lead by first creating a 
 [repo on R-Forge](http://boostheaders.r-forge.r-project.org/). And now the package is out, so what follows is a little demo.
 
-This example borrows something already implemented in my [RcppBDT]((http://cran.r-project.org/package=RcppBDT) package which wraps
+This example borrows something already implemented in my [RcppBDT](http://cran.r-project.org/package=RcppBDT) package which wraps
 code from [Boost Date_Time](http://www.boost.org/doc/libs/1_52_0/doc/html/date_time.html) for R.  
 Here, we compute the so-called [IMM Date](http://en.wikipedia.org/wiki/IMM_dates) -- generally the
 the third Wednesday of the month (in the last month of the quarter).  Boost has a function computing the _Nth day of the Mth week_ 
@@ -24,7 +24,6 @@ the compilation will see the headers files provided by BH.  Which happen to be t
 And that is all it takes.
 
 
-
 {% highlight cpp %}
 // Use brandnew CRAN package BH for Boost headers
 
@@ -46,7 +45,6 @@ Rcpp::Date getIMMDate(int mon, int year) {
 }
 {% endhighlight %}
 
-
 We can test this from R for 2013 by computing the first two:
 
 {% highlight r %}
@@ -56,7 +54,7 @@ getIMMDate(3, 2013)
 
 
 <pre class="output">
-[1] "2013-03-20"
+[1] &quot;2013-03-20&quot;
 </pre>
 
 
@@ -68,10 +66,9 @@ getIMMDate(6, 2013)
 
 
 <pre class="output">
-[1] "2013-06-19"
+[1] &quot;2013-06-19&quot;
 </pre>
 
-
 And for kicks, the same for 2033:
 
 {% highlight r %}
@@ -81,7 +78,7 @@ getIMMDate(3, 2033)
 
 
 <pre class="output">
-[1] "2033-03-16"
+[1] &quot;2033-03-16&quot;
 </pre>
 
 
@@ -93,10 +90,9 @@ getIMMDate(6, 2033)
 
 
 <pre class="output">
-[1] "2033-06-15"
+[1] &quot;2033-06-15&quot;
 </pre>
 
-
 The BH package is still pretty raw. For example, [yesterday's Rcpp
 Gallery post on Boost foreach](../boost-foreach)] does not build as
 we have not yet included the relevant Boost library. So far, BH reflects the needs of 

_posts/2013-05-16-using-rcppprogress.md

@@ -3,6 +3,8 @@ title: Using RcppProgress to control the long computations in C++
 author: Karl Forner
 license: GPL (>= 2)
 tags: interrupt openmp
+updated: Jul 09, 2017
+updateauthor: Matt Dziubinski
 summary: Demonstrates how to display a progress bar and interrupt C++ code.
 layout: post
 src: 2013-05-16-using-rcppprogress.Rmd
@@ -41,7 +43,6 @@ double long_computation(int nb) {
 {% endhighlight %}
 
 
-
 {% highlight r %}
     system.time(s  <- long_computation(1000))
 {% endhighlight %}
@@ -50,7 +51,7 @@ double long_computation(int nb) {
 
 <pre class="output">
    user  system elapsed 
-  0.116   0.000   0.116 
+  0.116   0.000   0.114 
 </pre>
 
 
@@ -62,11 +63,10 @@ double long_computation(int nb) {
 
 
 <pre class="output">
-[1] 1002
+[1] 1002.32
 </pre>
 
 
-
 ## Checking for user interrupts
 
 Let's modify our code to add a check for user interruption by calling the function
@@ -97,7 +97,6 @@ double long_computation2(int nb) {
 {% endhighlight %}
 
 
-
 {% highlight r %}
     system.time(s  <- long_computation2(3000)) # interrupt me
 {% endhighlight %}
@@ -106,7 +105,7 @@ double long_computation2(int nb) {
 
 <pre class="output">
    user  system elapsed 
-  1.044   0.000   1.044 
+  1.012   0.000   1.022 
 </pre>
 
 
@@ -118,11 +117,10 @@ double long_computation2(int nb) {
 
 
 <pre class="output">
-[1] 3002
+[1] 3002.32
 </pre>
 
 
-
 You may wonder why we put the `check_abort` call in the first loop instead
 that in the second.  The performance cost of `check_abort` call is not
 negligible. It should be put in a place called often enough (once per
@@ -139,6 +137,7 @@ it at a place called at least every second.
 {% highlight cpp %}
 // [[Rcpp::depends(RcppProgress)]]
 #include <progress.hpp>
+#include <progress_bar.hpp>
 // [[Rcpp::export]]
 double long_computation3(int nb, bool display_progress=true) {
     double sum = 0;
@@ -156,7 +155,6 @@ double long_computation3(int nb, bool display_progress=true) {
 {% endhighlight %}
 
 
-
 {% highlight r %}
     system.time(s  <- long_computation3(3000)) # interrupt me
 {% endhighlight %}
@@ -165,7 +163,7 @@ double long_computation3(int nb, bool display_progress=true) {
 
 <pre class="output">
    user  system elapsed 
-  1.072   0.000   1.073 
+  1.156   0.004   1.196 
 </pre>
 
 
@@ -177,22 +175,21 @@ double long_computation3(int nb, bool display_progress=true) {
 
 
 <pre class="output">
-[1] 3002
+[1] 3002.32
 </pre>
 
-
 ## OpenMP support
 
-First we need this to enable OpenMP support for gcc:
+First we need this to enable OpenMP support for `gcc`. In the early days we used
 
 
 {% highlight r %}
 Sys.setenv("PKG_CXXFLAGS"="-fopenmp")
 Sys.setenv("PKG_LIBS"="-fopenmp")
 {% endhighlight %}
 
-
-Future Rcpp versions should have a plugin which does this for us.
+and more recent version of Rcpp have a plugin
+Recent Rcpp versions should have a plugin which does this for us.
 
 Here is an OpenMP version of our function:
 
@@ -201,6 +198,7 @@ Here is an OpenMP version of our function:
 #ifdef _OPENMP
 #include <omp.h>
 #endif
+// [[Rcpp::plugins(openmp)]]
 // [[Rcpp::depends(RcppProgress)]]
 #include <progress.hpp>
 // [[Rcpp::export]]
@@ -224,7 +222,6 @@ double long_computation_omp(int nb, int threads=1) {
 }
 {% endhighlight %}
 
-
 Now check that it is parallelized:
 
 {% highlight r %}
@@ -235,7 +232,7 @@ Now check that it is parallelized:
 
 <pre class="output">
    user  system elapsed 
-  4.208   0.000   1.069 
+  2.848   0.004   0.990 
 </pre>
 
 
@@ -247,7 +244,7 @@ Now check that it is parallelized:
 
 
 <pre class="output">
-[1] 5002
+[1] 5002.14
 </pre>
 
 
@@ -260,7 +257,7 @@ Now check that it is parallelized:
 
 <pre class="output">
    user  system elapsed 
-  2.948   0.000   2.949 
+  2.836   0.004   2.851 
 </pre>
 
 
@@ -272,28 +269,29 @@ Now check that it is parallelized:
 
 
 <pre class="output">
-[1] 5002
+[1] 5002.32
 </pre>
 
-
 ## adding progress monitoring to the openMP function
 
 
 {% highlight cpp %}
 #ifdef _OPENMP
 #include <omp.h>
 #endif
+// [[Rcpp::plugins(openmp)]]
 // [[Rcpp::depends(RcppProgress)]]
 #include <progress.hpp>
+#include <progress_bar.hpp>
 // [[Rcpp::export]]
-double long_computation_omp2(int nb, int threads=1) {
+double long_computation_omp2(const int nb, int threads=1) {
 #ifdef _OPENMP
     if ( threads > 0 )
         omp_set_num_threads( threads );
 #endif
     Progress p(nb, true);
     double sum = 0;
-#pragma omp parallel for schedule(dynamic)   
+#pragma omp parallel for default(none) reduction(+ : sum) schedule(dynamic)
     for (int i = 0; i < nb; ++i) {
         double thread_sum = 0;
         if ( ! Progress::check_abort() ) {
@@ -309,37 +307,26 @@ double long_computation_omp2(int nb, int threads=1) {
 {% endhighlight %}
 
 
-
 {% highlight r %}
-    system.time(s <- long_computation_omp2(5000, 4))
+system.time(s <- long_computation_omp2(5000, 4))
 {% endhighlight %}
 
-
-
-<pre class="output">
-   user  system elapsed 
-  4.108   0.000   1.049 
-</pre>
-
-
 ## Test it now
 
 If you want to test it now in your R console, just paste the following code
 (after installing the 
 [RcppProgress](http://cran.r-project.org/web/packages/RcppProgress/index.html)
 package, of course):
 
-{% highlight r %}
-library(Rcpp)
-Sys.setenv("PKG_CXXFLAGS"="-fopenmp")
-Sys.setenv("PKG_LIBS"="-fopenmp")
 
-code='
+{% highlight cpp %}
 #ifdef _OPENMP
 #include <omp.h>
 #endif
+// [[Rcpp::plugins(openmp)]]
 // [[Rcpp::depends(RcppProgress)]]
 #include <progress.hpp>
+#include <progress_bar.hpp>
 
 // [[Rcpp::export]]
 double long_computation_omp2(int nb, int threads=1) {
@@ -364,9 +351,13 @@ double long_computation_omp2(int nb, int threads=1) {
 
     return sum + nb;
 }
-'
+{% endhighlight %}
 
-sourceCpp(code=code)
+and run
+
+
+{% highlight r %}
+Rcpp::sourceCpp(code=code)
 s <- long_computation_omp2(10000, 4)
 {% endhighlight %}