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POCompile R package with TBB
 

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  1. POCompile R package with TBB
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    <p>I want to compile R package by using TBB (Threading Building Blocks). I used a simple example in the internet to test whether it is possible to develop R packages with TBB or not.</p> <p>I create Makevars file which include these flags for gcc:</p> <pre><code>PKG_CPPFLAGS=-I/opt/tbb41_20121003oss/include/ -O3 -g3 -Wall -c -fmessage-length=0 PKG_LIBS=-L/opt/tbb41_20121003oss/build/linux_intel64_gcc_cc4.4.6_libc2.12_kernel2.6.32_release/ </code></pre> <p>And the source code is:</p> <pre><code>#include &lt;iostream&gt; #include &lt;string&gt; #include &lt;algorithm&gt; #include "tbb/parallel_for.h" #include "tbb/blocked_range.h" using namespace tbb; using namespace std; static const size_t N = 23; class SubStringFinder { const string str; size_t *max_array; size_t *pos_array; public: void operator() ( const blocked_range&lt;size_t&gt;&amp; r ) const { for ( size_t i = r.begin(); i != r.end(); ++i ) { size_t max_size = 0, max_pos = 0; for (size_t j = 0; j &lt; str.size(); ++j) if (j != i) { size_t limit = str.size()-max(i,j); for (size_t k = 0; k &lt; limit; ++k) { if (str[i + k] != str[j + k]) break; if (k &gt; max_size) { max_size = k; max_pos = j; } } } max_array[i] = max_size; pos_array[i] = max_pos; } } SubStringFinder(string &amp;s, size_t *m, size_t *p) : str(s), max_array(m), pos_array(p) { } }; extern "C" { int test() { string str[N] = { string("a"), string("b") }; for (size_t i = 2; i &lt; N; ++i) str[i] = str[i-1]+str[i-2]; string &amp;to_scan = str[N-1]; size_t num_elem = to_scan.size(); size_t *max = new size_t[num_elem]; size_t *pos = new size_t[num_elem]; parallel_for(blocked_range&lt;size_t&gt;(0, num_elem ), SubStringFinder( to_scan, max, pos ) ); // for (size_t i = 0; i &lt; num_elem; ++i) cout &lt;&lt; " " &lt;&lt; max[i] &lt;&lt; "(" &lt;&lt; pos[i] &lt;&lt; ")" &lt;&lt; endl; delete[] pos; delete[] max; } } </code></pre> <p>When I compile the code I get this error:</p> <pre><code> library/2.14/test/libs/test.so: undefined symbol: _ZTIN3tbb4taskE </code></pre> <p>If I remove this line I can compile the program:</p> <pre><code>parallel_for(blocked_range&lt;size_t&gt;(0, num_elem ), SubStringFinder( to_scan, max, pos ) ); </code></pre> <p>Which make the TBB library useless!</p> <p>In addition I added</p> <pre><code> export /opt/tbb41_20121003oss/build/linux_intel64_gcc_cc4.4.6_libc2.12_kernel2.6.32_release/ </code></pre> <p>to the .bashrc</p> <p>I use centos.</p>
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    1. PTQuestion
    1. USuser1436187
    1. USuser1436187
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    1. COThat is a **linker** error, not a compiler error. You need `PKG_LIBS` too.
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      1. POCompile R package with TBB
      1. USDirk Eddelbuettel
    2. COAdd -ltbb to PKG_LIBS in order to link with the TBB shared library
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      1. POCompile R package with TBB
      1. USAlexey Kukanov
 

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