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language, the use of loops in R, and especially nested loops, constitutes a significant performance bottleneck. Whenever possible you | language, the use of loops in R, and especially nested loops, constitutes a significant performance bottleneck. Whenever possible you | ||
should try to use vectorized forms of R functions and more functional elements of the R programming language like the family of | should try to use vectorized forms of R functions and more functional elements of the R programming language like the family of | ||
< | <code>apply</code> functions and the <code>ifelse</code> function. This will frequently offer you a far better performance gain by eliminating | ||
a loop altogether instead of simply parallelizing the (slow) execution of this loop across several CPU cores. | a loop altogether instead of simply parallelizing the (slow) execution of this loop across several CPU cores. | ||
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=== doParallel and makeCluster === <!--T:56--> | === doParallel and makeCluster === <!--T:56--> | ||
====Usage==== | ====Usage==== | ||
You must register the backend by feeding it the nodes name multiplied by the desired number of processes. For instance, with two nodes (node1 and node2) and two processes, we would create a cluster composed of : < | You must register the backend by feeding it the nodes name multiplied by the desired number of processes. For instance, with two nodes (node1 and node2) and two processes, we would create a cluster composed of : <code>node1 node1 node2 node2</code> hosts. The ''PSOCK'' cluster type will run commands through SSH connections into the nodes. | ||
====Running==== <!--T:57--> | ====Running==== <!--T:57--> | ||
1. Place your R code in a script file, in this case the file is called < | 1. Place your R code in a script file, in this case the file is called <code>test_makecluster.R</code>. | ||
{{File | {{File | ||
|name=test_makecluster.R | |name=test_makecluster.R | ||
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<!--T:62--> | <!--T:62--> | ||
2. Copy the following content in a job submission script called < | 2. Copy the following content in a job submission script called <code>job_makecluster.sh</code>: | ||
{{File | {{File | ||
|name=job_makecluster.sh | |name=job_makecluster.sh | ||