On 18 April 2008 at 13:03, tyler wrote: | Hi, | | I have only the vaguest notions of what parallel programing, but I think | I have a situation where it might be of use to me, or at least provide | me with the opportunity to learn more about it. Before I invest in | figuring out the nuts and bolts, can anyone confirm that this is a sane | approach, or provide alternatives that I could pursue? | | I'm running stochastic simulations, with the actual simulation in C | code, with an R interface to set up the parameters, format the output, | and save the resulting objects periodically through the run. The basic | layout is: | | R function sets up the run | R for(c = 0; c < CYCLES; c++) | call C function | C for(i = 0; i < TIME; i++) | immigration loop adds individuals to the recruit vector | birth loop adds individuals to the recruit vector | recruit vector is added to the community vector | death loop removes excess individuals | Return results to R, which processes and saves the objects | Repeat | | A typical run has 20 cycles, each with 500 time steps, and takes about | an hour. The immigration and birth loops are independent of each other, | and so could run simultaneously. They both add to the recruit vector, | but the order of the addition doesn't matter so long as both finish | before the recruit vector is added to the community vector. The | immigration, birth, and death loop iterate over arrays in a way that the | outcome at different locations is independent. i.e., the impact of the | birth vector on recruit vector position 0 has no influence on what the | birth vector does to recruit vector position 1. | | What I'm thinking of doing is running the birth and immigration loops as | separate threads, and possibly running each of those threads as a group | of threads - so a thread for a birth loop that iterates over the first N | positions, another thread for the second N positions and so on. | | I'm keen to learn about parallel programming, but I don't understand | enough yet to make sense of the information in the R extensions manual | and the various discussions on this list about R being thread-safe. Does | it matter if R is thread-safe if the actual simulation is being computed | in separate, shared C code? | | I'm running my current, sequential code, on a cluster that supports both | OpenMP and MPI, should I figure out how to use it.
As I recall, you use Debian so do $ sudo apt-get install r-cran-snow r-cran-rmpi to get R support working out-of-the box. Then study the examples for Snow on Luke's website. [ I also have some slides on my website from presentations I gave a few years ago. ] That allows you to _easily_ do the so-called embarassingly parallel: same problem, different parameters. Or, you could also loop over CYCLES across the cluster. Start with something simple to study it and then go from there. Hope this helps, Dirk -- Three out of two people have difficulties with fractions. ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
