Dear R users; I am using R for a project. I have some PHP forms that pass parameters to R for calculations, and publish the result in HTML format by CGIwithR. I'm using a Linux machine and every things work perfectly. However, it is too slow, it takes 5 to 10 seconds to run, and even if I start R from the Shell it takes the same amount of time, which is probably due to installing packages. My first question is that how can i make R run faster? and second if I am supposed to reduce the packages which are being loaded at initiation of R, how can I limit it to only the packages that i want? and third how can i make R not to get open each time, and let it sit on the server so that, when i pass something to it , i get result faster? Sincerely, Sean
My standard algorithm for improving speed is as follows:
1. Identify what takes the most time.
2. Try to find ways in R to speed it up, e.g., converting loops
to vector operations. Many tasks in R can be performed in a variety of
different ways to get the same result but with different time.
3. If that fails, convert the most time consuming part into
compiled code and link to it.
Use "system.time" to time a single expression and
"proc.time" to
store the time at multiple places in your code; precede any test with
garbage collection (gc) to reduce variations in the answers.
An "R site search" (www.r-project.org -> Search -> "R
site
search") for "timing R" produced 126 hits, the second of which
gave
"system.time"; you might skim the rest for other ideas. A similar
search for "compute speed" produced 64 hits, some of which will
doubtless interest you if you haven't already read them.
For more help on this, please be more specific, e.g., following
the posting guide! "http://www.R-project.org/posting-guide.html".
hope this helps. spencer graves
ebashi wrote:
>Dear R users;
>I am using R for a project. I have some PHP forms that
>pass parameters to R for calculations, and publish the
>result in HTML format by CGIwithR. I'm using a Linux
>machine and every things work perfectly. However, it
>is too slow, it takes 5 to 10 seconds to run, and
>even if I start R from the Shell it takes the same
>amount of time, which is probably due to installing
>packages. My first question is that how can i make R
>run faster? and second if I am supposed to reduce the
>packages which are being loaded at initiation of R,
>how can I limit it to only the packages that i want?
>and third how can i make R not to get open each time,
>and let it sit on the server so that, when i pass
>something to it , i get result faster?
>
>Sincerely,
>Sean
>
>______________________________________________
>R-help at stat.math.ethz.ch mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
>
A few things to add to what Spencer said: - Please give more info about your setup, as the posting guide asks you to (e.g., R version, OS [which Linux distro and which release?], hardware). These things matter! As an example, the time it takes to start an R process was dramatically reduced since R-2.0.0. If you are using older version, you need to upgrade. - See the example section of ?Startup, which has an example of how to specify packages to be loaded at startup. - There's a section on profiling R code in the `Writing R Extensions' manual, that may help you pinpoint the bottleneck. - Sometimes re-thinking the organization of the computation or algorithm can make a huge difference. I remember reading in an old computing book the staggering difference between FFT and doing the computation the na?ve way. Andy> From: Spencer Graves > > My standard algorithm for improving speed is as follows: > > 1. Identify what takes the most time. > > 2. Try to find ways in R to speed it up, e.g., > converting loops > to vector operations. Many tasks in R can be performed in a > variety of > different ways to get the same result but with different time. > > 3. If that fails, convert the most time consuming part into > compiled code and link to it. > > Use "system.time" to time a single expression and > "proc.time" to > store the time at multiple places in your code; precede any > test with > garbage collection (gc) to reduce variations in the answers. > > An "R site search" (www.r-project.org -> Search -> "R site > search") for "timing R" produced 126 hits, the second of which gave > "system.time"; you might skim the rest for other ideas. A similar > search for "compute speed" produced 64 hits, some of which will > doubtless interest you if you haven't already read them. > > For more help on this, please be more specific, e.g., following > the posting guide! "http://www.R-project.org/posting-guide.html". > > hope this helps. spencer graves > > ebashi wrote: > > >Dear R users; > >I am using R for a project. I have some PHP forms that > >pass parameters to R for calculations, and publish the > >result in HTML format by CGIwithR. I'm using a Linux > >machine and every things work perfectly. However, it > >is too slow, it takes 5 to 10 seconds to run, and > >even if I start R from the Shell it takes the same > >amount of time, which is probably due to installing > >packages. My first question is that how can i make R > >run faster? and second if I am supposed to reduce the > >packages which are being loaded at initiation of R, > >how can I limit it to only the packages that i want? > >and third how can i make R not to get open each time, > >and let it sit on the server so that, when i pass > >something to it , i get result faster? > > > >Sincerely, > >Sean > > > >______________________________________________ > >R-help at stat.math.ethz.ch mailing list > >https://stat.ethz.ch/mailman/listinfo/r-help > >PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > > > > > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > >
ebashi wrote:>Dear R users; >I am using R for a project. I have some PHP forms that >pass parameters to R for calculations, and publish the >result in HTML format by CGIwithR. I'm using a Linux >machine and every things work perfectly. However, it >is too slow, it takes 5 to 10 seconds to run, and >even if I start R from the Shell it takes the same >amount of time, which is probably due to installing >packages. My first question is that how can i make R >run faster? and second if I am supposed to reduce the >packages which are being loaded at initiation of R, >how can I limit it to only the packages that i want? >and third how can i make R not to get open each time, >and let it sit on the server so that, when i pass >something to it , i get result faster? > >Have a look at RSOAP, which does exactly what you suggest and allows you to commuicate with the R session via SOAP. I'm sure there are SOAP libraries available for PHP. See http://research.warnes.net/projects/rzope/rsoap/ Tim C