Re: [R] R Running slow on Ubuntu
Thanks guys. I'll look into this and tell you if I come up with anything. -R On Saturday, March 15, 2014, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Comparing with an unspecified benchmark makes answering this too hard. Following instructions in the Posting Guide will lead to more accurate Q and A. Note that you may not need to compile if you have not as yet followed the recommendations: http://cran.r-project.org/bin/linux/ubuntu/README. There are apparently compile-time options that can obtain noticeable improvements for certain classes of problems, but if you and your friend are both using standard installs that seems unlikely to explain the difference. I have not needed a custom compile (yet?). --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.us javascript:;Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On March 15, 2014 3:46:57 AM PDT, Augusto Cesar augusto.ce...@gmail.comjavascript:; wrote: My guess is that maybe the default Ubuntu binaries aren't compiled with MKL (Math Kernel Library) support and thus with no multithreading. I would suggest doing a quick research on how to re-compile R with MKL support and maybe you'll be good to go. On Fri, Mar 14, 2014 at 9:45 PM, Russell Bainer russ.bai...@gmail.comjavascript:; wrote: Hi All, I've run across an odd phenomenon and I am wondering if someone might be able to provide insight as to what is going on. I'm running some R code that was provided by a collaborator, who is not a very experienced R programmer (e.g., the code is functional but not very efficient). When I run it from the terminal or command line everything executes, albeit very slowly- the logfile suggests that the program is about 5% done after running over last weekend. Top indicates that it is maxing out one of my CPUs and chewing up a lot of memory, which I expect. The strange thing is that my collaborator insists that the code executes on the order of minutes on his 2012 macbook pro with 8G of memory. I am running it with ubuntu 12.04 on a dual-core i7 with 32G, and it's slow as molasses. That suggests a configuration issue of some kind with R that I might not be aware of (I am more experienced in R and usually don't write code that requires resources like that). I have played with my swappiness and the effect seems to be minimal. Can anyone suggest something else that could be going on? I have considered trying to run it directly on a unix server, but the code has a lot of third-party dependencies that would be a bit of work to set up for simple troubleshooting. And naturally I'd prefer that R be configured correctly in the event that I need to locally run something more intense in the future. Thanks in advance for any advice you can give. This message has been cross-posted omn the ubuntu forums. -R [[alternative HTML version deleted]] __ R-help@r-project.org javascript:; mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Running slow on Ubuntu
http://www.cybaea.net/Blogs/Faster-R-through-better-BLAS.html any help? On Mar 16, 2014 9:38 PM, Russell Bainer russ.bai...@gmail.com wrote: Thanks guys. I'll look into this and tell you if I come up with anything. -R On Saturday, March 15, 2014, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Comparing with an unspecified benchmark makes answering this too hard. Following instructions in the Posting Guide will lead to more accurate Q and A. Note that you may not need to compile if you have not as yet followed the recommendations: http://cran.r-project.org/bin/linux/ubuntu/README. There are apparently compile-time options that can obtain noticeable improvements for certain classes of problems, but if you and your friend are both using standard installs that seems unlikely to explain the difference. I have not needed a custom compile (yet?). --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.us javascript:;Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On March 15, 2014 3:46:57 AM PDT, Augusto Cesar augusto.ce...@gmail.com javascript:; wrote: My guess is that maybe the default Ubuntu binaries aren't compiled with MKL (Math Kernel Library) support and thus with no multithreading. I would suggest doing a quick research on how to re-compile R with MKL support and maybe you'll be good to go. On Fri, Mar 14, 2014 at 9:45 PM, Russell Bainer russ.bai...@gmail.com javascript:; wrote: Hi All, I've run across an odd phenomenon and I am wondering if someone might be able to provide insight as to what is going on. I'm running some R code that was provided by a collaborator, who is not a very experienced R programmer (e.g., the code is functional but not very efficient). When I run it from the terminal or command line everything executes, albeit very slowly- the logfile suggests that the program is about 5% done after running over last weekend. Top indicates that it is maxing out one of my CPUs and chewing up a lot of memory, which I expect. The strange thing is that my collaborator insists that the code executes on the order of minutes on his 2012 macbook pro with 8G of memory. I am running it with ubuntu 12.04 on a dual-core i7 with 32G, and it's slow as molasses. That suggests a configuration issue of some kind with R that I might not be aware of (I am more experienced in R and usually don't write code that requires resources like that). I have played with my swappiness and the effect seems to be minimal. Can anyone suggest something else that could be going on? I have considered trying to run it directly on a unix server, but the code has a lot of third-party dependencies that would be a bit of work to set up for simple troubleshooting. And naturally I'd prefer that R be configured correctly in the event that I need to locally run something more intense in the future. Thanks in advance for any advice you can give. This message has been cross-posted omn the ubuntu forums. -R [[alternative HTML version deleted]] __ R-help@r-project.org javascript:; mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R Running slow on Ubuntu
Hi All, I've run across an odd phenomenon and I am wondering if someone might be able to provide insight as to what is going on. I'm running some R code that was provided by a collaborator, who is not a very experienced R programmer (e.g., the code is functional but not very efficient). When I run it from the terminal or command line everything executes, albeit very slowly- the logfile suggests that the program is about 5% done after running over last weekend. Top indicates that it is maxing out one of my CPUs and chewing up a lot of memory, which I expect. The strange thing is that my collaborator insists that the code executes on the order of minutes on his 2012 macbook pro with 8G of memory. I am running it with ubuntu 12.04 on a dual-core i7 with 32G, and it's slow as molasses. That suggests a configuration issue of some kind with R that I might not be aware of (I am more experienced in R and usually don't write code that requires resources like that). I have played with my swappiness and the effect seems to be minimal. Can anyone suggest something else that could be going on? I have considered trying to run it directly on a unix server, but the code has a lot of third-party dependencies that would be a bit of work to set up for simple troubleshooting. And naturally I'd prefer that R be configured correctly in the event that I need to locally run something more intense in the future. Thanks in advance for any advice you can give. This message has been cross-posted omn the ubuntu forums. -R [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Running slow on Ubuntu
My guess is that maybe the default Ubuntu binaries aren't compiled with MKL (Math Kernel Library) support and thus with no multithreading. I would suggest doing a quick research on how to re-compile R with MKL support and maybe you'll be good to go. On Fri, Mar 14, 2014 at 9:45 PM, Russell Bainer russ.bai...@gmail.com wrote: Hi All, I've run across an odd phenomenon and I am wondering if someone might be able to provide insight as to what is going on. I'm running some R code that was provided by a collaborator, who is not a very experienced R programmer (e.g., the code is functional but not very efficient). When I run it from the terminal or command line everything executes, albeit very slowly- the logfile suggests that the program is about 5% done after running over last weekend. Top indicates that it is maxing out one of my CPUs and chewing up a lot of memory, which I expect. The strange thing is that my collaborator insists that the code executes on the order of minutes on his 2012 macbook pro with 8G of memory. I am running it with ubuntu 12.04 on a dual-core i7 with 32G, and it's slow as molasses. That suggests a configuration issue of some kind with R that I might not be aware of (I am more experienced in R and usually don't write code that requires resources like that). I have played with my swappiness and the effect seems to be minimal. Can anyone suggest something else that could be going on? I have considered trying to run it directly on a unix server, but the code has a lot of third-party dependencies that would be a bit of work to set up for simple troubleshooting. And naturally I'd prefer that R be configured correctly in the event that I need to locally run something more intense in the future. Thanks in advance for any advice you can give. This message has been cross-posted omn the ubuntu forums. -R [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Augusto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Running slow on Ubuntu
Comparing with an unspecified benchmark makes answering this too hard. Following instructions in the Posting Guide will lead to more accurate Q and A. Note that you may not need to compile if you have not as yet followed the recommendations: http://cran.r-project.org/bin/linux/ubuntu/README. There are apparently compile-time options that can obtain noticeable improvements for certain classes of problems, but if you and your friend are both using standard installs that seems unlikely to explain the difference. I have not needed a custom compile (yet?). --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On March 15, 2014 3:46:57 AM PDT, Augusto Cesar augusto.ce...@gmail.com wrote: My guess is that maybe the default Ubuntu binaries aren't compiled with MKL (Math Kernel Library) support and thus with no multithreading. I would suggest doing a quick research on how to re-compile R with MKL support and maybe you'll be good to go. On Fri, Mar 14, 2014 at 9:45 PM, Russell Bainer russ.bai...@gmail.com wrote: Hi All, I've run across an odd phenomenon and I am wondering if someone might be able to provide insight as to what is going on. I'm running some R code that was provided by a collaborator, who is not a very experienced R programmer (e.g., the code is functional but not very efficient). When I run it from the terminal or command line everything executes, albeit very slowly- the logfile suggests that the program is about 5% done after running over last weekend. Top indicates that it is maxing out one of my CPUs and chewing up a lot of memory, which I expect. The strange thing is that my collaborator insists that the code executes on the order of minutes on his 2012 macbook pro with 8G of memory. I am running it with ubuntu 12.04 on a dual-core i7 with 32G, and it's slow as molasses. That suggests a configuration issue of some kind with R that I might not be aware of (I am more experienced in R and usually don't write code that requires resources like that). I have played with my swappiness and the effect seems to be minimal. Can anyone suggest something else that could be going on? I have considered trying to run it directly on a unix server, but the code has a lot of third-party dependencies that would be a bit of work to set up for simple troubleshooting. And naturally I'd prefer that R be configured correctly in the event that I need to locally run something more intense in the future. Thanks in advance for any advice you can give. This message has been cross-posted omn the ubuntu forums. -R [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Running slow on Ubuntu
Installing the openbals library may help. Shige On Sat, Mar 15, 2014 at 12:00 PM, Jeff Newmiller jdnew...@dcn.davis.ca.uswrote: Comparing with an unspecified benchmark makes answering this too hard. Following instructions in the Posting Guide will lead to more accurate Q and A. Note that you may not need to compile if you have not as yet followed the recommendations: http://cran.r-project.org/bin/linux/ubuntu/README. There are apparently compile-time options that can obtain noticeable improvements for certain classes of problems, but if you and your friend are both using standard installs that seems unlikely to explain the difference. I have not needed a custom compile (yet?). --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On March 15, 2014 3:46:57 AM PDT, Augusto Cesar augusto.ce...@gmail.com wrote: My guess is that maybe the default Ubuntu binaries aren't compiled with MKL (Math Kernel Library) support and thus with no multithreading. I would suggest doing a quick research on how to re-compile R with MKL support and maybe you'll be good to go. On Fri, Mar 14, 2014 at 9:45 PM, Russell Bainer russ.bai...@gmail.com wrote: Hi All, I've run across an odd phenomenon and I am wondering if someone might be able to provide insight as to what is going on. I'm running some R code that was provided by a collaborator, who is not a very experienced R programmer (e.g., the code is functional but not very efficient). When I run it from the terminal or command line everything executes, albeit very slowly- the logfile suggests that the program is about 5% done after running over last weekend. Top indicates that it is maxing out one of my CPUs and chewing up a lot of memory, which I expect. The strange thing is that my collaborator insists that the code executes on the order of minutes on his 2012 macbook pro with 8G of memory. I am running it with ubuntu 12.04 on a dual-core i7 with 32G, and it's slow as molasses. That suggests a configuration issue of some kind with R that I might not be aware of (I am more experienced in R and usually don't write code that requires resources like that). I have played with my swappiness and the effect seems to be minimal. Can anyone suggest something else that could be going on? I have considered trying to run it directly on a unix server, but the code has a lot of third-party dependencies that would be a bit of work to set up for simple troubleshooting. And naturally I'd prefer that R be configured correctly in the event that I need to locally run something more intense in the future. Thanks in advance for any advice you can give. This message has been cross-posted omn the ubuntu forums. -R [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running *slow*
Thank you Michael and Patrick for your responses. Michael - your code ran in under 5 minutes, which I find stunning, and Patrick I have sent the Inferno doc to the copier for printing and reading this weekend. I now have 8 million values in my lookup table and want to replace each value in Dat with the index of that value in the lookup table. In line with Chapter 2 in the Inferno doc, I created a list of appropriate size first, rather than growing it, but still couldn't figure out how to do it without looping in R, so it still runs extremely slowly, even just to process the first 1000 values in Dat. My original code (before I tried specifiying the size of Dat2) was: Dat2 - c() for (i in 1:nrow(Dat)) { for (j in 1:2) { Dat2 - c(Dat2, match(Dat[i,j], ltable)) }} write(t(edgelist), EL.txt, ncolumns=2) Can anyone suggest a way of doing this without looping in R? Or is the bottleneck the c function? I am looking at apply this morning, but Gentleman (2009) suggests apply isn't very efficient. -- View this message in context: http://r.789695.n4.nabble.com/Running-slow-tp3878093p3881365.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running *slow*
Hi, Thomas, if I'm not completely mistaken Dat2 - match( t( Dat), ltable) should do what you want. Hth -- Gerrit On Fri, 7 Oct 2011, thomas.chesney wrote: Thank you Michael and Patrick for your responses. Michael - your code ran in under 5 minutes, which I find stunning, and Patrick I have sent the Inferno doc to the copier for printing and reading this weekend. I now have 8 million values in my lookup table and want to replace each value in Dat with the index of that value in the lookup table. In line with Chapter 2 in the Inferno doc, I created a list of appropriate size first, rather than growing it, but still couldn't figure out how to do it without looping in R, so it still runs extremely slowly, even just to process the first 1000 values in Dat. My original code (before I tried specifiying the size of Dat2) was: Dat2 - c() for (i in 1:nrow(Dat)) { for (j in 1:2) { Dat2 - c(Dat2, match(Dat[i,j], ltable)) }} write(t(edgelist), EL.txt, ncolumns=2) Can anyone suggest a way of doing this without looping in R? Or is the bottleneck the c function? I am looking at apply this morning, but Gentleman (2009) suggests apply isn't very efficient. -- View this message in context: http://r.789695.n4.nabble.com/Running-slow-tp3878093p3881365.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running *slow*
Gerrit, Looks like it does and in less than--an incredible--one minute! Thank you! -- View this message in context: http://r.789695.n4.nabble.com/Running-slow-tp3878093p3881588.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running *slow*
Making a bit more sense now: If you are translating code into R that has a double for loop, think. The R Inferno, Page 18. -- View this message in context: http://r.789695.n4.nabble.com/Running-slow-tp3878093p3881951.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Running *slow*
Anyone got any hints on how to make this code more efficient? An early version (which to be fair did more than this one is) ran for 330 hours and produced no output. I have a two column table, Dat, with 12,000,000 rows and I want to produce a lookup table, ltable, in a 1 dimensional matrix with one copy of each of the values in Dat: for (i in 1:nrow(Dat)) { for (j in 1:2) { #If next value is already in ltable, do nothing if (is.na(match(Dat[i,j], ltable))){ltable - rbind(ltable,Dat[i,j])} } } but it takes forever to produce anything. Any advice gratefully received. Thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running *slow*
?unique x - matrix(c(1:6, 6:1),ncol=2) x.temp - x dim(x.temp) - NULL unique(x.temp) Michael On Thu, Oct 6, 2011 at 8:37 AM, Thomas chesney@gmail.com wrote: Anyone got any hints on how to make this code more efficient? An early version (which to be fair did more than this one is) ran for 330 hours and produced no output. I have a two column table, Dat, with 12,000,000 rows and I want to produce a lookup table, ltable, in a 1 dimensional matrix with one copy of each of the values in Dat: for (i in 1:nrow(Dat)) { for (j in 1:2) { #If next value is already in ltable, do nothing if (is.na(match(Dat[i,j], ltable))){ltable - rbind(ltable,Dat[i,j])} } } but it takes forever to produce anything. Any advice gratefully received. Thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running *slow*
Probably most of the time you're waiting for this you are in Circle 2 of 'The R Inferno'. If the values are numbers, you might also be in Circle 1. On 06/10/2011 13:37, Thomas wrote: Anyone got any hints on how to make this code more efficient? An early version (which to be fair did more than this one is) ran for 330 hours and produced no output. I have a two column table, Dat, with 12,000,000 rows and I want to produce a lookup table, ltable, in a 1 dimensional matrix with one copy of each of the values in Dat: for (i in 1:nrow(Dat)) { for (j in 1:2) { #If next value is already in ltable, do nothing if (is.na(match(Dat[i,j], ltable))){ltable - rbind(ltable,Dat[i,j])} } } but it takes forever to produce anything. Any advice gratefully received. Thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Patrick Burns pbu...@pburns.seanet.com twitter: @portfolioprobe http://www.portfolioprobe.com/blog http://www.burns-stat.com (home of 'Some hints for the R beginner' and 'The R Inferno') __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running *slow*
Patrick is right, most of the time is probably taken up for the reasons documented in the (masterful) R Inferno, namely the rbind() calls. There is another problem though and it gets at the very core of R, and for that matter, all interpreted languages that I'm familiar with. I'll give a fairly elementary explanation and gloss over many of the subtleties that R core worries about so we mere mortals don't have to. At the end of the day, everything is looped, there's no way to get around it. However, from a code perspective we have a choice of looping in C or R. Whenever possible it is better to loop in C than R and most of the key built-in functions, like unique(), are designed to do just that. The reason for it is pretty straightforward: consider what has to happen to run a loop in R: Iterator is defined: a sequence of C calls start this first line of loop is hit - interpreted by R - sent to C code - executed - changed back into an R result - passed to the next line of the loop iterator is increased: C again second line of loop is hit - interpreted by R - sent to C code - executed - changed back into an R result - passed to the next line of the loop etc. Complicated and/or multiple lines of code only compound the problem because you have to go up and down multiple times at each iteration. Looping on the C level gets rid of all those translations between C/R, save 2, and thereby mightily increases efficiency. Hence, even if you are using the same (or heaven forbid a faster!) algorithm on the R level, it can look super slow because of all the moving up and down the ladder; I don't know how unique.C is implemented, but my guess is it's more or less like what you have now, with more efficient memory usage/preallocation, it just looks *much* faster because of the C architecture. DISCLAIMER: there are quite a few inaccuracies, most small, maybe a few large, in here, and I probably only am aware of a small fraction thereof, but this wasn't intended to be a super accurate explanation. On another note, I should explain my solution a little more clearly. A straight call to unique() would check for unique ROWS not values of x. I take x, make a copy so as not to harm the original object, strip if of its dimensionality (thereby converting it to a vector efficiently), and then apply unique() which will now find unique values. It's not a huge thing, but not immediately apparent from what I did. Hope this helps, Michael On Thu, Oct 6, 2011 at 11:59 AM, Patrick Burns pbu...@pburns.seanet.com wrote: Probably most of the time you're waiting for this you are in Circle 2 of 'The R Inferno'. If the values are numbers, you might also be in Circle 1. On 06/10/2011 13:37, Thomas wrote: Anyone got any hints on how to make this code more efficient? An early version (which to be fair did more than this one is) ran for 330 hours and produced no output. I have a two column table, Dat, with 12,000,000 rows and I want to produce a lookup table, ltable, in a 1 dimensional matrix with one copy of each of the values in Dat: for (i in 1:nrow(Dat)) { for (j in 1:2) { #If next value is already in ltable, do nothing if (is.na(match(Dat[i,j], ltable))){ltable - rbind(ltable,Dat[i,j])} } } but it takes forever to produce anything. Any advice gratefully received. Thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Patrick Burns pbu...@pburns.seanet.com twitter: @portfolioprobe http://www.portfolioprobe.com/blog http://www.burns-stat.com (home of 'Some hints for the R beginner' and 'The R Inferno') __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.