Thank you Jim and Gabor. It seems that for my purpose of comparing the computational effort (not I/O) the optimal thing is to use the sum of user and system CPU times to get the total CPU. It also seems like when there is not much I/O involved, which is the case for my algorithms, the total CPU is not that different from the total elapsed time.
Best regards, Ravi. ____________________________________________________________________ Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu ----- Original Message ----- From: jim holtman <jholt...@gmail.com> Date: Sunday, February 28, 2010 0:03 am Subject: Re: [R] Which system.time() component to use? To: Ravi Varadhan <rvarad...@jhmi.edu> Cc: Gabor Grothendieck <ggrothendi...@gmail.com>, r-help@r-project.org > A lot depends on what you are trying to measure. > > You should add the system and user CPU times to get a better idea of > the CPU utilization. For some classes of problems it might be good to > separate them if you were doing a lot of I/O or other system calls > that might be using time, but for 99% of the cases adding them is the > way to go. > > You also want to look at elapsed times. If the script is CPU bound > the elapsed and total CPU times should be close. In the case that > Gabor gave of sleeping for 60 seconds, no CPU time was used, but it > was 60 seconds of elapsed time. If there is a big difference, it > might be due to a lot of I/O or possible paging if you did not have > enough memory. > > On Sat, Feb 27, 2010 at 11:44 PM, Ravi Varadhan <rvarad...@jhmi.edu> wrote: > > > > Thanks, Gabor. Your reply is helpful, but it still doesn't answer > whether I should use the sum of the first two components of > system.time (user + system CPU) or only the first one (user CPU). > > > > Ravi. > > ____________________________________________________________________ > > > > Ravi Varadhan, Ph.D. > > Assistant Professor, > > Division of Geriatric Medicine and Gerontology > > School of Medicine > > Johns Hopkins University > > > > Ph. (410) 502-2619 > > email: rvarad...@jhmi.edu > > > > > > ----- Original Message ----- > > From: Gabor Grothendieck <ggrothendi...@gmail.com> > > Date: Saturday, February 27, 2010 9:47 pm > > Subject: Re: [R] Which system.time() component to use? > > To: Ravi Varadhan <rvarad...@jhmi.edu> > > Cc: r-help@r-project.org > > > > > >> Try this: > >> > >> > system.time(Sys.sleep(60)) > >> user system elapsed > >> 0.00 0.00 60.05 > >> > pt <- proc.time(); Sys.sleep(60); proc.time() - pt > >> user system elapsed > >> 0.00 0.00 60.01 > >> > >> On Sat, Feb 27, 2010 at 9:33 PM, Ravi Varadhan <rvarad...@jhmi.edu> > wrote: > >> > > >> > Hi, > >> > > >> > The `system.time(expr)' command provide 3 different times for > >> evaluating the expression `expr'; the first two are user and system > >> CPUs and the third one is total elapsed time. Suppose I want to > >> compare two different computational procedures for performing the same > >> task, which component of `system.time' is most meaningful in the sense > >> that it most accurately reflects the computational effort of the > >> algorithm, and does not depend upon the idiosyncrasies of the > >> operating system. > >> > > >> > I have always been using the first component of `system.time', which > >> is the user CPU. Should I use the sum of user and system CPU or is > >> the total elapsed time a better measure? I would appreciate UseR's > >> feedback on this. > >> > > >> > Thanks very much. > >> > > >> > Best, > >> > Ravi. > >> > ____________________________________________________________________ > >> > > >> > Ravi Varadhan, Ph.D. > >> > Assistant Professor, > >> > Division of Geriatric Medicine and Gerontology > >> > School of Medicine > >> > Johns Hopkins University > >> > > >> > Ph. (410) 502-2619 > >> > email: rvarad...@jhmi.edu > >> > > >> > ______________________________________________ > >> > R-help@r-project.org mailing list > >> > > >> > PLEASE do read the posting guide > >> > and provide commented, minimal, self-contained, reproducible code. > >> > > > > > ______________________________________________ > > R-help@r-project.org mailing list > > > > PLEASE do read the posting guide > > and provide commented, minimal, self-contained, reproducible code. > > > > > > -- > Jim Holtman > Cincinnati, OH > +1 513 646 9390 > > What is the problem that you are trying to solve? ______________________________________________ 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.
