Also, just came to know about dotcall64::.C64() (on CRAN) which allows for Fortran to be called using .Call(). -Naras On 12/23/20 8:34 AM, Balasubramanian Narasimhan wrote:> I think it should be pretty easy to fix up SUtools to use the .Call > instead of .Fortran following along the lines of > > https://github.com/wrathematics/Romp > > I too deal with a lot of f77 and so I will most likely finish it > before the new year, if not earlier. (Would welcome testers besides > myself.) > > Incidentally, any idea of what the performance hit is, quantitatively? > I confess I never paid attention to it myself as most Fortran code I > use seems pretty fast, i.e. glmnet. > > -Naras > > > On 12/23/20 3:57 AM, Koenker, Roger W wrote: >> Thanks to all and best wishes for a better 2021. >> >> Unfortunately I remain somewhat confused: >> >> ????o? Bill reveals an elegant way to get from my rudimentary >> registration setup to >> ????one that would explicitly type the C interface functions, >> >> ????o Ivan seems to suggest that there would be no performance gain >> from doing this. >> >> ????o? Naras?s pcLasso package does use the explicit C typing, but >> then uses .Fortran >> ????not .Call. >> >> ????o? Avi uses .Call and cites the Romp package >> https://github.com/wrathematics/Romp >> ????where it is asserted that "there is a (nearly) deprecated >> interface .Fortran() which you >> ????should not use due to its large performance overhead.? >> >> As the proverbial naive R (ab)user I?m left wondering: >> >> ????o? if I updated my quantreg_init.c file in accordance with Bill?s >> suggestion could I >> ????then simply change my .Fortran calls to .Call? >> >> ????o? and if so, do I need to include ALL the fortran subroutines in >> my src directory >> ????or only the ones called from R? >> >> ????o? and in either case could I really expect to see a significant >> performance gain? >> >> Finally, perhaps I should stipulate that my fortran is strictly f77, >> so no modern features >> are in play, indeed most of the code is originally written in ratfor, >> Brian Kernighan?s >> dialect from ancient times at Bell Labs. >> >> Again,? thanks to all for any advice, >> Roger >> >> >>> On Dec 23, 2020, at 1:11 AM, Avraham Adler <avraham.adler at gmail.com> >>> wrote: >>> >>> Hello, Ivan. >>> >>> I used .Call instead of .Fortran in the Delaporte package [1]. What >>> helped me out a lot was Drew Schmidt's Romp examples and descriptions >>> [2]. If you are more comfortable with the older Fortran interface, >>> Tomasz Kalinowski has a package which uses Fortran 2018 more >>> efficiently [3]. I haven't tried this last in practice, however. >>> >>> Hope that helps, >>> >>> Avi >>> >>> [1] >>> https://urldefense.com/v3/__https://CRAN.R-project.org/package=Delaporte__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPITBN5NK8$ >>> [2] >>> https://urldefense.com/v3/__https://github.com/wrathematics/Romp__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPISF5aCYs$ >>> [3] >>> https://urldefense.com/v3/__https://github.com/t-kalinowski/RFI__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPIbwXmXqY$ >>> >>> Tomasz Kalinowski >>> >>> >>> >>> On Tue, Dec 22, 2020 at 7:24 PM Balasubramanian Narasimhan >>> <naras at stanford.edu> wrote: >>>> To deal with such Fortran issues in several packages I deal with, I >>>> wrote the SUtools package >>>> (https://urldefense.com/v3/__https://github.com/bnaras/SUtools__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPIJ5BbDwA$ >>>> ) that you >>>> can try.? The current version generates the registration assuming >>>> implicit Fortran naming conventions though. (I've been meaning to >>>> upgrade it to use the gfortran -fc-prototypes-external flag which >>>> should >>>> be easy; I might just finish that during these holidays.) >>>> >>>> There's a vignette as well: >>>> https://urldefense.com/v3/__https://bnaras.github.io/SUtools/articles/SUtools.html__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPITq9-Quc$ >>>> >>>> >>>> -Naras >>>> >>>> >>>> On 12/19/20 9:53 AM, Ivan Krylov wrote: >>>>> On Sat, 19 Dec 2020 17:04:59 +0000 >>>>> "Koenker, Roger W" <rkoenker at illinois.edu> wrote: >>>>> >>>>>> There are comments in various places, including R-extensions ?5.4 >>>>>> suggesting that .Fortran is (nearly) deprecated and hinting that use >>>>>> of .Call is more efficient and now preferred for packages. >>>>> My understanding of ?5.4 and 5.5 is that explicit routine >>>>> registration >>>>> is what's important for efficiency, and your package already does >>>>> that >>>>> (i.e. calls R_registerRoutines()). The only two things left to add >>>>> would be types (REALSXP/INTSXP/...) and styles (R_ARG_IN, >>>>> R_ARG_OUT/...) of the arguments of each subroutine. >>>>> >>>>> Switching to .Call makes sense if you want to change the interface of >>>>> your native subroutines to accept arbitrary heavily structured SEXPs >>>>> (and switching to .External could be useful if you wanted to play >>>>> with >>>>> evaluation of the arguments). >>>>> >>>> ______________________________________________ >>>> R-devel at r-project.org mailing list >>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-devel__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPIr_nqkqg$ >>>> > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel
Yes, dotcall64 looks interesting. There is a paper about it here: https://www.sciencedirect.com/science/article/pii/S2352711018300785?via%3Dihub and the R spam package contains many examples of its use for fortran source.> On Dec 24, 2020, at 12:39 AM, Balasubramanian Narasimhan <naras at stanford.edu> wrote: > > Also, just came to know about dotcall64::.C64() (on CRAN) which allows for Fortran to be called using .Call(). > > -Naras > > On 12/23/20 8:34 AM, Balasubramanian Narasimhan wrote: >> I think it should be pretty easy to fix up SUtools to use the .Call instead of .Fortran following along the lines of >> >> https://urldefense.com/v3/__https://github.com/wrathematics/Romp__;!!DZ3fjg!r3_sswU4ZHCe3huoGUy2boX-Vr7aUS-RaExyeh_Rsv8gvGiABcqzvOOKZinG4kC7RtA$ >> I too deal with a lot of f77 and so I will most likely finish it before the new year, if not earlier. (Would welcome testers besides myself.) >> >> Incidentally, any idea of what the performance hit is, quantitatively? I confess I never paid attention to it myself as most Fortran code I use seems pretty fast, i.e. glmnet. >> >> -Naras >> >> >> On 12/23/20 3:57 AM, Koenker, Roger W wrote: >>> Thanks to all and best wishes for a better 2021. >>> >>> Unfortunately I remain somewhat confused: >>> >>> o Bill reveals an elegant way to get from my rudimentary registration setup to >>> one that would explicitly type the C interface functions, >>> >>> o Ivan seems to suggest that there would be no performance gain from doing this. >>> >>> o Naras?s pcLasso package does use the explicit C typing, but then uses .Fortran >>> not .Call. >>> >>> o Avi uses .Call and cites the Romp package https://urldefense.com/v3/__https://github.com/wrathematics/Romp__;!!DZ3fjg!r3_sswU4ZHCe3huoGUy2boX-Vr7aUS-RaExyeh_Rsv8gvGiABcqzvOOKZinG4kC7RtA$ where it is asserted that "there is a (nearly) deprecated interface .Fortran() which you >>> should not use due to its large performance overhead.? >>> >>> As the proverbial naive R (ab)user I?m left wondering: >>> >>> o if I updated my quantreg_init.c file in accordance with Bill?s suggestion could I >>> then simply change my .Fortran calls to .Call? >>> >>> o and if so, do I need to include ALL the fortran subroutines in my src directory >>> or only the ones called from R? >>> >>> o and in either case could I really expect to see a significant performance gain? >>> >>> Finally, perhaps I should stipulate that my fortran is strictly f77, so no modern features >>> are in play, indeed most of the code is originally written in ratfor, Brian Kernighan?s >>> dialect from ancient times at Bell Labs. >>> >>> Again, thanks to all for any advice, >>> Roger >>> >>> >>>> On Dec 23, 2020, at 1:11 AM, Avraham Adler <avraham.adler at gmail.com> wrote: >>>> >>>> Hello, Ivan. >>>> >>>> I used .Call instead of .Fortran in the Delaporte package [1]. What >>>> helped me out a lot was Drew Schmidt's Romp examples and descriptions >>>> [2]. If you are more comfortable with the older Fortran interface, >>>> Tomasz Kalinowski has a package which uses Fortran 2018 more >>>> efficiently [3]. I haven't tried this last in practice, however. >>>> >>>> Hope that helps, >>>> >>>> Avi >>>> >>>> [1] https://urldefense.com/v3/__https://CRAN.R-project.org/package=Delaporte__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPITBN5NK8$ >>>> [2] https://urldefense.com/v3/__https://github.com/wrathematics/Romp__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPISF5aCYs$ >>>> [3] https://urldefense.com/v3/__https://github.com/t-kalinowski/RFI__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPIbwXmXqY$ >>>> >>>> Tomasz Kalinowski >>>> >>>> >>>> >>>> On Tue, Dec 22, 2020 at 7:24 PM Balasubramanian Narasimhan >>>> <naras at stanford.edu> wrote: >>>>> To deal with such Fortran issues in several packages I deal with, I >>>>> wrote the SUtools package (https://urldefense.com/v3/__https://github.com/bnaras/SUtools__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPIJ5BbDwA$ ) that you >>>>> can try. The current version generates the registration assuming >>>>> implicit Fortran naming conventions though. (I've been meaning to >>>>> upgrade it to use the gfortran -fc-prototypes-external flag which should >>>>> be easy; I might just finish that during these holidays.) >>>>> >>>>> There's a vignette as well: >>>>> https://urldefense.com/v3/__https://bnaras.github.io/SUtools/articles/SUtools.html__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPITq9-Quc$ >>>>> >>>>> -Naras >>>>> >>>>> >>>>> On 12/19/20 9:53 AM, Ivan Krylov wrote: >>>>>> On Sat, 19 Dec 2020 17:04:59 +0000 >>>>>> "Koenker, Roger W" <rkoenker at illinois.edu> wrote: >>>>>> >>>>>>> There are comments in various places, including R-extensions ?5.4 >>>>>>> suggesting that .Fortran is (nearly) deprecated and hinting that use >>>>>>> of .Call is more efficient and now preferred for packages. >>>>>> My understanding of ?5.4 and 5.5 is that explicit routine registration >>>>>> is what's important for efficiency, and your package already does that >>>>>> (i.e. calls R_registerRoutines()). The only two things left to add >>>>>> would be types (REALSXP/INTSXP/...) and styles (R_ARG_IN, >>>>>> R_ARG_OUT/...) of the arguments of each subroutine. >>>>>> >>>>>> Switching to .Call makes sense if you want to change the interface of >>>>>> your native subroutines to accept arbitrary heavily structured SEXPs >>>>>> (and switching to .External could be useful if you wanted to play with >>>>>> evaluation of the arguments). >>>>>> >>>>> ______________________________________________ >>>>> R-devel at r-project.org mailing list >>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-devel__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPIr_nqkqg$ >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-devel__;!!DZ3fjg!r3_sswU4ZHCe3huoGUy2boX-Vr7aUS-RaExyeh_Rsv8gvGiABcqzvOOKZinGvMnBkW0$
I?ve recoded a version of one of my quantile regression fitting functions to use .C64 from dotCall64 rather than .Fortran. For a moderately large problem with n = 500,000 and p = 5, and solving for 1:49/50 quantiles the new version shows a 3% speedup, although for smaller problems it is actually slower that the .Fortran version. So, I?m (provisionally) unimpressed by the claims that .Fortran has a big ?overhead? performance penalty. Compared to the(more than) an order of magnitude (base 10) improvement that moving from R to fortran produces, 3% isn?t really worth the (admittedly) minimal additional coding effort.> On Dec 24, 2020, at 12:39 AM, Balasubramanian Narasimhan <naras at stanford.edu> wrote: > > Also, just came to know about dotcall64::.C64() (on CRAN) which allows for Fortran to be called using .Call(). > > -Naras > > On 12/23/20 8:34 AM, Balasubramanian Narasimhan wrote: >> I think it should be pretty easy to fix up SUtools to use the .Call instead of .Fortran following along the lines of >> >> https://urldefense.com/v3/__https://github.com/wrathematics/Romp__;!!DZ3fjg!r3_sswU4ZHCe3huoGUy2boX-Vr7aUS-RaExyeh_Rsv8gvGiABcqzvOOKZinG4kC7RtA$ >> I too deal with a lot of f77 and so I will most likely finish it before the new year, if not earlier. (Would welcome testers besides myself.) >> >> Incidentally, any idea of what the performance hit is, quantitatively? I confess I never paid attention to it myself as most Fortran code I use seems pretty fast, i.e. glmnet. >> >> -Naras >> >> >> On 12/23/20 3:57 AM, Koenker, Roger W wrote: >>> Thanks to all and best wishes for a better 2021. >>> >>> Unfortunately I remain somewhat confused: >>> >>> o Bill reveals an elegant way to get from my rudimentary registration setup to >>> one that would explicitly type the C interface functions, >>> >>> o Ivan seems to suggest that there would be no performance gain from doing this. >>> >>> o Naras?s pcLasso package does use the explicit C typing, but then uses .Fortran >>> not .Call. >>> >>> o Avi uses .Call and cites the Romp package https://urldefense.com/v3/__https://github.com/wrathematics/Romp__;!!DZ3fjg!r3_sswU4ZHCe3huoGUy2boX-Vr7aUS-RaExyeh_Rsv8gvGiABcqzvOOKZinG4kC7RtA$ where it is asserted that "there is a (nearly) deprecated interface .Fortran() which you >>> should not use due to its large performance overhead.? >>> >>> As the proverbial naive R (ab)user I?m left wondering: >>> >>> o if I updated my quantreg_init.c file in accordance with Bill?s suggestion could I >>> then simply change my .Fortran calls to .Call? >>> >>> o and if so, do I need to include ALL the fortran subroutines in my src directory >>> or only the ones called from R? >>> >>> o and in either case could I really expect to see a significant performance gain? >>> >>> Finally, perhaps I should stipulate that my fortran is strictly f77, so no modern features >>> are in play, indeed most of the code is originally written in ratfor, Brian Kernighan?s >>> dialect from ancient times at Bell Labs. >>> >>> Again, thanks to all for any advice, >>> Roger >>> >>> >>>> On Dec 23, 2020, at 1:11 AM, Avraham Adler <avraham.adler at gmail.com> wrote: >>>> >>>> Hello, Ivan. >>>> >>>> I used .Call instead of .Fortran in the Delaporte package [1]. What >>>> helped me out a lot was Drew Schmidt's Romp examples and descriptions >>>> [2]. If you are more comfortable with the older Fortran interface, >>>> Tomasz Kalinowski has a package which uses Fortran 2018 more >>>> efficiently [3]. I haven't tried this last in practice, however. >>>> >>>> Hope that helps, >>>> >>>> Avi >>>> >>>> [1] https://urldefense.com/v3/__https://CRAN.R-project.org/package=Delaporte__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPITBN5NK8$ >>>> [2] https://urldefense.com/v3/__https://github.com/wrathematics/Romp__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPISF5aCYs$ >>>> [3] https://urldefense.com/v3/__https://github.com/t-kalinowski/RFI__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPIbwXmXqY$ >>>> >>>> Tomasz Kalinowski >>>> >>>> >>>> >>>> On Tue, Dec 22, 2020 at 7:24 PM Balasubramanian Narasimhan >>>> <naras at stanford.edu> wrote: >>>>> To deal with such Fortran issues in several packages I deal with, I >>>>> wrote the SUtools package (https://urldefense.com/v3/__https://github.com/bnaras/SUtools__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPIJ5BbDwA$ ) that you >>>>> can try. The current version generates the registration assuming >>>>> implicit Fortran naming conventions though. (I've been meaning to >>>>> upgrade it to use the gfortran -fc-prototypes-external flag which should >>>>> be easy; I might just finish that during these holidays.) >>>>> >>>>> There's a vignette as well: >>>>> https://urldefense.com/v3/__https://bnaras.github.io/SUtools/articles/SUtools.html__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPITq9-Quc$ >>>>> >>>>> -Naras >>>>> >>>>> >>>>> On 12/19/20 9:53 AM, Ivan Krylov wrote: >>>>>> On Sat, 19 Dec 2020 17:04:59 +0000 >>>>>> "Koenker, Roger W" <rkoenker at illinois.edu> wrote: >>>>>> >>>>>>> There are comments in various places, including R-extensions ?5.4 >>>>>>> suggesting that .Fortran is (nearly) deprecated and hinting that use >>>>>>> of .Call is more efficient and now preferred for packages. >>>>>> My understanding of ?5.4 and 5.5 is that explicit routine registration >>>>>> is what's important for efficiency, and your package already does that >>>>>> (i.e. calls R_registerRoutines()). The only two things left to add >>>>>> would be types (REALSXP/INTSXP/...) and styles (R_ARG_IN, >>>>>> R_ARG_OUT/...) of the arguments of each subroutine. >>>>>> >>>>>> Switching to .Call makes sense if you want to change the interface of >>>>>> your native subroutines to accept arbitrary heavily structured SEXPs >>>>>> (and switching to .External could be useful if you wanted to play with >>>>>> evaluation of the arguments). >>>>>> >>>>> ______________________________________________ >>>>> R-devel at r-project.org mailing list >>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-devel__;!!DZ3fjg!s1-ihrZ9DPUtXpxdIpJPA1VedpZFt12Ahmn4CycOmile_uSahFZnJPn_5KPIr_nqkqg$ >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-devel__;!!DZ3fjg!r3_sswU4ZHCe3huoGUy2boX-Vr7aUS-RaExyeh_Rsv8gvGiABcqzvOOKZinGvMnBkW0$