On 8 June 2011 08:03, Douglas Bates <[email protected]> wrote: > On Tue, Jun 7, 2011 at 2:34 PM, baptiste auguie > <[email protected]> wrote: >> Hi Doug, >> >> On 8 June 2011 03:43, Douglas Bates <[email protected]> wrote: >>> >>> On Jun 6, 2011 4:17 AM, "baptiste auguie" <[email protected]> >>> wrote: >>>> >>>> Thank you for the explanations below. >>>> >>>> On 5 June 2011 10:40, Dirk Eddelbuettel <[email protected]> wrote: >>>> > >>>> > On 5 June 2011 at 10:12, baptiste auguie wrote: >>>> > | Hi Dirk and all, >>>> > | >>>> > | On 4 June 2011 12:04, Dirk Eddelbuettel <[email protected]> wrote: >>>> > | > >>>> > | > Baptiste, >>>> > | > >>>> > | > On 4 June 2011 at 11:45, baptiste auguie wrote: >>>> > | > | Dear list, >>>> > | > | >>>> > | > | My package cda, which I was hoping to release on CRAN, fails to >>>> > | > | compile on R-forge with error, >>>> > | > | >>>> > | > | ** testing if installed package can be loaded >>>> > | > | Error in dyn.load(file, DLLpath = DLLpath, ...) : >>>> > | > | unable to load shared object >>>> > '/tmp/RtmpbztUMm/Rinst1829c04c/cda/libs/cda.so': >>>> > | > | /tmp/RtmpbztUMm/Rinst1829c04c/cda/libs/cda.so: undefined symbol: >>>> > zgetri_ >>>> > | > | >>>> > | > | It builds fine on my local machines (Mac OS 10.5, 10.6). >>>> > | > | >>>> > | > | >From an older discussion on this list < >>>> > | > | >>>> > http://www.mail-archive.com/[email protected]/msg00678.html> >>>> > | > | the issue seems to be that Armadillo's inv() relies on a function >>>> > that >>>> > | > | is not provided by R, only by LAPACK. I have just replaced inv() >>>> > by >>>> > | > | pinv() and solve() in my code; merely to see what happens, but >>>> > chances >>>> > | > | are they also require a full LAPACK. >>>> > | >>>> > | Indeed, the error on R-forge is now with zgels_, required to solve >>>> > | linear systems. It seems one cannot solve Armadillo linear systems >>>> > | without LAPACK in the current situation. >>>> > >>>> > Yes. Doug, Romain and myself should address that, or at least make it >>>> > clear >>>> > what feature of the full Armadillo are lacking in RcppArmadillo. >>>> > >>>> > | > Sometime relatively early in the RcppArmadillo development process, >>>> > Doug >>>> > | > convinced Romain and myself to go for a pure template solution with >>>> > Armadillo >>>> > | > as all / most things found during the configure (or in this case, >>>> > cmake) >>>> > | > stage can be assumed 'found' given that we have around us by design. >>>> > So no >>>> > | > testing, no local library and full reliance and what R gives us. >>>> > | > >>>> > | > That was a brilliant idea, and has freed us from having to rely on >>>> > building >>>> > | > and shipping a library, having to tell users how to set PKG_LIBS etc >>>> > pp and I >>>> > | > firmly believe that this helped tremendously in getting >>>> > RcppArmadillo more >>>> > | > widely used. So I would not want to revert this. >>>> > | >>>> > | It sounds like a good choice, I agree. Yet solving a linear system is >>>> > | quite a crucial task in linear algebra; it would be nice if we could >>>> > | come up with a tutorial recipe for dummies like me. >>>> > | >>>> > | > >>>> > | > In any event, it seems that you need more LAPACK than R has for you. >>>> > That is >>>> > | > likely to be a dicey situation as you per se do not know whether R >>>> > was built >>>> > | > and linked with its own (subset) copy of LAPACK, or whether it uses >>>> > system >>>> > | > LAPACK libraries (as e.g. the Debian / Ubuntu systems do). So you >>>> > may be in >>>> > | > a spot bother and I not sure what I can recommend --- other than >>>> > trying your >>>> > | > luck at some short configure snippets that will run at package build >>>> > time to >>>> > | > determine whether the system you want to build cda on it 'rich' >>>> > enough to >>>> > | > support it. I can help you off list with some configure snippets as >>>> > some of >>>> > | > my packages have configure code; adding a test for zgetri should be >>>> > feasible. >>>> > | > >>>> > | > | Does anybody have any experience >>>> > | > | dealing with such issues w.r.t releasing a package on R-forge / >>>> > CRAN? >>>> > | > | Is there any chance they would consider installing LAPACK on those >>>> > | > | servers, or is there no point in asking such things? >>>> > | > >>>> > | > I don't think it is a matter of fixing the R-Forge server. I think >>>> > it is a >>>> > | > matter of making your package installable on the largest number of >>>> > user >>>> > | > systems. Also try win-builder.r-project.org to see how it fares on >>>> > that >>>> > | > platform. >>>> >>>> Unsurprisingly, it fails, with the same complaint as R-forge. >>>> >>>> > | >>>> > | I was under the impression that R-forge or CRAN, if it had LAPACK >>>> > | installed, could produce binaries for the relevant platforms, and >>>> > | users would not have to build the package themselves and would not be >>>> > | required of having LAPACK on their machine. That's probably a >>>> > | misconception, isn't it? >>>> > >>>> > If and only statically linked binaries or libraries where produced, >>>> > which is >>>> > generally not the case. Many OSs (Linux incl) ship source only and >>>> > otherwise >>>> > link dynamically, others (Windoze) use dynamic linking and OS X is for >>>> > all I >>>> > know somewhere in the middle (as you can get prebuild packages with >>>> > dynamic >>>> > linking or build from source). >>>> >>>> I see; so basically the user will always need to have a full LAPACK >>>> installed. Here's one question then, if R-core didn't consider >>>> necessary to include those particular functions from LAPACK, >>>> presumably that means that R defines its own routines to solve linear >>>> systems and invert matrices. Is there any possibility to use those >>>> routines with Armadillo? >>> >>> One important point has been missed in this discussion, which is that the >>> particular Lapack subroutine that is not found in the subset of Lapack >>> shipped with R is for general, complex-valued matrices (just google the name >>> zgetri). The way that Armadillo is structured it is either all-in or >>> all-out with respect to complex-valued matrices If you allow for complex >>> matrices then you must have all the supporting subroutines for whatever you >>> are calling. If you call inv() you need to allow for all the [sdcz]getri >>> routines to be available. >> >> The matrix I need to invert is definitely always complex; in fact, >> convenient complex algebra is the main attraction of Armadillo for me. > > Argh. Of course, I was being foolish. Because Armadillo is a > header-only library it does not access any Lapack subroutine until the > call is instantiated. I still haven't quite gotten used to thinking > only having the headers. > >>> >>> So one possibility is to check the Armadillo sources to see if you can >>> suppress the use of complex-valued matrices when compiling your package. A >>> quick glance indicates that this might now be easy. >>> >>> Otherwise, remember the first rule of numerical linear algebra which is, "If >>> your algorithm involves computing the inverse of a matrix you should rethink >>> the algorithm because there is a better way of doing it". So why do you >>> need inv()? >>> If the answer is to solve a linear system of equations then you >>> use solve(), you do not use inv(). If, for some truly unusual reason you >>> actually need the inverse (and, remember in 99.99% of the cases where people >>> think they need the inverse, they don't) then you use a combination of >>> solve() and eye(). >> >> I tried this, and in fact I do use solve() elsewhere in my code, which >> calls for another LAPACK routine (zgels.f) not present in R. The >> reason I still need inv() is that I have to solve about 300 times a >> linear system AX=B with the same matrix A but varying B. A quick >> timing last week revealed that using solve() 300 times was typically >> slower by a factor of two in my use case than using inv() once (or >> pinv() for that matter, it makes not appreciable difference). I'm >> happy to be shown otherwise though. > > I forgot that Armadillo doesn't provide a convenient way of using the > LU decomposition (that is one of the things that I find frustrating > about Armadillo). Did you try a single solve call in which the > right-hand side is an identity matrix? On looking at the Armadillo > sources it seems that it should call zgesv which is included in R's > subset of the Lapack routines.
It seems curious, looking at the bestiary of LAPACK functions, that so many of them seem to perform a similar task. I wonder what are the practical downsides of using a code that solves AX=I rather than one inverting A. Also, when I replaced inv() by solve() and pinv(), R-forge still failed to build complaining that zgesv_ was not present. I assumed it was used by solve(), but perhaps it was pinv(). I'll give it a try anyway, but I'd rather hope we can figure out a less ad hoc solution. Thanks, baptiste > > >> One option that I'd like to consider is whether the appropriate LAPACK >> routines could be wrapped and shipped in a separate package >> (discontinued rblas could provide a good starting point). Sadly, I >> know nothing about static/dynamic libraries and all this business.. >> >> Thanks, >> >> baptiste >> >>> >>>> > | Sorry for being dense, I don't know anything about linking R to >>> >>>> > | external dependencies. >>>> > >>>> > It can be done; there are many examples -- for example every package >>>> > using >>>> > the GSL. >>>> >>>> I just checked how RcppGSL does it, and well, this configure magic is >>>> way above my head. >>>> >>>> Best, >>>> >>>> baptiste >>>> _______________________________________________ >>>> Rcpp-devel mailing list >>>> [email protected] >>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel >>> >> > _______________________________________________ Rcpp-devel mailing list [email protected] https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
