[Rd] Calling a LAPACK subroutine from R

Berend Hasselman bhh @end|ng |rom x@4@||@n|
Thu Sep 12 09:15:37 CEST 2019 

Followup:

I have checked my package nleqslv which uses dgemv only from Fortran, on Kubuntu 18.04 with the development version of R.
No errors or problems.

Berend


> On 12 Sep 2019, at 08:57, Berend Hasselman <bhh using xs4all.nl> wrote:
> 
> 
> I have tried what I proposed in a virtual Kubuntu 18.04 which uses gfortran 7.4.
> I used the latest development version of R.
> 
> It worked just as on macOS.
> 
> Berend
> 
> 
>> On 11 Sep 2019, at 22:07, Göran Broström <goran.brostrom using umu.se> wrote:
>> 
>> Berend,
>> 
>> I do not think this works with gfortran 7+. I am calling the BLAS subroutine dgemv from Fortran code in my package eha, and the check (with R-devel) gives:
>> 
>> gmlfun.f:223:1: warning: type of ‘dgemv’ does not match original declaration [-Wlto-type-mismatch]
>>     &     score, ione)
>> ^
>> /home/gobr0002/R/src/R-devel/include/R_ext/BLAS.h:107:1: note: type mismatch in parameter 12
>> F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
>> 
>> Type of a Fortran subroutine is matched against type of a C function?! My conclusion is that it is impossible to call a BLAS subroutine with a character parameter from Fortran code (nowadays). Calling from C code is fine, on the other hand(!).
>> 
>> I have recently asked about this on R-pkg-devel, but not received any useful answers, and my submission to CRAN is rejected. I solve it by making a personal copy of dgemv and changing the character parameter to integer, and adding Jack Dongarra, Jeremy Du Croz, Sven Hammarling, and Richard Hanson as authors of eha. And a Copyright note, all in the DESCRIPTION file. Ugly but what can I do (except rewriting the Fortran code in C with f2c)?
>> 
>> Göran
>> 
>> On 2019-09-11 21:38, Berend Hasselman wrote:
>>> The Lapack library is loaded automatically by R itself when it needs it  for doing some calculation.
>>> You can force it to do that with a (dummy) solve for example.
>>> Put this at start of your script:
>>> <code>
>>> # dummy code to get LAPACK library loaded
>>> X1 <- diag(2,2)
>>> x1 <- rep(2,2)
>>> # X1;x1
>>> z <- solve(X1,x1)
>>> </code>
>>> followed by the rest of your script.
>>> You will get a warning (I do) that  "passing a character vector  to .Fortran is not portable".
>>> On other systems this may gave fatal errors. This is quick and very dirty. Don't do it.
>>> I believe there is a better and much safer way to achieve what you want.
>>> Here goes.
>>> Create a folder (directory) src in the directory where your script resides.
>>> Create a wrapper for "dpbtrf" file in a file xdpbtrf.f that takes an integer instead of character
>>> <xdpbtrf.f>
>>> c intermediate for dpbtrf
>>>      SUBROUTINE xDPBTRF( kUPLO, N, KD, AB, LDAB, INFO )
>>> c      .. Scalar Arguments ..
>>>      integer         kUPLO
>>>      INTEGER         INFO, KD, LDAB, N
>>> c  .. Array Arguments ..
>>>      DOUBLE PRECISION   AB( LDAB, * )
>>>      character UPLO
>>> c     convert integer argument to character
>>>      if(kUPLO .eq. 1 ) then
>>>          UPLO = 'L'
>>>      else
>>>          UPLO = 'U'
>>>      endif
>>>      call dpbtrf(UPLO,N,KD,AB,LDAB,INFO)
>>>      return
>>>      end
>>> </xdpbtrf.f>
>>> Instead of a character argument UPLO it takes an integer argument kUPLO.
>>> The meaning should be obvious from the code.
>>> Now create a shell script in the folder of your script to generate a dynamic library to be loaded in your script:
>>> <mkso.sh>
>>> # Build a binary dynamic library for accessing Lapack dpbtrf
>>> # syntax checking
>>> SONAME=xdpbtrf.so
>>> echo Strict syntax checking
>>> echo ----------------------
>>> gfortran -c -fsyntax-only -fimplicit-none -Wall src/*.f || exit 1
>>> LAPACK=$(R CMD config LAPACK_LIBS)
>>> R CMD SHLIB --output=${SONAME} src/*.f ${LAPACK} || exit 1
>>> </mkso.sh>
>>> To load the dynamic library xdpbtrf.so  change your script into this
>>> <yourscript>
>>> dyn.load("xdpbtrf.so")
>>> n <- 4L
>>> phi <- 0.64
>>> AB <- matrix(0, 2, n)
>>> AB[1, ] <- c(1, rep(1 + phi^2, n-2), 1)
>>> AB[2, -n] <- -phi
>>> round(AB, 3)
>>> AB.ch <- .Fortran("xdpbtrf", kUPLO=1L, N = as.integer(n),
>>>                            KD = 1L, AB = AB, LDAB = 2L, INFO = as.integer(0))$AB
>>> AB.ch
>>> </yourscript>
>>> and you are good to go.
>>> You should always do something  as described above when you need to pass character arguments to Fortran code.
>>> All of this was tested and run on macOS using the CRAN version of R.
>>> Berend Hasselman
>>>> On 11 Sep 2019, at 15:47, Giovanni Petris <gpetris using uark.edu> wrote:
>>>> 
>>>> Sorry for cross-posting, but I realized my question might be more appropriate for r-devel...
>>>> 
>>>> Thank you,
>>>> Giovanni
>>>> 
>>>> ________________________________________
>>>> From: R-help <r-help-bounces using r-project.org> on behalf of Giovanni Petris <gpetris using uark.edu>
>>>> Sent: Tuesday, September 10, 2019 16:44
>>>> To: r-help using r-project.org
>>>> Subject: [R] Calling a LAPACK subroutine from R
>>>> 
>>>> Hello R-helpers!
>>>> 
>>>> I am trying to call a LAPACK subroutine directly from my R code using .Fortran(), but R cannot find the symbol name. How can I register/load the appropriate library?
>>>> 
>>>>> ### AR(1) Precision matrix
>>>>> n <- 4L
>>>>> phi <- 0.64
>>>>> AB <- matrix(0, 2, n)
>>>>> AB[1, ] <- c(1, rep(1 + phi^2, n-2), 1)
>>>>> AB[2, -n] <- -phi
>>>>> round(AB, 3)
>>>>     [,1]  [,2]  [,3] [,4]
>>>> [1,]  1.00  1.41  1.41    1
>>>> [2,] -0.64 -0.64 -0.64    0
>>>>> 
>>>>> ### Cholesky factor
>>>>> AB.ch <- .Fortran("dpbtrf", UPLO = 'L', N = as.integer(n),
>>>> +                  KD = 1L, AB = AB, LDAB = 2L, INFO = as.integer(0))$AB
>>>> Error in .Fortran("dpbtrf", UPLO = "L", N = as.integer(n), KD = 1L, AB = AB,  :
>>>> Fortran symbol name "dpbtrf" not in load table
>>>>> sessionInfo()
>>>> R version 3.6.0 (2019-04-26)
>>>> Platform: x86_64-apple-darwin18.5.0 (64-bit)
>>>> Running under: macOS Mojave 10.14.6
>>>> 
>>>> Matrix products: default
>>>> BLAS/LAPACK: /usr/local/Cellar/openblas/0.3.6_1/lib/libopenblasp-r0.3.6.dylib
>>>> 
>>>> locale:
>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>> 
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>> 
>>>> loaded via a namespace (and not attached):
>>>> [1] compiler_3.6.0 tools_3.6.0
>>>> 
>>>> Thank you in advance for your help!
>>>> 
>>>> Best,
>>>> Giovanni Petris
>>>> 
>>>> 
>>>> 
>>>> --
>>>> Giovanni Petris, PhD
>>>> Professor
>>>> Director of Statistics
>>>> Department of Mathematical Sciences
>>>> University of Arkansas - Fayetteville, AR 72701
>>>> 
>>>> 
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