[Rd] Fw: Calling a LAPACK subroutine from R
Göran Broström
gor@n@bro@trom @end|ng |rom umu@@e
Wed Sep 11 22:07:54 CEST 2019
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
>>
>>
>> ______________________________________________
>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwICAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=C3DNvy_azplKSvJKgvsgjA&m=C-MwKl__0xz-98RBbu7QNXJjqWkRr4xp6c0cz9Dck7A&s=a1vAu3mcXKObTLwP19vOmRPq55h6oQTh_vnS6BEibF0&e=
>> PLEASE do read the posting guide https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwICAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=C3DNvy_azplKSvJKgvsgjA&m=C-MwKl__0xz-98RBbu7QNXJjqWkRr4xp6c0cz9Dck7A&s=qFGlplF9cOSmnDUvugsPRDn4iZS7v-LuWNAvfY69sbA&e=
>> and provide commented, minimal, self-contained, reproducible code.
>>
>> ______________________________________________
>> R-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
> R-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
More information about the R-devel
mailing list