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 at r-project.org> on behalf of Giovanni Petris <gpetris at uark.edu> Sent: Tuesday, September 10, 2019 16:44 To: r-help at 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 at 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&ePLEASE 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&eand provide commented, minimal, self-contained, reproducible code.
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 at 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 at r-project.org> on behalf of Giovanni
Petris <gpetris at uark.edu>
> Sent: Tuesday, September 10, 2019 16:44
> To: r-help at 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 at 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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)?
G?ran
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 at 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 at r-project.org> on behalf of
Giovanni Petris <gpetris at uark.edu>
>> Sent: Tuesday, September 10, 2019 16:44
>> To: r-help at 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 at 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 at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
On 11/09/2019 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>another way is to use directly dyn.load(): lapack.path <- paste0(file.path(R.home(), ifelse(.Platform$OS.type == "windows", ???????? file.path("bin", .Platform$r_arch, "Rlapack"), file.path("lib", "libRlapack"))), ???????? .Platform$dynlib.ext) dyn.load(lapack.path) followed by your code. Best, Serguei.> > 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 at 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 at r-project.org> on behalf of Giovanni Petris <gpetris at uark.edu> >> Sent: Tuesday, September 10, 2019 16:44 >> To: r-help at 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 at 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 at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
Hi guys,
interestingly, my problem seems to be solved by writing a FORTRAN
wrapper for the Fortran code! (As long as the check doesn't get
smarter...). This is the relevant part of my Fortran code:
-----------------------------------------------------------
subroutine gmlfun(what,
& totevent, totrs, ns,
& antrs, antevents, size,
& totsize, eventset, riskset,
& nn, antcov, covar, offset,
& beta, gamma,
& loglik, h1, h2, h11, h21, h22,
& score)
......
call gmlfun1(what,
& totevent, totrs, ns,
& antrs, antevents, size,
& totsize, eventset, riskset,
& nn, antcov, covar, offset,
& beta, gamma,
& loglik, h1, h2, h11, h21, h22,
& score)
return
end
C ***
C
subroutine gmlfun1(what,
& totevent, totrs, ns,
& antrs, antevents, size,
& totsize, eventset, riskset,
& nn, antcov, covar, offset,
& beta, gamma,
& loglik, h1, h2, h11, h21, h22,
& score)
.....
C
call dcopy(nn, offset, ione, score, ione)
call dgemv(trans, nn, antcov, one, covar, nn, beta, ione, one,
& score, ione)
.....
return
end
-----------------------------------------------------------------
gmlfun is called directly by .Fortran, and in my original code gmlfun
was gmlfun1. Now gmlfun is just a wrapper that calls gmlfun1, which
calls dgemv, and no complaints!
This is apparently what Berend (and now myself) gets away with: Quite
bizarre in my mind.
Or: Is this an R-blessed solution?
Thanks, G?ran
On 2019-09-12 11:25, Tomas Kalibera wrote:> On 9/12/19 11:07 AM, G?ran Brostr?m wrote:
>> Kurt, see below:
>>
>> On 2019-09-12 08:42, Kurt Hornik wrote:
>>>>>>>> G?ran Brostr?m writes:
>>>
>>> G?ran,
>>>
>>> Pls allow me to join the discussions on your pending CRAN
submission.
>>>
>>> First, the current solution with the copy of the BLAS sources is
not
>>> quite perfect.? You now have
>>>
>>> Authors at R: c(person("G?ran", "Brostr?m",
role = c("aut", "cre"),
>>> ???????????????????? email = "goran.brostrom at umu.se"),
>>> ????????????? person("Jack", "Dongarra", role =
"aut"),
>>> ????????????? person("Jeremy", "Du Croz", role
= "aut"),
>>> ????????????? person("Sven", "Hammarling", role
= "aut"),
>>> ????????????? person("Richard", "Hanson", role
= "aut"),
>>> ????????????? person("Jianming", "Jin", role =
"aut"))
>>> Copyright: The blas Developers 2014-2018.
>>>
>>> I think the last 5 persons should get a ctb role instead of aut,
and you
>>> should add
>>>
>>> ?? person("The blas Developers", role = "cph",
comment = "....")
>>>
>>> with a suitable comment explaining what the copyright is held for.
>>>
>>> However, I would still hope that you can do without the copy by
>>> following the recipe in section "Fortran character
strings" in "Writing
>>> R Extensions".? This says:
>>>
>>>
************************************************************************
>>> Alternatively, do as R does as from version 3.6.1-patched and pass
the
>>> character length(s) from C to Fortran.? A portable way to do this
is
>>> ????? // before any R headers, or define in PKG_CPPFLAGS
>>> ????? #define USE_FC_LEN_T
>>> ????? #include <Rconfig.h>
>>> ????? #include <R_ext/BLAS.h>
>>> ????? #ifndef FCONE
>>> ????? # define FCONE
>>> ????? #endif
>>> ????? ...
>>> ????????????? F77_CALL(dgemm)("N", "T",
&nrx, &ncy, &ncx, &one, x,
>>> ????????????????????????????? &nrx, y, &nry, &zero, z,
&nrx FCONE
>>> FCONE);
>>> (Note there is no comma before or between the 'FCONE'
invocations.)? It
>>> is strongly recommended that packages which call from C/C++
BLAS/LAPACK
>>> routines with character arguments adopt this approach.
>>>
************************************************************************
>>>
>>> Does this really not work for you?
>>
>> Of course it would work: I call dgemv (and other BLAS routines)
>> frequently from C code in my package, that is not the problem. I am
>> just wondering why Berend gets away with direct calls to dgemv from
>> Fortran without using the 12th hidden parameter FCLEN (FCONE), when I
>> fail. I suspect an oversight in the R checking system.
>
> The hidden argument will be added by the Fortran compiler, at the call
> site. If BLAS is built with the same Fortran compiler as your Fortran
> code which calls it, there should be no problem (often it will work also
> when the compilers are different, but that depends on how different they
> are). If you can't find why it is not working for you, please create a
> minimum reproducible but complete example. Please try looking also at
> existing packages with Fortran code, including "stats" for
instance.
> There are several people who are trying to help you on the mailing
> lists, it would be easier for them if they knew exactly what you were
> doing.
>
> Best
> Tomas
>
>
>>
>> I can write a C wrapper for my Fortran function that calls dgemv and
>> call it in R by .C, but is that really guaranteed to work, when the
>> checking routine gets sharper?
>
>>
>> Best, G,
>>
>>> Best
>>> -k
>>>
>>>
>>>> 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)?
>>>
>>>> G?ran
>>>
>>>> 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
at 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 at r-project.org> on
behalf of Giovanni
>>>>>> Petris <gpetris at uark.edu>
>>>>>> Sent: Tuesday, September 10, 2019 16:44
>>>>>> To: r-help at 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 at r-project.org mailing list -- To UNSUBSCRIBE
and more, see
>>>>>>
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>>>>>>
>>>>>> PLEASE do read the posting guide
>>>>>>
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>>>>>> and provide commented, minimal, self-contained,
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>>>>>>
>>>>>> ______________________________________________
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>>>>>
>>>>> ______________________________________________
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>
>