Matthieu Stigler
2009-Jan-13 13:07 UTC
[R] Using fortran code which call LAPACK subroutines
Hello
I'm trying to run a fortran code which use LAPACK subroutines. I think I
should use some points shown in the manual 5.5 Creating shared objects
but it is too technical for me :-(... Could anyone help me for the
procedure to do:
-which part of the manual is relevant for this type of question?
actually I'm speaking from writing R extensions, should I read R admin?
-point 1.2 says: /Recent versions of Autoconf in fact allow an already
set |FLIBS| to override the test for the FORTRAN linker flags. Also,
recent versions of R can detect external BLAS and LAPACK libraries./
but nevertheless I have to include something more? or modify the script?
-should I compile from SHLIB with other options or include it directly
into a package and cretae a makevars or PACKAGE_LIBS...? I'm lost...
The subroutine I try to use is delcols.f
(http://www.maths.manchester.ac.uk/~clucas/updating/addcols.f) which calls
* .. External Subroutines ..
EXTERNAL DGEQRF, DLASR, DROT, DROTG, XERBLA
Thank you very much!!
Charles C. Berry
2009-Jan-13 18:59 UTC
[R] Using fortran code which call LAPACK subroutines
On Tue, 13 Jan 2009, Matthieu Stigler wrote:> Hello > > I'm trying to run a fortran code which use LAPACK subroutines. I think I > should use some points shown in the manual 5.5 Creating shared objects but it > is too technical for me :-(...Be sure to look over section 6, esp. 6.17 The headers for DGEQRF, DLASR, DROT, DROTG are all in Blas.h or Lapack.h (although you will see them in lower case). XERBLA in libRBlas.so but is not in the R API, so if your code needs to use it you'll have to add a header like the one in main.c or add your own version. I think you can probably do what you want with just PKG_LIBS=${LAPACK_LIBS} $(BLAS_LIBS) ${FLIBS} in Makevars and R CMD INSTALL <your-package> with just the default settings. HTH, Chuck Could anyone help me for the procedure to do:> > -which part of the manual is relevant for this type of question? actually I'm > speaking from writing R extensions, should I read R admin? > > -point 1.2 says: /Recent versions of Autoconf in fact allow an already set > |FLIBS| to override the test for the FORTRAN linker flags. Also, recent > versions of R can detect external BLAS and LAPACK libraries./ > but nevertheless I have to include something more? or modify the script? > > -should I compile from SHLIB with other options or include it directly into a > package and cretae a makevars or PACKAGE_LIBS...? I'm lost... > > > The subroutine I try to use is delcols.f > (http://www.maths.manchester.ac.uk/~clucas/updating/addcols.f) which calls > > * .. External Subroutines .. > EXTERNAL DGEQRF, DLASR, DROT, DROTG, XERBLA > > > Thank you very much!! > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >Charles C. Berry (858) 534-2098 Dept of Family/Preventive Medicine E mailto:cberry at tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
Matthieu Stigler
2009-Jan-15 16:51 UTC
[R] Using fortran code which call LAPACK subroutines
Prof Brian Ripley a ?crit :> On Tue, 13 Jan 2009, Charles C. Berry wrote: > >> On Tue, 13 Jan 2009, Matthieu Stigler wrote: >> >>> Hello >>> >>> I'm trying to run a fortran code which use LAPACK subroutines. I >>> think I should use some points shown in the manual 5.5 Creating >>> shared objects but it is too technical for me :-(... >> >> >> >> Be sure to look over section 6, esp. 6.17 >> >> The headers for DGEQRF, DLASR, DROT, DROTG are all in Blas.h or >> Lapack.h (although you will see them in lower case). >> >> XERBLA in libRBlas.so but is not in the R API, so if your code needs >> to use it you'll have to add a header like the one in main.c or add >> your own version. > > Not in Fortran code, though: see below > > I think Matthieu had not read quite a lot of the documentation: given > how carefully it was written, that was disrespectful (as was the lack > of a proper signature: see the posting guide: Charles aka Chuck has > been exemplary). >Sorry if this could be seen as disrespectful, I nevertheless don't think that having difficulties to read a good but complex (and difficult for a newbie) documentation is a sign of disrespect.> To put it simply: if you are ashamed of who you are, so are the most > prolific helpers here. Some people resent being milked for free > consultancy for commercial firms, and many of us will go many miles > out of our way for third-world NGOs/academia. >Oh, I forgot to write my name... I'm sorry, well even if you could see it from my address I should have written. I understand your worry about commercial firms, personnaly, I'm trying to contribute myself to R through extensions of package tsDyn http://code.google.com/p/tsdyn/wiki/ThresholdCointegration>> I think you can probably do what you want with just >> >> >> PKG_LIBS=${LAPACK_LIBS} $(BLAS_LIBS) ${FLIBS} >> >> in Makevars >> >> and >> R CMD INSTALL <your-package> >> >> with just the default settings. >This did the job (just had to copy/paste the xerbla in a proper .f file in src)! Thank you so much!> Agreed. > > >> HTH, >> >> Chuck >> >> Could anyone help me for the procedure to do: >>> >>> -which part of the manual is relevant for this type of question? >>> actually I'm speaking from writing R extensions, should I read R admin? >>> >>> -point 1.2 says: /Recent versions of Autoconf in fact allow an >>> already set |FLIBS| to override the test for the FORTRAN linker >>> flags. Also, recent versions of R can detect external BLAS and >>> LAPACK libraries./ >>> but nevertheless I have to include something more? or modify the >>> script? >>> >>> -should I compile from SHLIB with other options or include it >>> directly into a package and cretae a makevars or PACKAGE_LIBS...? >>> I'm lost... >>> >>> >>> The subroutine I try to use is delcols.f >>> (http://www.maths.manchester.ac.uk/~clucas/updating/addcols.f) which >>> calls >>> >>> * .. External Subroutines .. >>> EXTERNAL DGEQRF, DLASR, DROT, DROTG, XERBLA >>> >>> >>> Thank you very much!! >>> >> >> Charles C. Berry (858) 534-2098 >> Dept of Family/Preventive >> Medicine >> E mailto:cberry at tajo.ucsd.edu UC San Diego >> http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego >> 92093-0901 >> >> ______________________________________________ >> R-help at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >