[Rd] Matrix with random number

[Fabio Mathias]

Hello! 

 I have a program in Fortran and would like to build a matrix with random 
numbers, I have a function in C. 
 However, I have problems with the use of function in R. 

 Code to compile: R CMD SHLIB mat.f myrbeta.c -o func.so


Code in C.

#include 
#include 

void F77_SUB(fseedi)(void){
  GetRNGstate();
}

void F77_SUB(fseedo)(void){
  PutRNGstate();
}

void F77_SUB(myrbeta)(double *px, double *pa, double *pb){

  *px = rbeta(*pa,*pb);
}



Code in Fortran

    subroutine mat(x,l,c)
    integer l,c
    double precision x(l,c)
    integer i,j
     do j = 1, c
       do i = 1, l
        call fseedi()

     x(i,j) = call myrbeta(1,4,5) ! It's correct?
        call fseedo()
   enddo
  enddo
    end


Thanks very much!


-- 
              Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária

 Fábio Mathias Corrêa   UFLA



  

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[Rd] Matrix with random number

[Fabio Mathias]

Hello! 

 I have a program in Fortran and would like to build a matrix with random 
numbers, I have a function in C. 
 However, I have problems with the use of function in R. 

 Code to compile: R CMD SHLIB mat.f myrbeta.c -o func.so


Code in C.

#include 
#include 

void F77_SUB(fseedi)(void){
  GetRNGstate();
}

void F77_SUB(fseedo)(void){
  PutRNGstate();
}

void F77_SUB(myrbeta)(double *px, double *pa, double *pb){

  *px = rbeta(*pa,*pb);
}



Code in Fortran

    subroutine mat(x,l,c)
    integer l,c
    double precision x(l,c)
    integer i,j
     do j = 1, c
       do i = 1, l
        call fseedi()

     x(i,j) = call myrbeta(1,4,5) ! It's correct?
        call fseedo()
   enddo
  enddo
    end


The code of the error in R is: 
dyn.load("func.so")
Error in dyn.load("func.so") : 
  unable to load shared library 
'/home/julio/Orientados/Fabio/Fortran/mat-fortran/func.so':
  /home/julio/Orientados/Fabio/Fortran/mat-fortran/func.so: undefined symbol: 
callmyrbeta_



Thanks very much!

 Fábio Mathias Corrêa   UFLA



  

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Re: [Rd] Matrix with random number

[Fabio Mathias]

Thanks Mr. Barry Rowlingson

However, the matrix appears to zeros! 

 Notice the code below! Please!

Code in fortran

    subroutine mat(x,l,c,a)
    integer l,c
    double precision x(l,c), a
    integer i,j
     do j = 1, c
       do i = 1, l
        call fseedi()
     x(i,j) = myrbeta(a,1,2)
        call fseedo()
   enddo
  enddo
    end

In R:

dyn.load("func.so")
x <- matrix(0,5,6)
l <- nrow(x)
c <-
 ncol(x)
a <- 0

..Fortran("mat", x = x, l, c, as.double(a))

Results:

$x
 [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0

[[2]]
[1] 5

[[3]]
[1] 6

[[4]]
[1] 1


Thanks!!!


 Fábio Mathias Corrêa   UFLA




  

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Re: [Rd] Matrix with random number

[Fabio Mathias]

Thanks very much!

 Fábio Mathias Corrêa   UFLA


--- Em qua, 1/7/09, Kjell Konis  escreveu:

De: Kjell Konis 
Assunto: Re: [Rd] Matrix with random number
Para: "Fabio Mathias" 
Cc: r-devel@r-project.org
Data: Quarta-feira, 1 de Julho de 2009, 8:30

Hi Fabio,

Your function myrbeta returns void so assigning the output isn't going to 
work.  Instead you need to call it like a FORTRAN subroutine.  Also, I added 
arguments for the parameters of the beta and moved the fseedi and fseedo calls 
outside of the loop.

This is a pretty basic FORTRAN programming question and there are lots of books 
that can help you learn FORTRAN.


    subroutine mat(x,l,c,pa,pb)
    integer l,c
    double precision x(l,c), a
    integer i,j
    call fseedi()
    do j = 1, c
       do i = 1, l
         call myrbeta(x(i,j),pa,pb)
        enddo
      enddo
    call fseedo()
    end


In R call it like this:

storage.mode(x) <- "double"
..Fortran("mat", x = x, as.integer(l), as.integer(c), as.double(1), 
as.double(2))


Cheers,
Kjell



On 30 juin 09, at 20:02, Fabio Mathias wrote:

> Thanks Mr. Barry Rowlingson
> 
> However, the matrix appears to zeros!
> 
> Notice the code below! Please!
> 
> Code in fortran
> 
>     subroutine mat(x,l,c,a)
>     integer l,c
>     double precision x(l,c), a
>     integer i,j
>      do j = 1, c
>        do i = 1, l
>         call fseedi()
>          x(i,j) = myrbeta(a,1,2)
>         call fseedo()
>            enddo
>           enddo
>     end
> 
> In R:
> 
> dyn.load("func.so")
> x <- matrix(0,5,6)
> l <- nrow(x)
> c <-
> ncol(x)
> a <- 0
> 
> ..Fortran("mat", x = x, l, c, as.double(a))
> 
> Results:
> 
> $x
>      [,1] [,2] [,3] [,4] [,5] [,6]
> [1,]    0    0    0    0    0    0
> [2,]    0    0    0    0    0    0
> [3,]    0    0    0    0    0    0
> [4,]    0    0    0    0    0    0
> [5,]    0    0    0    0    0    0
> 
> [[2]]
> [1] 5
> 
> [[3]]
> [1] 6
> 
> [[4]]
> [1] 1
> 
> 
> Thanks!!!
> 
> 
>              Fábio Mathias Corrêa                       UFLA
> 
> 
> 
> 
>      
>
> [[elided Yahoo spam]]
> 
>     [[alternative HTML version deleted]]
> 
> 




  

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[Rd] Generate random numbers in Fortran

[Fabio Mathias]

Hi!!!
It would like to know if it exists a form to use the functions to
generate variates in FORTRAN with the same easiness I use that them in
C? Or not?
If yes. They would have some example? I would like to use the functions rbeta, 
rlnorm and others!


Sorry my english..rsrsrs

Thanks!!! 


             Fábio Mathias Corrêa    University Federal of the 
Lavras - Brazil



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Re: [Rd] Generate random numbers in Fortran

[Fabio Mathias]

As I am wanting to generate a beta, then I created a function in C to
generate a beta, but the problem appears when I go to compile

My function in C is

#include 
#include 
#include 

void F77_SUB(myrbeta)(double* px)
{ 
    GetRNGstate();
    *px = rbeta(1.00,3.00);
    PutRNGstate();
}

My function in Fortran is

subroutine blah(a)
double precision (a)
call myrbeta(RND)
end

The error

fmc...@fmcron-desktop:~/teste$ R CMD SHLIB mat.c blah.f
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c mat.c -o mat.o
gfortran   -fpic  -g -O2 -c blah.f -o blah.o
blah.f:1.1:

subroutine 
blah(a)                                                     
 
1
Erro: Non-numeric character in statement label at (1)
blah.f:1.1:

subroutine 
blah(a)                                                     
 
1
Erro: Unclassifiable statement at (1)
blah.f:2.1:

double precision 
(a)                                                   
 
1
Erro: Non-numeric character in statement label at (1)
blah.f:2.1:

double precision 
(a)                                                   
 
1
Erro: Unclassifiable statement at (1)
blah.f:4.1:

end                                                                    
 
1
Erro: Non-numeric character in statement label at (1)
blah.f:4.1:

end                                                                    
 
1
Erro: Unclassifiable statement at (1)
make: ** [blah.o] Erro 1


             Fábio Mathias 
Corrêa                       UFLA


--- Em sex, 13/2/09, Kjell Konis  escreveu:
De: Kjell Konis 
Assunto: Re: [Rd] Generate random numbers in Fortran
Para: "fabio.u...@yahoo.com.br" 
Cc: "r-devel@r-project.org" 
Data: Sexta-feira, 13 de Fevereiro de 2009, 16:49

Take a look at section 6.6 in Writing R Extensions. It describes how to call C
functions from FORTRAN. Basically it just boils down to this, in a C file define
the functions

void F77_SUB(fseedi)(void)
{
  int x = 100;
  seed_in(&x);
}


void F77_SUB(fseedo)(void)
{
  int x = 100;
  seed_out(&x);
}


void F77_SUB(myrunif)(double* px)
{
*px = unif_rand();
}


Then you could write a FORTRAN subroutine like

  subroutine blah()
  implicit double precision (a-h,o-z)
  call fseedi()
  call myrunif(RND)
  call fseedo()
  end

The fseed* subroutines only need to be called once, fseedi at the beginning of
your FORTRAN code and fseedo at the end.

HTH,
Kjell


On 13 févr. 09, at 17:32, Fabio Mathias wrote:

> Hi!!!
> It would like to know if it exists a form to use the functions to
> generate variates in FORTRAN with the same easiness I use that them in
> C? Or not?
> If yes. They would have some example? I would like to use the functions
rbeta, rlnorm and others!
> 
> 
> Sorry my english..rsrsrs
> 
> Thanks!!!
> 
> 
>  Fábio Mathias CorrêaUniversity Federal of the Lavras -
Brazil
> 
> 
> 
>  Veja quais são os assuntos do momento no Yahoo! +Buscados
> 
>   [[alternative HTML version deleted]]
> 
> 




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[Rd] how to change nlme() contrast parametrization?

[Fabio Mathias]

How to set the nlme() function to return the answer without the intercept 
parametrization?

#=
library(nlme)
Soybean[1:3, ]

(fm1Soy.lis <- nlsList(weight ~ SSlogis(Time, Asym, xmid, scal),
   data = Soybean))

(fm1Soy.nlme <- nlme(fm1Soy.lis))
fm2Soy.nlme <- update(fm1Soy.nlme, weights = varPower())

plot(ranef(fm2Soy.nlme, augFrame = TRUE),
 form = ~ Year * Variety, layout = c(3,1))

soyFix <- fixef(fm2Soy.nlme)

options(contrasts = c("contr.treatment", "contr.poly"))
(fm3Soy.nlme <-
 update(fm2Soy.nlme,
    fixed = Asym + xmid + scal ~ Year,
    start = c(soyFix[1], 0, 0, soyFix[2], 0, 0, soyFix[3], 0, 0)))

# here I wouldn't like give the intercept parametrization but
# the parameters by tratament with standard error. See:

# before:
# Fixed effects: list(Asym ~ Year * Variety, xmid ~ Year + Variety, scal - 1 
~  Year) 
#   Value Std.Error  DF  t-value p-value
# Asym.(Intercept)   19.43400 0.9537402 352 20.37661  0.
# Asym.Year1989  -8.84208 1.0721164 352 -8.24731  0.
# Asym.Year1990  -3.70719 1.1770024 352 -3.14969  0.0018

# after (I would like this):
# Fixed effects: list(Asym ~ Year * Variety, xmid ~ Year + Variety, scal - 1 
~  Year) 
#   Value Std.Error  DF  t-value p-value
# Asym.Year1988   19.43400 0.9537402 352 20.37661  0.
# Asym.Year1989  -8.84208 1.0721164 352 -8.24731  0.
# Asym.Year1990  -3.70719 1.1770024 352 -3.14969  0.0018

#=

Thanks in advance.


 Fábio Mathias Corrêa   UFLA



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[Rd] how to change nlme() contrast parametrization?

[Fabio Mathias]

How to set the nlme() function to return the answer without the intercept 
parametrization?

#=
library(nlme)
Soybean[1:3, ]

(fm1Soy.lis <- nlsList(weight ~ SSlogis(Time, Asym, xmid, scal),
   data = Soybean))

(fm1Soy.nlme <- nlme(fm1Soy.lis))
fm2Soy.nlme <- update(fm1Soy.nlme, weights = varPower())

plot(ranef(fm2Soy.nlme, augFrame = TRUE),
 form = ~ Year * Variety, layout = c(3,1))

soyFix <- fixef(fm2Soy.nlme)

options(contrasts = c("contr.treatment", "contr.poly"))
(fm3Soy.nlme <-
 update(fm2Soy.nlme,
    fixed = Asym + xmid + scal ~ Year,
    start = c(soyFix[1], 0, 0, soyFix[2], 0, 0, soyFix[3], 0, 0)))

# here I wouldn't like give the intercept parametrization but
# the parameters by tratament with standard error. See:

# before:
# Fixed effects: list(Asym ~ Year * Variety, xmid ~ Year + Variety, scal - 1 
~  Year) 
#   Value Std.Error  DF  t-value p-value
# Asym.(Intercept)   19.43400 0.9537402 352 20.37661  0.
# Asym.Year1989  -8.84208 1.0721164 352 -8.24731  0.
# Asym.Year1990  -3.70719 1.1770024 352 -3.14969  0.0018

# after (I would like this):
# Fixed effects: list(Asym ~ Year * Variety, xmid ~ Year + Variety, scal - 1 
~  Year) 
#   Value Std.Error  DF  t-value p-value
# Asym.Year1988   19.43400 0.9537402 352 20.37661  0.
# Asym.Year1989  -8.84208 1.0721164 352 -8.24731  0.
# Asym.Year1990  -3.70719 1.1770024 352 -3.14969  0.0018

#=

Thanks in advance.


 Fábio Mathias Corrêa   UFLA



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[Rd] Namespace File

[Fabio Mathias Corrêa]

Dear Colleagues,

I am developing a library. However I am having the following problem with the 
file NAMESPACE.

My file contains:

useDynLib(Bayesthres, vuA)

export(Bayesthres, 
random.effects, 
fixed.effects,
)

exportClasses("Bayesthres")

 


My function is:


Avuall <- function(Zz, Dd, A, Vu, FL)
  {
m <- dim(A)[1]
n <- dim(A)[2]
tc <- length(Vu)
ifc <- unlist(lapply(FL$fl, function(x) length(levels(x
il <-  1
ic <- ifc[1]
for(i in 2:tc){
  ic[i] <- ifc[i]+ic[i-1]
  il[i] <- ic[i]-ifc[i]+1
}
storage.mode(A) <- "double"
Aux <- .Fortran("vuA", as.double(Vu), A=A, as.integer(ic), as.integer(il), 
as.integer(m), 

as.integer(n), as.integer(tc), PACKAGE="Bayesthres")$A
V <- rbind(Zz, cbind(Dd,Aux))
return(V)
  }


The vuA file was written in Fortran95. It's within the src directory.

However the following error appears in R CMD check

Error in .Fortran("vuA", as.double(Vu), A = A, as.integer(ic), as.integer(il),  
: 

name simbol in Fortran "vua" not is in DLL library "Bayesthres"
Error : unable to load R code in package 'Bayesthres'
ERROR: lazy loading failed for package ‘Bayesthres’

Where can I be wrong?

Thank you very much!


  Fábio Mathias Corrêa
 Departamento de Estatística
   Universidade Estadual de Santa Cruz




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[Rd] Namespace File

[Fabio Mathias Corrêa]

Dear colleagues,


Problem solved with:


".First.lib" <- function(lib, pkg)
{
  library.dynam("Bayesthres", package = pkg, lib.loc = lib)
  return(invisible(0))
}





 
  Fábio Mathias Corrêa
 Departamento de Estatística
   Universidade Estadual de Santa Cruz




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[Rd] Namespace File

[Fabio Mathias Corrêa]

Dear Simon

By using useDynLib (Bayesthres) in NAMESPACE file. Appeared another error:

Error in dyn.load("Bayesthres.so") : 
  unable to load shared object '/home/fmc/Bayesthres/Bayesthres.so':
  /home/fmc/Bayesthres/Bayesthres.so: cannot open shared object file: No such 
file or directory
ERROR: lazy loading failed for package ‘Bayesthres’
* removing ‘/home/fmc/Bayesthres.Rcheck/Bayesthres’

 
Now he is not recognizing the file Bayesthres.so

Grateful for the help.



  Fábio Mathias Corrêa
 Departamento de Estatística
   Universidade Estadual de Santa Cruz




- Mensagem original 
De: Simon Urbanek 
Para: Fabio Mathias Corrêa 
Cc: r-devel@r-project.org
Enviadas: Quarta-feira, 15 de Dezembro de 2010 13:41:34
Assunto: Re: [Rd] Namespace File


On Dec 15, 2010, at 6:57 AM, Fabio Mathias Corrêa wrote:

> Dear colleagues,
> 
> 
> Problem solved with:
> 
> 
> ".First.lib" <- function(lib, pkg)
> {
>  library.dynam("Bayesthres", package = pkg, lib.loc = lib)
>  return(invisible(0))
> }
> 

Well, that's shooting at a clay pigeon with a missile ;). You could have done 
the same simply using
useDynLib(Bayesthres)
in the NAMESPACE.

Your issue is very likely just a mixup of cases as there is no "vuA" symbol in 
Fortran as all symbols are lower-case (at the object file level).

Cheers,
Simon


 
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[Rd] Namespace File

[Fabio Mathias Corrêa]

Dear,

I am using Ubuntu linux and R2.12.0
The trial version is in my home.

\home\Bayesthres~$

To perform the R CMD check

\home~$ R CMD check Bayesthres

Within the directory Bayesthres, have:

Directories: inst, man, R and src

Files: DESCRIPTION AND NAMESPACE

Best wishes

Fábio




... but that's an entirely wrong place - I suspect you have some real issues in 
the way your package is constructed. Are you sure you have the correct layout 
and are using the *packaged* sources and not your working tree? (You didn't 
tell 
us anything about the package so there are many things that may be wrong - also 
you omitted the most basic details such as R version and platform...)

Cheers,
Simon


 
  Fábio Mathias Corrêa
 Departamento de Estatística
   Universidade Estadual de Santa Cruz




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[Rd] Namespace File

[Fabio Mathias Corrêa]

 The inst has CITATION only.

Best wishes



  Fábio Mathias Corrêa
 Departamento de Estatística
   Universidade Estadual de Santa Cruz





What is in inst? Make sure you have no binaries there.

Cheers,
Simon


> 
> 
>  Fábio Mathias Corrêa
> Departamento de Estatística
>   Universidade Estadual de Santa Cruz
> 
> 
> 
> 
> 



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[Rd] Namespace File

[Fabio Mathias Corrêa]

See the complete log

f...@raquel-laptop ~ $ R CMD check Bayesthres
* using log directory ‘/home/fmc/Bayesthres.Rcheck’
* using R version 2.12.0 (2010-10-15)
* using platform: i486-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘Bayesthres/DESCRIPTION’ ... OK
* this is package ‘Bayesthres’ version ‘0.1-0’
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ‘Bayesthres/src’ contains object files.
* checking for executable files ... OK
* checking whether package ‘Bayesthres’ can be installed ... ERROR
Installation failed.
See ‘/home/fmc/Bayesthres.Rcheck/00install.out’ for details.


File 00install.out

Error in dyn.load("Bayesthres.so") : 
  unable to load shared object '/home/fmc/Bayesthres/Bayesthres.so':
  /home/fmc/Bayesthres/Bayesthres.so: cannot open shared object file: No such 
file or directory
ERROR: lazy loading failed for package ‘Bayesthres’
* removing ‘/home/fmc/Bayesthres.Rcheck/Bayesthres’

Best wishes



 
  Fábio Mathias Corrêa
 Departamento de Estatística
   Universidade Estadual de Santa Cruz




- Mensagem original 
De: Simon Urbanek 
Para: Fabio Mathias Corrêa 
Cc: R-devel 
Enviadas: Quarta-feira, 15 de Dezembro de 2010 17:10:21
Assunto: Re: [Rd] Namespace File


On Dec 15, 2010, at 1:56 PM, Fabio Mathias Corrêa wrote:

> Dear,
> 
> I am using Ubuntu linux and R2.12.0
> The trial version is in my home.
> 
> \home\Bayesthres~$
> 
> To perform the R CMD check
> 
> \home~$ R CMD check Bayesthres
> 

That is in general not a good idea, especially if you ever run things inside by 
hand for testing (because that will pollute the build). Make sure you clean 
your 
tree and use R CMD build followed by R CMD check on the resulting tar ball. 
Does 
the issue persist?


> Within the directory Bayesthres, have:
> 
> Directories: inst, man, R and src
> 

What is in inst? Make sure you have no binaries there.

Cheers,
Simon


> 
> ... but that's an entirely wrong place - I suspect you have some real issues 
> in 
>
> the way your package is constructed. Are you sure you have the correct layout 
> and are using the *packaged* sources and not your working tree? (You didn't 
>tell 
>
> us anything about the package so there are many things that may be wrong - 
> also 
>
> you omitted the most basic details such as R version and platform...)
> 
> Cheers,
> Simon
> 
> 
> 
>  Fábio Mathias Corrêa
> Departamento de Estatística
>   Universidade Estadual de Santa Cruz
> 
> 
> 
> 
> 




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[Rd] Compile error gfortran-4.6

[Fabio Mathias Corrêa]

Dears,

I am writing a code in Fortran using OpenMP directives.

When compiling the code in gfortran 4.4 does not occur any problem.

When compiling the code in gfortran 4.6, an error message appears.

In other compilers the error does not occur.


A small example.


## Code in Fortran

       subroutine hello()
       implicit none
       integer :: nthreads, tid
       integer :: omp_get_num_threads, omp_get_thread_num
       integer :: omp_get_max_threads, omp_set_num_threads

       print *, 'Máximo de threads', omp_get_max_threads()

       !$omp parallel 
       tid = omp_get_thread_num()
       print *, 'Hello World from thread = ', tid
       print *, 'Number of threads =', omp_get_thread_num()
       !$omp end parallel
       end subroutine hello


### Compiling and testing

system("R CMD COMPILE hello.f90 FCFLAGS=-fopenmp")
system("R CMD SHLIB hello.o")

dyn.load("hello.so")

.Fortran("hello")

### Error message

/home/fmcron/Documentos/Fortran/OpenMP/exemplos/hello.so: undefined symbol: 
_gfortran_transfer_character_write



Thanks

 
        Fábio Mathias Corrêa


   Universidade Estadual de Santa Cruz
Departamento de Ciências Exatas e da Terra - DCET


Campus Soane Nazaré de Andrade, km 16 Rodovia Ilhéus-Itabuna
CEP 45662-900. Ilhéus-Bahia


Tel.: 73-3680-5076
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[Rd] Compile error with gfortran-4.6

[Fabio Mathias Corrêa]

Dears,

I am writing a code in Fortran using OpenMP directives.

When compiling the code in gfortran 4.4 does not occur any problem.

When compiling the code in gfortran 4.6, an error message appears.

In other compilers the error does not occur.


A small example.


## Code in Fortran

       subroutine hello()
       implicit none
       integer :: nthreads, tid
       integer :: omp_get_num_threads, omp_get_thread_num
       integer :: omp_get_max_threads, omp_set_num_threads

       print *, 'Máximo de threads', omp_get_max_threads()

       !$omp parallel 
       tid = omp_get_thread_num()
       print *, 'Hello World from thread = ', tid
       print *, 'Number of threads =', omp_get_thread_num()
       !$omp end parallel
       end subroutine hello


### Compiling and testing

system("R CMD COMPILE hello.f90 FCFLAGS=-fopenmp")
system("R CMD SHLIB hello.o")

dyn.load("hello.so")

.Fortran("hello")

### Error message

/home/fmcron/Documentos/Fortran/OpenMP/exemplos/hello.so: undefined symbol: 
_gfortran_transfer_character_write



Thanks

 
        Fábio Mathias Corrêa


   Universidade Estadual de Santa Cruz
Departamento de Ciências Exatas e da Terra - DCET


Campus Soane Nazaré de Andrade, km 16 Rodovia Ilhéus-Itabuna
CEP 45662-900. Ilhéus-Bahia
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[Rd] Problem with gfortran-4.6

[Fabio Mathias Corrêa]

Dears,

I am writing a code in Fortran using OpenMP directives.

When compiling the code in gfortran 4.4 does not occur any problem.

When compiling the code in gfortran 4.6, an error message appears.

In other compilers the error does not occur.


A small example.


## Code in Fortran

       subroutine hello()
       implicit none
       integer :: nthreads, tid
       integer :: omp_get_num_threads, omp_get_thread_num
       integer :: omp_get_max_threads, omp_set_num_threads

       print *, 'Máximo de threads', omp_get_max_threads()

       !$omp parallel 
       tid = omp_get_thread_num()
       print *, 'Hello World from thread = ', tid
       print *, 'Number of threads =', omp_get_thread_num()
       !$omp end parallel
       end subroutine hello


### Compiling and testing

system("R CMD COMPILE hello.f90 FCFLAGS=-fopenmp")
system("R CMD SHLIB hello.o")

dyn.load("hello.so")

.Fortran("hello")

### Error message

/home/fmcron/Documentos/Fortran/OpenMP/exemplos/hello.so: undefined symbol: 
_gfortran_transfer_character_write



Thanks



        Fábio Mathias Corrêa


   Universidade Estadual de Santa Cruz
Departamento de Ciências Exatas e da Terra - DCET


Campus Soane Nazaré de Andrade, km 16 Rodovia Ilhéus-Itabuna
CEP 45662-900. Ilhéus-Bahia


Tel.: 73-3680-5076 

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Re: [Rd] Compile error with gfortran-4.6

[Fabio Mathias Corrêa]

Dear prof. Brian Ripley,

Thanks for help!

I compiled using the command:


MAKEFLAGS="FCFLAGS=-fopenmp" R CMD SHLIB hello.f90


I use linux mint Maya, R 3.0.1 and gfortran 4.6.3.

Thanks,

 
        Fábio Mathias Corrêa


   Universidade Estadual de Santa Cruz
Departamento de Ciências Exatas e da Terra - DCET
Campus Soane Nazaré de Andrade, km 16 Rodovia Ilhéus-Itabuna
CEP 45662-900. Ilhéus-Bahia


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[Rd] Changing the compiler gfortran to ifort

[Fabio Mathias Corrêa]

I tried the manual R Installation and Administration to change the gcc compiler 
to icc and ifort for gfotran. However I could not find the correct path for the 
R to identify the icc and ifort.
In which file I define the change of compiler?

Thanks very much!!!

     Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA
Brazil


  

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[Rd] Problem with function in fortran 95

[Fabio Mathias Corrêa]

I am writing a function in fortran 95, but the intrinsic function MATMUL is not 
working properly. Here's an example.

SUBROUTINE mymult(x,y,res,m,n)
IMPLICIT NONE
INTEGER :: m,n
REAL :: x, y, res
DIMENSION :: x(m,n), y(n,m), res(m,m)
res = MATMUL(x,y)
END SUBROUTINE mymult

R CMD SHLIB mat.f95

In R:

dyn.load("mat.so")
x   <- matrix(1:20,5)
l   <- nrow(x)
c   <- ncol(x)
y   <- matrix(20:1,c)
res <- matrix(0,l,l)
dim(x)
dim(y)
dim(res)
l
c
.Fortran("mymult", x,y,res,l,c)

[[1]]
 [,1] [,2] [,3] [,4]
[1,]16   11   16
[2,]27   12   17
[3,]38   13   18
[4,]49   14   19
[5,]5   10   15   20

[[2]]
 [,1] [,2] [,3] [,4] [,5]
[1,]   20   16   1284
[2,]   19   15   1173
[3,]   18   14   1062
[4,]   17   13951

[[3]]
 [,1] [,2] [,3] [,4] [,5]
[1,]00000
[2,]00000
[3,]00000
[4,]00000
[5,]00000

[[4]]
[1] 5

[[5]]
[1] 4


Linux Ubuntu 8.04 and use compiler gfortran 4.2.
The problem is the compiler?

Thanks!

   Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA
  Brazil


  

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[Rd] Problem with function in fortran 95

[Fabio Mathias Corrêa]

Thanks very much!!!

   Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA



--- Em sex, 14/8/09, Simone Giannerini  escreveu:

> De: Simone Giannerini 
> Assunto: Re: [Rd] Problem with function in fortran 95
> Para: "Fabio Mathias Corrêa" 
> Cc: r-devel@r-project.org
> Data: Sexta-feira, 14 de Agosto de 2009, 9:19
> Fabio,
> 
> I see two problems with your code:
> 
> 1. R type numeric corresponds to FORTRAN Real*8 (or double
> precision)
> so that line 4 of your mat.f95 becomes:
> 
> REAL*8 :: x, y, res
> 
> 2. your R code won't ever succeed because you pass integer
> matrices
> (x,y,res) to a subroutine that expects REAL*8 data.
> you need to coerce all your matrices to "double" as
> follows:
> 
> storage.mode(x) <- "double"
> storage.mode(y) <- "double"
> storage.mode(res) <- "double"
> 
> Finally, you can call the corrected function:
> 
> .Fortran("mymult", x,y,res,as.integer(l),as.integer(c))
> [[1]]
>      [,1] [,2] [,3] [,4]
> [1,]    1   
> 6   11   16
> [2,]    2   
> 7   12   17
> [3,]    3   
> 8   13   18
> [4,]    4   
> 9   14   19
> [5,]   
> 5   10   15   20
> 
> [[2]]
>      [,1] [,2] [,3] [,4] [,5]
> [1,]   20   16   12 
>   8    4
> [2,]   19   15   11 
>   7    3
> [3,]   18   14   10 
>   6    2
> [4,]   17   13   
> 9    5    1
> 
> [[3]]
>      [,1] [,2] [,3] [,4] [,5]
> [1,]  604  468  332 
> 196   60
> [2,]  678  526  374 
> 222   70
> [3,]  752  584  416 
> 248   80
> [4,]  826  642  458 
> 274   90
> [5,]  900  700  500  300  100
> 
> [[4]]
> [1] 5
> 
> [[5]]
> [1] 4
> 
> 
> All these issues are discussed in the "Writing R
> Extensions" manual,
> please read it carefully.
> 
> Ciao
> 
> Simone
> 
> 
> 
> On Wed, Aug 12, 2009 at 1:32 PM, Fabio Mathias
> Corrêa
> wrote:
> > I am writing a function in fortran 95, but the
> intrinsic function MATMUL is not working properly. Here's an
> example.
> >
> >        SUBROUTINE mymult(x,y,res,m,n)
> >        IMPLICIT NONE
> >        INTEGER :: m,n
> >        REAL :: x, y, res
> >        DIMENSION :: x(m,n), y(n,m), res(m,m)
> >        res = MATMUL(x,y)
> >        END SUBROUTINE mymult
> >
> > R CMD SHLIB mat.f95
> >
> > In R:
> >
> > dyn.load("mat.so")
> > x   <- matrix(1:20,5)
> > l   <- nrow(x)
> > c   <- ncol(x)
> > y   <- matrix(20:1,c)
> > res <- matrix(0,l,l)
> > dim(x)
> > dim(y)
> > dim(res)
> > l
> > c
> > .Fortran("mymult", x,y,res,l,c)
> >
> > [[1]]
> >     [,1] [,2] [,3] [,4]
> > [1,]    1    6   11   16
> > [2,]    2    7   12   17
> > [3,]    3    8   13   18
> > [4,]    4    9   14   19
> > [5,]    5   10   15   20
> >
> > [[2]]
> >     [,1] [,2] [,3] [,4] [,5]
> > [1,]   20   16   12    8    4
> > [2,]   19   15   11    7    3
> > [3,]   18   14   10    6    2
> > [4,]   17   13    9    5    1
> >
> > [[3]]
> >     [,1] [,2] [,3] [,4] [,5]
> > [1,]    0    0    0    0    0
> > [2,]    0    0    0    0    0
> > [3,]    0    0    0    0    0
> > [4,]    0    0    0    0    0
> > [5,]    0    0    0    0    0
> >
> > [[4]]
> > [1] 5
> >
> > [[5]]
> > [1] 4
> >
> >
> > Linux Ubuntu 8.04 and use compiler gfortran 4.2.
> > The problem is the compiler?
> >
> > Thanks!
> >
> >    Fábio Mathias Corrêa
> > Estatística e Experimentação Agropecuária/UFLA
> >                      Brazil
> >
> >
> >    
>  
> > Veja quais são os assuntos do momento no Yahoo!
> +Buscados
> > http://br.maisbuscados.yahoo.com
> >
> > __
> > R-devel@r-project.org
> mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> 
> 
> 
> -- 
> __
> 
> Simone Giannerini
> Dipartimento di Scienze Statistiche "Paolo Fortunati"
> Universita' di Bologna
> Via delle belle arti 41 - 40126  Bologna,  ITALY
> Tel: +39 051 2098262  Fax: +39 051 232153
> http://www2.stat.unibo.it/giannerini/
> __
> 


  

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[Rd] Problem in matrix definition?

[Fabio Mathias Corrêa]

I'm implementing a function to compute the moore-penrose inverse, using a code 
from the article: Fast Computation of Moore-Penrose Inverse Matrices. Neural 
Information Processing - Letters and Reviews. Vol.8, No.2, August 2005

However, the R presents an error message when I use the geninv.

The odd thing is that the error occurs for some arrays, however they have the 
same size. And the R indicates the lack of compatibility between the matrix!

Below is an example:

Creating the function geninv

geninv <- function(x)
{
 m <- dim(x)[1]
 n <- dim(x)[2]
 tr <- 0
 if(m < n) {
   a <- tcrossprod(x)
   n <- m
   tr <- 1
 }
 else  a <- crossprod(x)
 dA <- diag(a)
 tol=min(dA[dA>0])*1e-9
 L = a*0
 r = 0
 for(k in 1:n){
  r = r+1
  L[k:n,r] = a[k:n,k]-(L[k:n,1:(r-1)]%*%(t(L[k,1:(r-1)])))
  if(L[k,r] > tol){
L[k,r] <- sqrt(L[k,r])
if (k < n) L[(k+1):n,r] <- L[(k+1):n,r]/L[k,r]
  }
  else r <- r-1
 }
 L <- L[,1:r]
 M <- solve(crossprod(L))
 if (tr == 1) Y <- t(x)%*%L%*%M%*%M%*%t(L)
 else Y <- L%*%M%*%M%*%t(L)%*%t(x)
 return(Y)
 }
 
# Perfect result! This result is identical of the function ginv!

library(MASS)
mp <- 10
np <- 5
a <- matrix(c(1:mp*np),mp,np)
dim(a) # 10,5
geninv(a)
ginv(a)

# Problem
a <- matrix(c(1:50),mp,np) # The difference is the vector (1:50)
dim(a) # 10,5

geninv(a)
Error in L[k:n, 1:(r - 1)] %*% (t(L[k, 1:(r - 1)])) : 
  arguments are not compatible


The problem this in matrix definition?

Thanks very much!

   Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA



  

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[Rd] Problem in matrix definition?

[Fabio Mathias Corrêa]

The problem is that arrays are the same size. The only difference is how they 
were built!

The way to build the matrix should not influence in the outcome!

Below is the commented code in MatLab!

Neural Information Processing - Letters and Reviews Vol.8, No.2, August 2005

function Y = geninv(G)
% Returns the Moore-Penrose inverse of the argument
% Transpose if m < n
   [m,n]=size(G); transpose=false;
   if m0))*1e-9;
   L=zeros(size(A));
   r=0;
   for k=1:n
  r=r+1;
  L(k:n,r)=A(k:n,k)-L(k:n,1:(r-1))*L(k,1:(r-1))';
% Note: for r=1, the substracted vector is zero
  if L(k,r)>tol
 L(k,r)=sqrt(L(k,r));
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Re: [Rd] Problem in matrix definition?

[Fabio Mathias Corrêa]

Thanks very much!!!

   Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA


  

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[Rd] Compiling with High Performance Fortran

[Fabio Mathias Corrêa]

Dear,

I looked in the list something on as to compile a code with access the High 
Performance FORTRAN using R CMD SHLIB, but I did not find. Would like to know 
if the accepted R this type of language?

Thanks!


   Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA



  

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[Rd] Fortran with OpenMP

[Fabio Mathias Corrêa]

Dear,

I wrote a code in Fortran using OpenMP. When testing the code in Fortran it was 
working. However, changing the code for the R, it does not indicate the use of 
threads, it should indicate.
I know that the R accepts the directives of OpenMP, but I can not use them 
correctly in R.
Below is a small sample code that should work with the use of OpenMP, but does 
not work when I use the R. 

SUBROUTINE A1(N, A, B)
  INCLUDE "omp_lib.h"
  INTEGER :: I, N
  DOUBLE PRECISION, DIMENSION(N) :: B(N), A(N)
  LOGICAL :: OMP_IN_PARALLEL

!$OMP PARALLEL DO 
  WRITE(*,*) OMP_IN_PARALLEL()
!$OMP DO
  DO I=2,N
B(I) = (A(I) + A(I-1)) / 2.0
  ENDDO
!$OMP END DO
!$OMP END PARALLEL
END SUBROUTINE A1

# Compiling

R CMD SHLIB teste.f95 -o teste.so -fopenmp


# Output of the R

a <- rnorm(10)
b <- rnorm(10)
N <- length(a)
dyn.load("teste.so")
.Fortran("A1", as.integer(n), as.double(a),as.double(b))

F# Should return TRUE and not FALSE

[[1]]
[1] 5

[[2]]
 [1] -1.0885364  0.4170852 -0.4627566  0.5662825 -1.9792053  1.0347733
 [7]  1.1615486  1.1752779  1.4337560 -0.2803431

[[3]]
 [1] -0.52768479 -0.33572564 -0.02283571  0.05176294 -0.70646140 -0.15066979
 [7] -0.82335438  1.20606866 -1.65533309  1.04965146


Somebody to say would know me where is the error?

Thank you very much!

   Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA



  

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[Rd] Changing options in R CMD SHLIB

[Fabio Mathias Corrêa]

Dear,

When trying to use directive OpenMP in my code, I observed that the directive 
ones were being considered as commentaries. 
Compiling with command R CMD SHLIB xxx.f95 - fopenmp and calling the function 
in the R verified that threads was not being considered. 
I was to observe the options of the compiler

R CMD SHLIB --help

Usage: R CMD SHLIB [options] files | linker options

Build a shared library for dynamic loading from the specified source or
object files (which are automagically made from their sources) or
linker options.  If not given via '--output', the name for the shared
library is determined from the first source or object file.

Options:
  -h, --help        print short help message and exit
  -v, --version        print version info and exit
  -o, --output=LIB    use LIB as (full) name for the built library
  -c, --clean        remove files created during compilation
  --preclean        remove files created during a previous run
  -n, --dry-run        dry run, showing commands that would be used

Windows only:
  -d, --debug        build a debug DLL


How can I enable -fopenmp for use with R CMD SHLIB? 


   Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA




  

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Re: [Rd] Changing options in R CMD SHLIB

[Fabio Mathias Corrêa]

I use linux Mint and R.2.9.2

Thank you!

   Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA



--- Em ter, 20/10/09, Prof Brian Ripley  escreveu:

> De: Prof Brian Ripley 
> Assunto: Re: [Rd] Changing options in R CMD SHLIB
> Para: "Fabio Mathias Corrêa" 
> Cc: r-devel@r-project.org
> Data: Terça-feira, 20 de Outubro de 2009, 5:08
> Please see the manual -- 'Writing R
> Extensions'.  If you want to use 
> custom compiler flags, you use a Makevars or personal
> .Makevars file.
> Something like
> 
> PKG_FCFLAGS=-fopenmp
> 
> (you haven't told us your OS or version of R).
> 
> On Mon, 19 Oct 2009, Fabio Mathias Corrêa wrote:
> 
> > Dear,
> >
> > When trying to use directive OpenMP in my code, I
> observed that the directive ones were being considered as
> commentaries.
> > Compiling with command R CMD SHLIB xxx.f95 - fopenmp
> and calling the function in the R verified that threads was
> not being considered.
> > I was to observe the options of the compiler
> >
> > R CMD SHLIB --help
> >
> > Usage: R CMD SHLIB [options] files | linker options
> >
> > Build a shared library for dynamic loading from the
> specified source or
> > object files (which are automagically made from their
> sources) or
> > linker options.  If not given via '--output', the
> name for the shared
> > library is determined from the first source or object
> file.
> >
> > Options:
> >   -h, --help        print short help message
> and exit
> >   -v, --version        print version info and
> exit
> >   -o, --output=LIB    use LIB as (full) name for
> the built library
> >   -c, --clean        remove files created
> during compilation
> >   --preclean        remove files created during
> a previous run
> >   -n, --dry-run        dry run, showing
> commands that would be used
> >
> > Windows only:
> >   -d, --debug        build a debug DLL
> >
> >
> > How can I enable -fopenmp for use with R CMD SHLIB?
> >
> >
> >    Fábio Mathias Corrêa
> > Estatística e Experimentação Agropecuária/UFLA
> 
> -- 
> Brian D. Ripley,           
>       rip...@stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,         
>    Tel:  +44 1865 272861 (self)
> 1 South Parks Road,         
>            +44 1865
> 272866 (PA)
> Oxford OX1 3TG, UK           
>     Fax:  +44 1865 272595


  

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Re: [Rd] Changing options in R CMD SHLIB

[Fabio Mathias Corrêa]

Dear,

I managed to use directives OpenMP in R.
To compile I used the gfortran directly. For example:

gfortran-shared-O2 teste.f90-fopenmp-fPIC

By using the code in R, it works perfectly!

However, I need to use some specific libraries of R, for use in C functions in 
Fortran 95.

When compiling using the command:

gfortran-shared-O2-o teste.f90 myrandom.c func.out -fopenmp -fPIC

However, I need to indicate the path for the compiler to use the files of the 
type: Rmath.h, R.h and others.

I observed the project ROMP and the library Rcsdp. The developers of the 
library Rcsdp in the installation file present the following modification in 
the compiler for enable the OpenMP. 


CFLAGS=CFLAGS=-O3 -march=nocona -m64 -fprefetch-loop-arrays -ftree-vectorize 
-ftree-vectorizer-verbose=1 -fopenmp  -ansi -Wall -DNOSHORTS -DBIT64 
-DUSEOPENMP -I../include


LIBS=LIBS=-static -L../lib -lsdp -llapack -lptf77blas -lptcblas -latlas -lgomp 
-lrt -lpthread -lgfortran -lm 



 I already tried

~/Fortran/parallel/tri $ export PKG_FCFLAGS= -fopenmp
bash: export: `-fopenmp': not a valid identifier


I could indicate the path of the files R.h, Rmath.h and other to the gfortran? 
How? 

Thank you!

   Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA




  

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Re: [Rd] Changing options in R CMD SHLIB

[Fabio Mathias Corrêa]

Thank you very much!!!

Problem solved!!

I use

export PKG_FCFLAGS=-fopenmp

> dyn.load("teste.so")
> system.time(abc3 <- .Fortran("mxv", as.integer(m), as.integer(n), 
> as.double(a), b, as.double(c)))
 In parallel region - Thread ID1
 In parallel region - Thread ID1
 In parallel region - Thread ID1
 In parallel region - Thread ID1
 In parallel region - Thread ID1
 In parallel region - Thread ID0
 In parallel region - Thread ID0
 In parallel region - Thread ID0
 In parallel region - Thread ID0
 In parallel region - Thread ID0
   user  system elapsed
  0   0   0 



   Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA



--- Em ter, 20/10/09, Prof Brian Ripley  escreveu:

> De: Prof Brian Ripley 
> Assunto: Re: [Rd] Changing options in R CMD SHLIB
> Para: "Fabio Mathias Corrêa" 
> Cc: r-devel@r-project.org
> Data: Terça-feira, 20 de Outubro de 2009, 5:08
> Please see the manual -- 'Writing R
> Extensions'.  If you want to use 
> custom compiler flags, you use a Makevars or personal
> .Makevars file.
> Something like
> 
> PKG_FCFLAGS=-fopenmp
> 
> (you haven't told us your OS or version of R).
> 
> On Mon, 19 Oct 2009, Fabio Mathias Corrêa wrote:
> 
> > Dear,
> >
> > When trying to use directive OpenMP in my code, I
> observed that the directive ones were being considered as
> commentaries.
> > Compiling with command R CMD SHLIB xxx.f95 - fopenmp
> and calling the function in the R verified that threads was
> not being considered.
> > I was to observe the options of the compiler
> >
> > R CMD SHLIB --help
> >
> > Usage: R CMD SHLIB [options] files | linker options
> >
> > Build a shared library for dynamic loading from the
> specified source or
> > object files (which are automagically made from their
> sources) or
> > linker options.  If not given via '--output', the
> name for the shared
> > library is determined from the first source or object
> file.
> >
> > Options:
> >   -h, --help        print short help message
> and exit
> >   -v, --version        print version info and
> exit
> >   -o, --output=LIB    use LIB as (full) name for
> the built library
> >   -c, --clean        remove files created
> during compilation
> >   --preclean        remove files created during
> a previous run
> >   -n, --dry-run        dry run, showing
> commands that would be used
> >
> > Windows only:
> >   -d, --debug        build a debug DLL
> >
> >
> > How can I enable -fopenmp for use with R CMD SHLIB?
> >
> >
> >    Fábio Mathias Corrêa
> > Estatística e Experimentação Agropecuária/UFLA
> 
> -- 
> Brian D. Ripley,           
>       rip...@stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,         
>    Tel:  +44 1865 272861 (self)
> 1 South Parks Road,         
>            +44 1865
> 272866 (PA)
> Oxford OX1 3TG, UK           
>     Fax:  +44 1865 272595


  

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[Rd] Error when compiling code in C

[Fabio Mathias Corrêa]

Dear,


I used the command in the terminal to compile code FORTRAN with directive OpenMP

export PKG_FCFLAGS=-fopenmp

It functioned perfectly for pure code FORTRAN.

However, when I call a function in C in code FORTRAN, the function in C is not 
compiled.

The following error appears

~/Fortran/parallel $ R CMD SHLIB para.f95 myrandom.c -o func.so -fopenmp

gfortran -fopenmp -fpic -g -O -c  para.f95 -o para.o
gcc -std=gnu99 -I/usr/share/R/include  -fpic  -g -O2 -c myrandom.c -o 
myrandom.c@
gfortran -shared -o func.so para.o myrandom.o -fopenmp -L/usr/lib64/R/lib -lR
gfortran: myrandom.o: No such file or directory
make: *** [func.so] Error 1

When compile only the function in code FORTRAN. The archive is compiled!

If compile only the function in C, the error I appear!

What it is occurring is that instead of generating an archive myrandom.o the 
compiler is generating an archive myrandom.c@

What I must make?

Thank you very much!


   Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA





  

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