f2py and Fortran90 gfortran_filename error

[Tyler]

Hello All:

Since my last post I have attempted to use the f2py program which
comes with numpy. I am able to create a <module_name>.so file fine;
however, when I import it into Python, I receive the following
message:


Traceback (most recent call last):
File "<stdin>", line 1, in ?
ImportError: ./matsolve2.so: undefined symbol: _gfortran_filename


The steps I used to create the matsolve2.so file are as follows:

(1) Created a Fortran90 program matsolve.f90

Note: The program compiles fine and prints the proper output for the
simple matrix specified. I have also attached below the file
matsolve.f90 if it helps at all.

(2) f2py matsolve.f90 -m matsolve2 -h matsolve2.pyf
(3) f2py -c matsolve2.pyf --f90exec=/usr/bin/gfortran matsolve.f90

Note: I had to specify the f90 path as f2py did not automatically find
it.

Any suggestions are greatly appreciated.

Cheers,

t.

! MATSOLVE.f90
!
! Start main program
PROGRAM MATSOLVE
IMPLICIT NONE
INTEGER,PARAMETER :: n=3
INTEGER :: i,j
REAL,DIMENSION(n) :: x,b
REAL,DIMENSION(n,n) :: A,L,U
! Initialize the vectors and matrices with a test case from text
! Using the one given in Appendix A from Thompson.
! Known vector "b"
b(1) = 12.
b(2) = 11.
b(3) = 2.

! Known coefficient matrix "A", and initialize L and U
DO i=1,n
DO j=1,n
L(i,j) = 0.
U(i,j) = 0.
END DO
END DO

A(1,1) = 3.
A(1,2) = -1.
A(1,3) = 2.

A(2,1) = 1.
A(2,2) = 2.
A(2,3) = 3.

A(3,1) = 2.
A(3,2) = -2.
A(3,3) = -1.


! Call subroutine to create L and U matrices from A
CALL lumake(L,U,A,n)
! Print results
PRINT *, '-----------------------'
DO i=1,n
DO j=1,n
PRINT *, i, j, A(i,j), L(i,j), U(i,j)
END DO
END DO
PRINT *, '-----------------------'

! Call subroutine to solve for "x" using L and U
CALL lusolve(x,L,U,b,n)

! Print results
PRINT *, '-----------------------'
DO i=1,n
PRINT *, i, x(i)
END DO
PRINT *, '-----------------------'

END PROGRAM MATSOLVE


! Create subroutine to make L and U matrices
SUBROUTINE lumake(LL,UU,AA,n1)
IMPLICIT NONE
INTEGER,PARAMETER :: n=3
INTEGER :: i,j,k
REAL :: LUSUM
INTEGER,INTENT(IN) :: n1
REAL,DIMENSION(n,n),INTENT(IN) :: AA
REAL,DIMENSION(n,n),INTENT(OUT) :: LL,UU

! We first note that the diagonal in our UPPER matrix is
! going to be UU(j,j) = 1.0, this allows us to initialize
! the first set of expressions
UU(1,1) = 1.

! Find first column of LL
DO i = 1,n1
LL(i,1) = AA(i,1)/UU(1,1)
END DO

! Now find first row of UU
DO j = 2,n1
UU(1,j) = AA(1,j)/LL(1,1)
END DO

! Now find middle LL elements
DO j = 2,n1
DO i = j,n1
LUSUM = 0.
DO k = 1,j-1
LUSUM = LUSUM + LL(i,k)*UU(k,j)
END DO
LL(i,j) = AA(i,j) - LUSUM
END DO

! Set Diagonal UU
UU(j,j) = 1.

! Now find middle UU elements
DO i = j+1,n1
LUSUM = 0.
DO k = 1,j-1
LUSUM = LUSUM + LL(j,k)*UU(k,i)
END DO
UU(j,i) = (AA(j,i) - LUSUM)/LL(j,j)
END DO
END DO
END SUBROUTINE lumake


! Make subroutine to solve for x
SUBROUTINE lusolve(xx,L2,U2,bb,n2)
IMPLICIT NONE
INTEGER,PARAMETER :: n=3
INTEGER :: i,j,k
REAL :: LYSUM,UXSUM
REAL,DIMENSION(n):: y
INTEGER,INTENT(IN) :: n2
REAL,DIMENSION(n),INTENT(IN) :: bb
REAL,DIMENSION(n,n),INTENT(IN) :: L2,U2
REAL,DIMENSION(n),INTENT(OUT) :: xx

! Initialize
DO i=1,n2
y(i) = 0.
xx(i) = 0.
END DO

! Solve L.y = b
y(1) = bb(1)/L2(1,1)
DO i = 2,n2
LYSUM = 0.
DO k = 1,i-1
LYSUM = LYSUM + L2(i,k)*y(k)
END DO
y(i) = (bb(i) - LYSUM)/L2(i,i)
END DO

! Now do back subsitution for U.x = y
xx(n2) = y(n2)/U2(n2,n2)
DO j = n2-1,1,-1
UXSUM = 0.
DO k = j+1,n2
UXSUM = UXSUM + U2(j,k)*xx(k)
END DO
xx(j) = y(j) - UXSUM
END DO
END SUBROUTINE lusolve

 

[Robert Kern]

Hello All:

Since my last post I have attempted to use the f2py program which
comes with numpy.

It's better to ask these questions on numpy-discussion, instead. There are more
f2py users per capita there.

http://www.scipy.org/Mailing_Lists

I am able to create a <module_name>.so file fine;
however, when I import it into Python, I receive the following
message:

Traceback (most recent call last):
File "<stdin>", line 1, in ?
ImportError: ./matsolve2.so: undefined symbol: _gfortran_filename


The steps I used to create the matsolve2.so file are as follows:

(1) Created a Fortran90 program matsolve.f90

Note: The program compiles fine and prints the proper output for the
simple matrix specified. I have also attached below the file
matsolve.f90 if it helps at all.

(2) f2py matsolve.f90 -m matsolve2 -h matsolve2.pyf
(3) f2py -c matsolve2.pyf --f90exec=/usr/bin/gfortran matsolve.f90

Note: I had to specify the f90 path as f2py did not automatically find
it.

You want to specify the *kind* of Fortran compiler such that f2py knows what
compile/link flags to use. Only use the --f90exec option to inform f2py that the
actual executable is named something odd or is in an unexpected place, like
/opt/gfortran/bin/gfortran-4.3, for example. The correct option to use is

--fcompiler=gnu95

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco

 

[Tyler]

It's better to ask these questions on numpy-discussion, instead. There are more
f2py users per capita there.

http://www.scipy.org/Mailing_Lists









You want to specify the *kind* of Fortran compiler such that f2py knows what
compile/link flags to use. Only use the --f90exec option to inform f2py that the
actual executable is named something odd or is in an unexpected place, like
/opt/gfortran/bin/gfortran-4.3, for example. The correct option to use is

--fcompiler=gnu95

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco

Hi Robert:

Thanks for the advice and I'll try posting to the mailing list you
mentioned. For what it's worth, the option, --fcompiler=gnu95 yileds
the following error in the second calling of f2py:

error: don't know how to compile Fortran code on platform 'posix' with
'gnu95' compiler. Supported compilers are:
compaq,absoft,intel,gnu,sun,f,vast,ibm,lahey,intelv,intele,pg,compaqv,mips,hpux,intelev,nag)

Cheers,

t.

 

[Beliavsky]

It's better to ask these questions on numpy-discussion, instead. There are more
f2py users per capita there.

http://www.scipy.org/Mailing_Lists

I wish the Google Groups interface to the list http://groups.google.com/group/Numpy-discussion
worked. When I use it to post my messages bounce, but messages from
the list do show up on Google Groups. The "bounces" say

"This mailing list is now defunct. Please use
(e-mail address removed) to discuss NumPy, Numeric, and numarray.

http://projects.scipy.org/mailman/listinfo/numpy-discussion"

Yes, I know I could follow these instructions, but I prefer to use
Google Groups.

 

[Robert Kern]

I wish the Google Groups interface to the list http://groups.google.com/group/Numpy-discussion
worked. When I use it to post my messages bounce, but messages from
the list do show up on Google Groups. The "bounces" say

"This mailing list is now defunct. Please use
(e-mail address removed) to discuss NumPy, Numeric, and numarray.

http://projects.scipy.org/mailman/listinfo/numpy-discussion"

Yes, I know I could follow these instructions, but I prefer to use
Google Groups.

Well, you'll have to find out who set up that interface or whoever at Google is
in charge of maintaining such gatewayed groups to let them know that the mailing
list has migrated. I used the "Send email to the owner" link, but I have no idea
who that is supposed to go to.

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco

 

[Robert Kern]

Beliavsky wrote:

Well, you'll have to find out who set up that interface or whoever at Google is
in charge of maintaining such gatewayed groups to let them know that the mailing
list has migrated. I used the "Send email to the owner" link, but I have no idea
who that is supposed to go to.

It worked.

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco