I am trying to wrap some Fortran modules to be called from Python using the ctypes library. I am going directly from Fortran to Python without writing any C code. Simply compiling a shared library.
Yet I am struggling with what the best approach should be for memory allocation, namely who should own the data. Should I allocate inside the Fortran module and then expose the data using ctypes or should I allocate with numpy and pass as argument to Fortran.
I am also open to doing the intermediary step and write the C wrappers (F->C->Python). But then the same question arises.
Thanks!
PS: I know F2Py exists I know how to use it but I am interested in going the ctypes way.
mod.f90:
module angio_global
use iso_c_binding
implicit none
integer :: lx,ly
real*8 :: raio_init
real*8,allocatable :: phi(:,:)
real*8 :: epsilon,rho_phi
contains
subroutine init_fields(phi_,lx_,ly_)
integer ,intent(in) :: lx_,ly_
real*8,intent(in) :: phi_(lx_,ly_)
integer :: i,j
real*8 :: dx,dy
lx = lx_
ly = ly_
allocate(phi(0:lx+1,0:ly+1))
phi(1:lx,1:ly) = phi_
raio_init = 20.0_dp
epsilon = 1.0_dp
rho_phi = 1.0_dp
do j=1,ly
do i=1,lx
dx = i-lx/2.0_dp
dy = j-ly/2.0_dp
if(dx**2+dy**2<raio_init**2) phi(i,j) = 1.0_dp
enddo
enddo
end subroutine
subroutine wrap_init_fields(phi_,lx_,ly_) bind(c)
integer(c_int),intent(in),value :: lx_,ly_
real(c_double),intent(in) :: phi_(lx_,ly_)
call init_fields(phi_,lx_,ly_)
end subroutine
subroutine wrap_get_phi(phi_,lx_,ly_) bind(c)
integer(c_int),intent(in),value :: lx_,ly_
real(c_double),intent(inout) :: phi_(lx_,ly_)
phi_ = phi(1:lx,1:ly)
end subroutine
end module
caller.py:
from ctypes import CDLL, c_int, c_double,c_float
import numpy as np
from numpy.ctypeslib import ndpointer
import matplotlib.pyplot as plt
angio = CDLL('./global.so')
def init_fields(phi):
Nx,Ny = np.shape(phi)
phi_ptr = ndpointer(dtype=phi.dtype,shape=phi.shape,flags="F_CONTIGUOUS")
angio.wrap_init_fields.argtypes = [phi_ptr,c_int,c_int]
angio.wrap_init_fields(phi,Nx,Ny)
return
def get_phi(phi):
Nx,Ny = np.shape(phi)
phi_ptr = ndpointer(dtype=phi.dtype,shape=phi.shape,flags="F_CONTIGUOUS")
angio.wrap_get_phi.argtypes = [phi_ptr,c_int,c_int]
angio.wrap_get_phi(phi,Nx,Ny)
phi = np.zeros((200,200),dtype = np.float64,order="F")-1.0
init_fields(phi)
Related
I need to get wall time in single precision. MPI_WTIME however returns the value in double precision. To work around this I try:
subroutine wtime
real(kind=8) :: t_now
real :: wt
t_now = MPI_WTIME()
if ( t_now > 1e38 ) then
wt = 1e30
else if ( t_now < 1e-38 ) then
wt = 0
end if
end subroutine wtime
Is there a fortran equivalent of MPI_WTIME() that I can use instead to get wall time in single precision?
I compile my code with the flag -real-size 32 so by default real is of kind 4.
I want to build a function with default arguments. However, any of the following simple methods fail to compile with F2PY printing the following simple and no-informing error message "error: f2py target file '/tmp/....' not generated".
1st using optional
module a
contains
integer function func(j)
implicit none
integer, optional :: j
if(present(j)) then
func = j
else
func = 0
endif
end function
end module
The other is function overloading using interface
module test
interface func
module procedure :: func0, func1
end interface
contains
integer function func0()
implicit none
func0 = 0
end function
integer function func1(j)
implicit none
integer, intent(in) :: j
func1 = j
end function
end module
Appreciate your help.
You can initialize the expression using the F2PY directive.
integer function func(j)
implicit none
integer :: j
!f2py integer :: j = 0
func = j
end function
I am new to OpenMP. I want to solve a stiff ODE system for a range of parameter values using parallel do loops. I use the following code in Fortran given below. However, I do not know whether calling a stiff solver(as a subroutine) inside a parallel do loop is allowed or not? Also, I want to write the time series data into files with filenames such as "r_value_s__value.txt" in the subroutine before the return to the main program. Can anyone help. Below is the code and the error. I used gfortran with flags -fopenmp to compile.
PROGRAM OPENMP_PARALLEL_STIFF
USE omp_lib
IMPLICIT NONE
INTEGER :: I, J
INTEGER, PARAMETER :: RTOT=10, STOT=15
INTEGER :: TID
INTEGER, PARAMETER :: NUM_THREADS=8
DOUBLE PRECISION :: T_INITIAL, T_FINAL
CALL OMP_SET_NUM_THREADS(NUM_THREADS)
CALL CPU_TIME(T_INITIAL)
PRINT*, "TIME INITIAL ",T_INITIAL
!$OMP PARALLEL DO PRIVATE(I,J,TID)
DO I=1,RTOT
DO J=1,STOT
TID=OMP_GET_THREAD_NUM()
CALL STIFF_DRIVER(TID,I,J,RTOT,STOT)
END DO
END DO
!$OMP END PARALLEL DO
CALL CPU_TIME(T_FINAL)
PRINT*, "TIME FINAL ",T_FINAL
PRINT*, "TIME ELAPSED ",(T_FINAL-T_INITIAL)/NUM_THREADS
END PROGRAM OPENMP_PARALLEL_STIFF
SUBROUTINE STIFF_DRIVER(TID,II,JJ,RTOT,STOT)
USE USEFUL_PARAMETERS_N_FUNC
USE DVODE_F90_M
! Type declarations:
IMPLICIT NONE
! Number of odes for the problem:
INTEGER :: SERIAL_NUMBER, TID
INTEGER :: II, JJ, RTOT, STOT, IND
INTEGER :: J, NTOUT
INTEGER :: ITASK, ISTATE, ISTATS, I
! parameters : declaration
DOUBLE PRECISION, PARAMETER :: s0=0.450D0, dr=1.0D-4, ds=1.0D-2
DOUBLE PRECISION, DIMENSION(NEQ) :: Y, YOUT
DOUBLE PRECISION :: ATOL, RTOL, RSTATS, T, TOUT, EPS, TFINAL, DELTAT
DIMENSION :: RSTATS(22), ISTATS(31)
DOUBLE PRECISION :: bb, cc, ba, ba1, eta
CHARACTER(len=45) :: filename
TYPE (VODE_OPTS) :: OPTIONS
SERIAL_NUMBER=3011+II+(JJ-1)*RTOT
IND=TID+3011+II+(JJ-1)*RTOT
WRITE (*,12)SERIAL_NUMBER,TID
12 FORMAT ("SL. NO. ",I5," THREAD NO.",I3)
r=(II-1)*dr
s=s0+JJ*ds
EPS = 1.0D-9
! Open the output file:
WRITE (filename,93)r,s
93 FORMAT ("r_",f6.4,"_s_",f4.2,".txt")
OPEN (UNIT=IND,FILE=filename,STATUS='UNKNOWN',ACTION='WRITE')
! Parameters for the stiff ODE system
q0 = 0.60D0; v = 3.0D0
Va = 20.0D-4; Vs = 1.0D-1
e1 = 1.0D-1; e2 = 1.10D-5; e3 = 2.3D-3; e4=3.0D-4
del = 1.7D-4; mu = 5.9D-4
al = 1.70D-4; be = 8.9D-4; ga = 2.5D-1
! S and r dependent parameters
e1s = e1/s; e2s = e2/(s**2); e3s = e3/s; e4s = e4/s
dels = del*s; rs = r*s
e1v = e1/v; e2v = e2/(v**2); e3v = e3/v; e4v = e4/v
delv = del*v; rv = r*v
! SET INITIAL PARAMETERS for INTEGRATION ROUTINES
T = 0.0D0
TFINAL = 200.0D0
DELTAT = 0.10D0
NTOUT = INT(TFINAL/DELTAT)
RTOL = EPS
ATOL = EPS
ITASK = 1
ISTATE = 1
! Set the initial conditions: USING MODULE USEFUL_PARAMETERS_N_FUNC
CALL Y_INITIAL(NEQ,Y)
! Set the VODE_F90 options:
OPTIONS = SET_OPTS(DENSE_J=.TRUE.,USER_SUPPLIED_JACOBIAN=.FALSE., &
RELERR=RTOL,ABSERR=ATOL,MXSTEP=100000)
! Integration:
DO I=1,NTOUT
TOUT = (I-1)*DELTAT
CALL DVODE_F90(F_FUNC,NEQ,Y,T,TOUT,ITASK,ISTATE,OPTIONS)
! Stop the integration in case of an error
IF (ISTATE<0) THEN
WRITE (*,*)"ISTATE ", ISTATE
STOP
END IF
! WRITE DATA TO FILE
WRITE (IND,*) TOUT,T, Y(NEQ-2)
END DO
CLOSE(UNIT=IND)
RETURN
END SUBROUTINE STIFF_DRIVER
At line ** of file openmp_parallel_stiff.f90 (unit = 3013)
Fortran runtime error: File already opened in another unit
The issue is the format that you chose: f6.4 for r will overflow for r>=10. Then, the output will be six asterisks ****** (depending on the compiler) for all values of r>=10 on all threads. The same holds true for s.
I would suggest to either limit/check the range of these values or extend the format to honor more digits.
As #francescalus mentioned, another possibility is hit a combination of II and JJ where r and s are identical.
Just for the fun of it - let's do the math:
r=(II-1)*dr
s=s0+JJ*ds
From r=s follows
(II-1)*dr = s0+JJ*ds
or
II = 1 + s0/dr + JJ*ds/dr
Using the constants s0=0.450D0, dr=1.0D-4, ds=1.0D-2 yields
II = 4501 + JJ*10
So, whenever this combination is true for two (or more) threads at a time, you run into the observed issue.
Simple solution for this case: add the thread number to the file name.
I took an example of data transfer between Host and Device for CUDA Fortran and found this:
Host Code:
program incTest
use cudafor
use simpleOps_m
implicit none
integer, parameter :: n = 256
integer :: a(n), b, i
integer, device :: a_d(n)
a = 1
b = 3
a_d = a
call inc<<<1,n>>>(a_d, b)
a = a_d
if (all(a == 4)) then
write(*,*) 'Success'
endif
end program incTest
Device Code:
module simpleOps_m
contains
attributes(global) subroutine inc(a, b)
implicit none
integer :: a(:)
integer, value :: b
integer :: i
i = threadIdx%x
a(i) = a(i)+b
end subroutine inc
end module simpleOps_m
The expected outcome is the console presenting "Success", but this did not happen. Nothing appears in the screen, nothing errors or messages.
This happen because don't enter in if, because a_d has the same value that before call inc subroutine.
I'm using:
OS: Linux - Ubuntu 16
Cuda 8
PGI to compile
Commands to compile:
pgf90 -Mcuda -c Device.cuf
pgf90 -Mcuda -c Host.cuf
pgf90 -Mcuda -o HostDevice Device.o Host.o
./HostDevice
I tried other examples and they did not work too.
I tried using simple Fortran (.f90) code with the same commands to compile and it works!
How can I fix this problem?
What type of device are you using? (If you don't know, post the output from the "pgaccelinfo" utility).
My best guess is that you have a Pascal based device in which case you need to compile with "-Mcuda=cc60".
For example, if I add error checking to the example code, we see that we get an invalid device kernel error when running on a Pascal without the "cc60" as part of the compilation.
% cat test.cuf
module simpleOps_m
contains
attributes(global) subroutine inc(a, b)
implicit none
integer :: a(:)
integer, value :: b
integer :: i
i = threadIdx%x
a(i) = a(i)+b
end subroutine inc
end module simpleOps_m
program incTest
use cudafor
use simpleOps_m
implicit none
integer, parameter :: n = 256
integer :: a(n), b, i, istat
integer, device :: a_d(n)
a = 1
b = 3
a_d = a
call inc<<<1,n>>>(a_d, b)
istat=cudaDeviceSynchronize()
istat=cudaGetLastError()
a = a_d
if (all(a == 4)) then
write(*,*) 'Success'
else
write(*,*) 'Error code:', cudaGetErrorString(istat)
endif
end program incTest
% pgf90 test.cuf -Mcuda
% a.out
Error code:
invalid device function
% pgf90 test.cuf -Mcuda=cc60
% a.out
Success
Now I am facing the problem that in a module, with a seed I am generating random numbers to be used in a loop of a function but each time I call that function, the same random numbers are generated (because the seed is obviously the same) but it's supposed that it must continue the series or at least it must be different between calls. One solution could be that the main program gives a new seed to be used in the module but I think it there could be another elegant solution.
I am using Mersenne Twister generator by suggestion of many people.
Added
My function in my module (it is a package of functions) escentially makes such a Metropolis test using random numbers generated by a seed, for some reason compilation complains if I put
module mymod
uses mtmod
call sgrnd(4357)!<-- this line causes compilation error
contains
myfunc(args)
implicit none
// declarations etc
!call sgrnd(4357) <-- if I put this call here compilator says ok,
!but re-start random number series each time this function is called :(
....
!the following part is inside a loop
if (prob < grnd()) then
!grnd() is random number generated
return
else continue testing to the end of the loop cycle
end myfunc
But if I put that function in the contains of the main program (using mtmod too) and call sgrnd(4357) before contains section and the calls to myfunc, now everything compile and run nicely. For clarity, I didn't want to put that long function in the main program, it has 70 lines of code, but it seems I have no escape. Notice that so, the seed is once called. The simulations have now physical meanings but with that price payed.
I always used this subroutine (I'm running a MonteCarlo simulation), call it in the beginning of your main program and tis should do the job:
(Source: gfortran 4.6.1)
c initialize a random seed from the system clock at every run (fortran 95 code)
subroutine init_random_seed()
INTEGER :: i, n, clock
INTEGER, DIMENSION(:), ALLOCATABLE :: seed
CALL RANDOM_SEED(size = n)
ALLOCATE(seed(n))
CALL SYSTEM_CLOCK(COUNT=clock)
seed = clock + 37 * (/ (i - 1, i = 1, n) /)
CALL RANDOM_SEED(PUT = seed)
DEALLOCATE(seed)
end
You can find here a subroutine that uses system time to re-seed the random number generator. You shouldn't have to do this every time you call random_number(), just each time you re-start the program.
Honestly, it didn't take me more than ten minutes to find this with Google.
In order to recover my points taken, I was obliged to find my own answer, here it is (after one hour of tries)
main program is
program callrtmod
use mymod
implicit none
real::x
x=1.0
write(*,*) x+writerandnum()
write(*,*) x+writerandnum()
write(*,*) x+writerandnum()
end program callrtmod
here's my module
module mymod
implicit none
!-------------mt variables-------------
! Default seed
integer, parameter :: defaultsd = 4357
! Period parameters
integer, parameter :: N = 624, N1 = N + 1
! the array for the state vector
integer, save, dimension(0:N-1) :: mt
integer, save :: mti = N1
!--------------------------------------
contains
function writerandnum
implicit none
real(8)::writerandnum
writerandnum = grnd()
!if you please, you could perform a Metropolis test here too
end function writerandnum
!Initialization subroutine
subroutine sgrnd(seed)
implicit none
integer, intent(in) :: seed
mt(0) = iand(seed,-1)
do mti=1,N-1
mt(mti) = iand(69069 * mt(mti-1),-1)
enddo
!
return
end subroutine sgrnd
!---------------------------------------------------------------------------
!the function grnd was here
!---------------------------------------------------------------------------
subroutine mtsavef( fname, forma )
character(*), intent(in) :: fname
character, intent(in) :: forma
select case (forma)
case('u','U')
open(unit=10,file=trim(fname),status='UNKNOWN',form='UNFORMATTED', &
position='APPEND')
write(10)mti
write(10)mt
case default
open(unit=10,file=trim(fname),status='UNKNOWN',form='FORMATTED', &
position='APPEND')
write(10,*)mti
write(10,*)mt
end select
close(10)
return
end subroutine mtsavef
subroutine mtsaveu( unum, forma )
integer, intent(in) :: unum
character, intent(in) :: forma
select case (forma)
case('u','U')
write(unum)mti
write(unum)mt
case default
write(unum,*)mti
write(unum,*)mt
end select
return
end subroutine mtsaveu
subroutine mtgetf( fname, forma )
character(*), intent(in) :: fname
character, intent(in) :: forma
select case (forma)
case('u','U')
open(unit=10,file=trim(fname),status='OLD',form='UNFORMATTED')
read(10)mti
read(10)mt
case default
open(unit=10,file=trim(fname),status='OLD',form='FORMATTED')
read(10,*)mti
read(10,*)mt
end select
close(10)
return
end subroutine mtgetf
subroutine mtgetu( unum, forma )
integer, intent(in) :: unum
character, intent(in) :: forma
select case (forma)
case('u','U')
read(unum)mti
read(unum)mt
case default
read(unum,*)mti
read(unum,*)mt
end select
return
end subroutine mtgetu
!===============================================
!Random number generator
! real(8) function grnd()
function grnd !agregue yo
implicit integer(a-z)
real(8) grnd !agregue yo
! Period parameters
integer, parameter :: M = 397, MATA = -1727483681
! constant vector a
integer, parameter :: LMASK = 2147483647
! least significant r bits
integer, parameter :: UMASK = -LMASK - 1
! most significant w-r bits
! Tempering parameters
integer, parameter :: TMASKB= -1658038656, TMASKC= -272236544
dimension mag01(0:1)
data mag01/0, MATA/
save mag01
! mag01(x) = x * MATA for x=0,1
TSHFTU(y)=ishft(y,-11)
TSHFTS(y)=ishft(y,7)
TSHFTT(y)=ishft(y,15)
TSHFTL(y)=ishft(y,-18)
if(mti.ge.N) then
! generate N words at one time
if(mti.eq.N+1) then
! if sgrnd() has not been called,
call sgrnd( defaultsd )
! a default initial seed is used
endif
do kk=0,N-M-1
y=ior(iand(mt(kk),UMASK),iand(mt(kk+1),LMASK))
mt(kk)=ieor(ieor(mt(kk+M),ishft(y,-1)),mag01(iand(y,1)))
enddo
do kk=N-M,N-2
y=ior(iand(mt(kk),UMASK),iand(mt(kk+1),LMASK))
mt(kk)=ieor(ieor(mt(kk+(M-N)),ishft(y,-1)),mag01(iand(y,1)))
enddo
y=ior(iand(mt(N-1),UMASK),iand(mt(0),LMASK))
mt(N-1)=ieor(ieor(mt(M-1),ishft(y,-1)),mag01(iand(y,1)))
mti = 0
endif
y=mt(mti)
mti = mti + 1
y=ieor(y,TSHFTU(y))
y=ieor(y,iand(TSHFTS(y),TMASKB))
y=ieor(y,iand(TSHFTT(y),TMASKC))
y=ieor(y,TSHFTL(y))
if(y .lt. 0) then
grnd=(dble(y)+2.0d0**32)/(2.0d0**32-1.0d0)
else
grnd=dble(y)/(2.0d0**32-1.0d0)
endif
return
end function grnd
end module mymod
test my solution and vote me up ;) [of course, as you see, I modified mt.f90 code to be included conveniently in my module, so I can keep separately the main program from the randon numbers generation part, so I can do a Metropolis test aside the main program. The main program just wants to know if a trial was accepted or not. My solution does give more clarity to the main progam]