I am doing something I've done time after time, setting an array to zero in Fortran 90. However, for some reason in this case it is not working, and I have no idea why.
I allocate the array and use A = 0.d0 but when I write out one of the components it prints as 0.4xxx
My array is a module-level array if this makes any difference, and I am initializing it within a subroutine.
Does anybody have an idea why this could be happening?
EDIT: Sorry I have been away therefore haven't responded. This is still happening. I am using gfortran 4.3. I have changed a few things to see if they will help but they haven't. Notice below that I set the elements to zero two ways. Within the loop they are definitely being set to zero, but after the loop at least one element is becoming non-zero for no apparent reason. I know that all other elements are non-zero as well. I changed the array concerned to be a local subroutine array but this has no effect. The following is the code that is giving me wrong output:
subroutine coeff_cube(f, Ng,x_max_8,coeffs)
integer, intent(in) :: Ng
real(8), intent(in) :: f(Ng,Ng,Ng)
real(8), intent(in) :: x_max_8
integer :: i,j,k,ii,jj,kk
real(8) :: Ints(Ng,nmax+1)
real(8), intent(out) :: coeffs(nmax+1,nmax+1,nmax+1)
call cube_ints(x_max_8,Ng,Ints)
write(*,*) "NOW NMAX IS: ", nmax !Prints '24'
coeffs = 0.0d0
do i=1,nmax+1
do j=1,nmax+1
do k=1,nmax+1
coeffs(i,j,k) = 0.d0
write(*,*) coeffs(i,j,k) !Prints 0.0000000000000000 for all i,j,k
end do
end do
end do
write(*,*) coeffs(1,3,28) !Prints a non-zero number
coeffs(1,3,28) = 0.0d0
write(*,*) coeffs(1,3,28) !Prints 0.0000000000000000
do k=1,nmax+1
i=1
j=1
if (i+j+k .GT. nmax+1)then
exit
end if
do j=1,nmax+1
i=1
if (i+j+k .GT. nmax+1)then
exit
end if
do i=1,nmax+1
if (i+j+k .GT. nmax+1)then
exit
end if
do kk=1,Ng
do jj = 1,Ng
do ii = 1,Ng
coeffs(i,j,k) = coeffs(i,j,k) + &
& f(ii,jj,kk)*Ints(ii,i)*Ints(jj,j)*Ints(kk,k)
if(i==1.AND.j==3.AND.k==28)then
if (kk==1) then
write(*,*) coeffs(i,j,k)
end if
end if
end do
end do
end do
end do
end do
end do
write(*,*) coeffs(1,3,28) !Prints 0.0000000000000000
end subroutine
Does anyone have any ideas?
Thanks.
Sorry I have figured it out...
It does in fact set the array to zero, however for some reason I am writing an element that is not in the array (out of bounds). I would have expected it to give me an error rather than write out any old thing, but I guess that's just fortran...
Are you aware that you can initialize an entire array with a single statement?
coeffs = 0.0d
will set all elements of the array to 0.
Related
I'm writing a subroutine that transform a regular vector into the one with only non-zero elements. Say, vector a=(0,0,1,2,3)' (n by 1). Then the non-zero vector is c=(1,2,3), and the row index is recorded as ic=(0,0,0,1,2,3) where ic(1)=0, ic(i+1)-ic(i) is the number of non-zero elements in i-th row. The vector index jc=(1,1,1) with size 3 as there are 3 non-zero entries. See the sparse matrix wiki for FYI: https://en.wikipedia.org/wiki/Sparse_matrix.
Despite its simplicity, I'm having troubles in running the following code named sparsem.f90
!This subroutine coverts a regular sparse matrix a into a CSR form
MODULE SPARSEM
CONTAINS
SUBROUTINE vsparse(a,c,jc,ic,counta,ierr,myid)
IMPLICIT NONE
REAL(8), INTENT(IN):: a(:)
INTEGER, INTENT(IN):: counta,myid
REAL(8), INTENT(OUT):: c(counta)
INTEGER, INTENT(OUT):: jc(counta),ic(size(a)+1)
INTEGER:: ierr,countaa,i
character(len=90):: filename
ierr=0
jc=0
c=0.0d0
ic=0
PRINT *, 'SIZE OF A IN VSPARSE', size(a),count(a>0.0d0),counta
IF (COUNT(a>0.0d0) /= counta) THEN
ierr=1
PRINT *, 'ERROR: number count of non-zero a(i,j) is not', counta
ELSE
countaa=0
ic(1)=0
DO i=1,size(a)
IF (a(i) > 0.0d0 ) THEN
countaa=countaa+1
c(countaa)=a(i)
ic(i+1)=ic(i)+1
jc(countaa)=1
IF (countaa<100) PRINT *,'checkcheckcheck', a(i), &
countaa,jc(countaa),c(countaa)，jc(1:5)
ELSE
ic(i+1)=ic(i)
END IF
END DO
PRINT *, 'JCJCJCJC',jc(1:5)
END IF
IF (myid==7) THEN
WRITE(filename,'("sparsedens_dcheck",I1,".txt")') myid+1
OPEN(UNIT=212101, FILE="/home/wenya/Workspace/Model4/valuef/"//filename,ACTION='write',status='replace')
DO i=1,counta+1
IF (i<=counta) THEN
WRITE(212101,*) c(i),jc(i)
ELSE
WRITE(212101,*) 0.0D0,0
END IF
END DO
CLOSE(212101)
END IF
return
END SUBROUTINE vsparse
END MODULE SPARSEM
So the three print jc codes shall give 1 1 1 1 1.... Yet starting from the second print jc code, the result is 6750960 6750691 6750692 .... The array of jc has size 9,000,000. And I know the first 2250000 element is 0.
To replicate this problem, here is the main program
PROGRAM MAIN
USE SPARSEM
IMPICIT NONE
REAL(8):: dens_last(9000000)
REAL(8), ALLOCATABLE :: dens(:)
INTEGER, ALLOCATABLE :: ic(:),jc(:)
INTEGER:: i
dens_last(1:2250000)=0.0d0
dens_last(2250001:9000000)=1.0d0/6750000.0d0
ncount=count(dens_last>0.0d0)
ALLOCATE(dens(ncount), ic(9000000+1), jc(ncount)_
CALL VSPASEM(dens_last, dens, jc, ic, ncount,ierr)
DEALLOCATE(dens,ic,jc)
END PROGRAM MAIN
I am using gfortran 6.3.0 and openmpi latest version on a UBUNTU 17.04 computer. Although openmpi is not used in this example, it's used in the rest of the program. Any thoughts? Thanks!
I am trying to read values from two files and write only the same values in the new(third) file. Is there any code or function I can use? What I have tried is that reading two files with DO statement and named them variable1(i), variable2(j), however I think comparing them is not easy for me, which is not working in the way of variable1(i) = variable (j)
Example:
file 1:
a1,b1,c1,d1,e1,a2,b2,c2,d2,e2,.........
f(a1),f(b1),f(c1),.......
Obviously I don't know the function, I just know the results.
file 2:
e2,e2,c1,c1,c1,c1,a2,a1,..........
new file 3:
f(e2),f(e2),f(c1),f(c1),f(c1),f(a2),f(a1)......
here's my code and the error is occurring because the number of data in two file is different
real*8 refjd(64285),pha(64285)
real*8 timejd(55436),epha(55436)
real*8 phs
format(47x,f10.2)
open(4,file="neic56.out")
do j=1,55436
read(4,55)timejd(j)
close(4)
format(f10.2,1x,f8.4)
open(3,file="74-17.out")
do i=1,64285
read(3,44)refjd(i),pha(i)
close(3)
end do
if(timejd(j) .EQ. refjd(i)) then
epha(j)=pha(i)
phs=epha(j)/360.
open(5,file="ejplphase.dat")
write(5,66)phs
end if
format(f6.4)
end do
end
A naive algorithm that would do the job is the following:
program filesOut
implicit none
integer :: i, j
real*8 :: refjd(64285), pha(64285)
real*8 :: timejd(55436)
real*8 :: phs
100 format(47x,f10.2)
open(15, file="neic56.out", status='old')
do j=1,55436
read(15,100) timejd(j)
end do
close(15)
200 format(f10.2,1x,f8.4)
open(25,file="74-17.out", status='old')
do i=1,64285
read(25,200) refjd(i), pha(i)
end do
close(25)
300 format(f6.4)
open(35,file="ejplphase.dat", status='unknown')
outerloop: do i = 1, size(timejd)
do j = 1, size(refjd)
if (timejd(i) == refjd(j)) then
phs = pha(j)/360.
write(35,300) phs
cycle outerloop
end if
end do
end do outerloop
close(35)
end program
There are some improvements that could be made to increase the efficiency depending on the specifications of your problem.
There are several threads with similar titles of mine, but I do not believe they are the same. One was very similar fortran pass allocated array to main procedure, but the answer required Fortran 2008. I am after a Fortran 90/95 solution.
Another very good, and quite similar thread is Dynamic array allocation in fortran90. However in this method while they allocate in the subroutine, they don't ever appear to deallocate, which seems odd. My method looks on the surface at least to be the same, yet when I print the array in the main program, only blank spaces are printed. When I print in the subroutine itself, the array prints to screen the correct values, and the correct number of values.
In the following a MAIN program calls a subroutine. This subroutine reads data into an allocatable array, and passes the array back to the main program. I do this by using small subroutines each designed to look for specific terms in the input file. All of these subroutines are in one module file. So there are three files: Main.f90, input_read.f90 and filename.inp.
It seems then that I do not know how to pass an array that is allocatable in program Main.f90 as well as in the called subroutine where it is actually allocated, sized, and then deallocated before being passed to program Main. This perhaps sounds confusing, so here is the code for all three programs. I apologize for the poor formatting when I pasted it. I tried to separate all the rows.
main.f90:
Program main
use input_read ! the module with the subroutines used for reading filename.inp
implicit none
REAL, Allocatable :: epsilstar(:)
INTEGER :: natoms
call Obtain_LJ_Epsilon(epsilstar, natoms)
print*, 'LJ Epsilon : ', epsilstar
END Program main
Next is the module with a subroutine (I removed all but the necessary one for space), input_read.f90:
module input_read
contains
!===============================================================
!===============================================================
Subroutine Obtain_LJ_Epsilon(epsilstar,natoms)
! Reads epsilon and sigma parameters for Lennard-Jones Force-Field and also
! counts the number of types of atoms in the system
!===============================================================
!===============================================================
INTEGER :: error,line_number,natoms_eps,i
CHARACTER(120) :: string, next_line, next_next_line,dummy_char
CHARACTER(8) :: dummy_na,dummy_eps
INTEGER,intent(out) :: natoms
LOGICAL :: Proceed
real, intent(out), allocatable :: epsilstar(:)
error = 0
line_number = 0
Proceed = .true.
open(10,file='filename.inp',status='old')
!=============================================
! Find key word LJ_Epsilon
!=============================================
DO
line_number = line_number + 1
Read(10,'(A120)',iostat=error) string
IF (error .NE. 0) THEN
print*, "Error, stopping read input due to an error reading line"
exit
END IF
IF (string(1:12) == '$ LJ_epsilon') THEN
line_number = line_number + 1
exit
ELSE IF (string(1:3) == 'END' .or. line_number > 2000) THEN
print*, "Hit end of file before reading '$ LJ_epsilon' "
Proceed = .false.
exit
ENDIF
ENDDO
!========================================================
! Key word found, now determine number of parameters
! needing to be read
!========================================================
natoms_eps = -1
dummy_eps = 'iii'
do while ((dummy_eps(1:1) .ne. '$') .and. (dummy_eps(1:1) .ne. ' '))
natoms_eps = natoms_eps + 1
read(10,*) dummy_eps
enddo !we now know the number of atoms in the system (# of parameters)
close(10)
Allocate(epsilstar(natoms_eps))
epsilstar = 0.0
!============================================================
! Number of parameters found, now read their values
!============================================================
if(Proceed) then
open(11,file='filename.inp',status='old')
do i = 1,line_number-1
read(11,*) ! note it is not recording anything for this do loop
enddo
do i = 1,natoms_eps
read(11,*) dummy_char
read(dummy_char,*) epsilstar(i) ! convert string read in to real, and store in epsilstar
enddo
close(11)
PRINT*, 'LJ_epsilon: ', epsilstar ! printing to make sure it worked
endif
deallocate(epsilstar)
END Subroutine Obtain_LJ_Epsilon
end module input_read
And finally the input file: filename.inp
# Run_Type
NVT
# Run_Name
Test_Name
# Pressure
1.0
# Temperature
298.15
# Number_Species
# LJ_epsilon
117.1
117.1
117.1
# LJ_sigma
3.251
3.251
3.251
END
And again, I can't figure out how to pass the allocated epsilstar array to the main program. I have tried passing an unallocated array to the subroutine from the main.f90, allocating it inside, passing it back, and deallocating it in the main.f90, but that did not work. I have tried it as the code currently is... the code works (i.e. is bug free) but it does not pass epsilstar from the subroutine where it correctly finds it and creates an array.
It turns out that the mistake I made was in deallocating the array in the subroutine before passing it to the main program. By NOT deallocating, the array was sent back fine. Also, I do not deallocate in the main program either.
Hermite Interpolation woes
I am trying to find the Newton Dividing Differences for the function and derivative values of a given set of x's. I'm running into serious problems with my code working for tiny examples, but failing on bigger one's. As is clearly visible, my answers are very much larger than they original function values.
Does anybody have any idea what I'm doing wrong?
program inter
implicit none
integer ::n,m
integer ::i
real(kind=8),allocatable ::xVals(:),fxVals(:),newtonDivDiff(:),dxVals(:),zxVals(:),zdxVals(:),zfxVals(:)
real(kind=8) ::Px
real(kind=8) ::x
Open(Unit=8,File="data/xVals")
Open(Unit=9,File="data/fxVals")
Open(Unit=10,File="data/dxVals")
n = 4 ! literal number of data pts
m = n*2+1
!after we get the data points allocate the space
allocate(xVals(0:n))
allocate(fxVals(0:n))
allocate(dxVals(0:n))
allocate(newtonDivDiff(0:n))
!allocate the zvalue arrays
allocate(zxVals(0:m))
allocate(zdxVals(0:m))
allocate(zfxVals(0:m))
!since the size is the same we can read in one loop
do i=0,n
Read(8,*) xVals(i)
Read(9,*) fxVals(i)
Read(10,*) dxVals(i)
end do
! contstruct the z illusion
do i=0,m,2
zxVals(i) = xVals(i/2)
zxVals(i+1) = xVals(i/2)
zdxVals(i) = dxVals(i/2)
zdxVals(i+1) = dxVals(i/2)
zfxVals(i) = fxVals(i/2)
zfxVals(i+1) = fxVals(i/2)
end do
!slightly modified business as usual
call getNewtonDivDiff(zxVals,zdxVals,zfxVals,newtonDivDiff,m)
do i=0,n
call evaluatePolynomial(m,newtonDivDiff,xVals(i),Px,zxVals)
print*, xVals(i) ,Px
end do
close(8)
close(9)
close(10)
stop
deallocate(xVals,fxVals,dxVals,newtonDivDiff,zxVals,zdxVals,zfxVals)
end program inter
subroutine getNewtonDivDiff(xVals,dxVals,fxVals,newtonDivDiff,n)
implicit none
integer ::i,k
integer, intent(in) ::n
real(kind=8), allocatable,dimension(:,:) ::table
real(kind=8),intent(in) ::xVals(0:n),dxVals(0:n),fxVals(0:n)
real(kind=8), intent(inout) ::newtonDivDiff(0:n)
allocate(table(0:n,0:n))
table = 0.0d0
do i=0,n
table(i,0) = fxVals(i)
end do
do k=1,n
do i = k,n
if( k .eq. 1 .and. mod(i,2) .eq. 1) then
table(i,k) = dxVals(i)
else
table(i,k) = (table(i,k-1) - table(i-1,k-1))/(xVals(i) - xVals(i-k))
end if
end do
end do
do i=0,n
newtonDivDiff(i) = table(i,i)
!print*, newtonDivDiff(i)
end do
deallocate(table)
end subroutine getNewtonDivDiff
subroutine evaluatePolynomial(n,newtonDivDiff,x,Px,xVals)
implicit none
integer,intent(in) ::n
real(kind=8),intent(in) ::newtonDivDiff(0:n),xVals(0:n)
real(kind=8),intent(in) ::x
real(kind=8), intent(out) ::Px
integer ::i
Px = newtonDivDiff(n)
do i=n,1,-1
Px = Px * (x- xVals(i-1)) + newtonDivDiff(i-1)
end do
end subroutine evaluatePolynomial
Values
x f(x) f'(x)
1.16, 1.2337, 2.6643
1.32, 1.6879, 2.9989
1.48, 2.1814, 3.1464
1.64, 2.6832, 3.0862
1.8, 3.1553, 2.7697
Output
1.1599999999999999 62.040113431002474
1.3200000000000001 180.40121445431600
1.4800000000000000 212.36319446149312
1.6399999999999999 228.61845650513027
1.8000000000000000 245.11610836104515
You are accessing array newtonDivDiff out of bounds.
You are first allocating it as 0:n (main program's n) then you are passing to subroutine getNewtonDivDiff as 0:n (the subroutine's n) but you pass m (m=n*2+1) to the argument n. That means you tell the subroutine that the array has bounds 0:m which is 0:9, but it has only bounds 0:4.
It is quite difficult to debug the program as it stands, I had to use valgrind. If you move your subroutines to a module and change the dummy arguments to assumed shape arrays (:,:) then the bound checking in gfortran (-fcheck=all) will catch the error.
Other notes:
kind=8 is ugly, 8 can mean different things for different compilers. If you want 64bit variables, you can use kind=real64 (real64 comes from module iso_fortran_env in Fortran 2008) or use selected_real_kind() (Fortran 90 kind parameter)
You do not have to deallocate your local arrays in the subroutines, they are deallocated automatically.
Your deallocate statement in the main program is after the stop statement, it will never be executed. I would just delete the stop, there is no reason to have it.
My problem is that I don't know how to call subroutines when I use mpi scheme in Fortran.
I have written this small code named TRY.f90 in which there is a subroutine named CONCENTRATION.f90. How should I change CONCENTRATION.f90 in order to make the code works?
PROGRAM TRY
USE MPI
integer status(mpi_status_size)
INTEGER I, J, K, II, IERR, MY_ID, NUM_PROCS, PSP
INTEGER , PARAMETER :: GRIDX =64, GRIDY=64
REAL , DIMENSION(gridx,gridy) :: PSI
PSI=0
PRINT*, 'VARIABLE'
CALL MPI_INIT(IERR)
CALL MPI_COMM_RANK(MPI_COMM_WORLD,MY_ID,IERR)
CALL MPI_COMM_SIZE(MPI_COMM_WORLD,NUM_PROCS,IERR)
CALL CONCENTRATION(GRIDX, GRIDY, NUM_PROCS, MY_ID , PSI)
IF (MY_ID .NE. 0) THEN
CALL mpi_send( PSI(1+MY_ID*GRIDX/NUM_PROCS:(MY_ID+1)*GRIDX/NUM_PROCS:1,1:GRIDY:1),&
(GRIDX/NUM_PROCS)*GRIDY,mpi_real, 0,10,mpi_comm_world,ierr)
END IF
IF (MY_ID .EQ. 0) THEN
DO II=1,NUM_PROCS-1
CALL mpi_recv(PSI(1+II*GRIDX/NUM_PROCS:(II+1)*GRIDX/NUM_PROCS:1,1:GRIDY:1),&
(GRIDX/NUM_PROCS)*GRIDY,mpi_real, &
II,10,mpi_comm_world,status,ierr)
END DO
END IF
CALL MPI_FINALIZE(IERR)
END PROGRAM TRY
I am using a subroutine named CONCENTRATION.f90 which is:
SUBROUTINE CONCENTRATION(GRIDX, GRIDY, NUM_PROCS, MY_ID , PSI)
implicit none
INTEGER*8, INTENT(IN) :: GRIDX, GRIDY
INTEGER , INTENT(IN) :: NUM_PROCS, MY_ID
REAL*8 , DIMENSION(GRIDX,GRIDY), INTENT(OUT) :: PSI
INTEGER*8 I, J
DO I=1+MY_ID*GRIDX/NUM_PROCS, (MY_ID+1)*GRIDX/NUM_PROCS
DO J=1,GRIDY
PSI(I,J)=2.0
END DO
END DO
END SUBROUTINE CONCENTRATION
The code currently gives me error since I think I should have made some changes on the subroutine CONCENTRATION.f90. Or I should also change the way I call the subroutine.
Could you please tell me what are those changes? Thanks for your helps in advance
Your program segfaults because of type mismatch. In the main program you have declared PSI as an array of REAL:
REAL , DIMENSION(gridx,gridy) :: PSI
while in the CONCENTRATION subroutine you use another type of REAL*8:
REAL*8 , DIMENSION(GRIDX,GRIDY), INTENT(OUT) :: PSI
By default REAL is 4 bytes long while REAL*8 (or DOUBLE PRECISION or REAL(KIND=8)) is 8 bytes long. So you are giving to CONCENTRATION an array that is 2 times smaller than what it believes to be and all ranks from NUM_PROCS/2 onwards write past the end of the PSI array and thus cause segfaults. If you run with one process only, then even rank 0 will segfault.
You should also read about MPI collective operations. MPI_GATHER and MPI_GATHERV do exactly what you are trying to achieve whith multiple sends and receives here.
The only change would be to declare concentration as reentrant. That could be the default for Fortran 90. (The bulk of my experience is F77, and reentrant is not the default there.)