[petsc-users] Back to struct in Fortran to represent field with dof > 1
Christophe Ortiz
christophe.ortiz at ciemat.es
Sun Sep 29 06:16:44 CDT 2013
Hi Barry,
I just looked at exf1.F. It seems you sent me a wrong file. It does not
correspond to ex1f90. There is no vecgetarraymystruct in the file you sent
me. Could you please send me the correct version of ex1f90 so I can test it
? Many thanks in advance.
Christophe
CIEMAT
Laboratorio Nacional de Fusión por Confinamiento Magnético
Unidad de Materiales
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2013/9/27 Barry Smith <bsmith at mcs.anl.gov>
>
> On Sep 27, 2013, at 3:06 PM, Christophe Ortiz <christophe.ortiz at ciemat.es>
> wrote:
>
> > The files were not attached. Could you please send them again ?
> >
> > Thanks.
> > Christophe
> >
> > El 27/09/2013 21:28, "Barry Smith" <bsmith at mcs.anl.gov> escribió:
> >
> > Please find attached a new version of the code. ex1.c and ex1f90.F
> please run it as is and send me all the output.
> >
> > It works correctly with gfortran and the intel 12.x ifort compiler, I
> believe it should now work for all fortran compilers. If it does not work
> as expected please send me the name and version of your fortran compiler.
> >
> > Barry
> >
> > On Sep 27, 2013, at 8:22 AM, Christophe Ortiz <
> christophe.ortiz at ciemat.es> wrote:
> >
> > > There was a misunderstanding. There are n entries in total in the
> vector. I thought it was a vector of n points, with 3 components associated
> to each point, ie 3*n entries. This is clear now.
> > >
> > > I've tested your example and I checked the values assigned to the
> components with your piece of code:
> > >
> > > call VecGetArrayMyStruct(x,xarray,ierr)
> > > do i=1,10
> > > xarray(i)%a = i
> > > xarray(i)%b = 100*i
> > > xarray(i)%c = 10000*i
> > > enddo
> > >
> > > call VecRestoreArrayMyStruct(x,xarray,ierr)
> > >
> > >
> > > I did it with:
> > >
> > > call VecGetArrayMyStruct(x,xarray,ierr)
> > > do i = 1 , 10
> > > write(*,*) xarray(i)%a,xarray(i)%b,xarray(i)%c
> > > end do
> > >
> > > call VecRestoreArrayMyStruct(x,xarray,ierr)
> > >
> > > I obtained the following:
> > >
> > > 1.00000000000000 2.00000000000000 3.00000000000000
> > > 2.00000000000000 3.00000000000000 4.00000000000000
> > > 3.00000000000000 4.00000000000000 5.00000000000000
> > > 4.00000000000000 5.00000000000000 6.00000000000000
> > > 5.00000000000000 6.00000000000000 7.00000000000000
> > > 6.00000000000000 7.00000000000000 8.00000000000000
> > > 7.00000000000000 8.00000000000000 9.00000000000000
> > > 8.00000000000000 9.00000000000000 10.0000000000000
> > > 9.00000000000000 10.0000000000000 1000.00000000000
> > > 10.0000000000000 1000.00000000000 100000.000000000
> > >
> > > First column if ok (1st component), but the other two columns show
> wrong numbers. For component 2 and 3, only the very last value is ok. It
> seems values from component b are copied from a, and those from component c
> from b, with an offset.
> > >
> > > What do you think ?
> > >
> > > Christophe
> > >
> > >
> > > On Fri, Sep 27, 2013 at 2:47 PM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> > >
> > > Indices start in fortran arrays from 1 by default so don't even try
> zero
> > >
> > > I've attached a new version that has three components,
> > > 30 TOTAL vector entries and 10 for each component. Please run it and
> send the results back.
> > >
> > > Barry
> > >
> > > On Sep 27, 2013, at 5:40 AM, Christophe Ortiz <
> christophe.ortiz at ciemat.es> wrote:
> > >
> > > > Hi Barry,
> > > >
> > > > I made some tests with your code that allows to use struct in
> Fortran90. It compiles and does not complain with the struct with 2
> components but...it exhibits some strange behaviour. Here are the
> behaviours I observed. To make it simple, I used n=10.
> > > >
> > > > - After using call VecSet(x,one,ierr), I checked the values of each
> component of the vector using
> > > >
> > > > call VecGetArrayMyStruct(x,xarray,ierr)
> > > > do i = 0 , n
> > > > write(*,*) i , xarray(i)%a, xarray(i)%b
> > > > end do
> > > > call VecRestoreArrayMyStruct(x,xarray,ierr)
> > > >
> > > > I checked the values from i= 0 to n since I was not sure what was
> the convention (0- or 1-based). I obtained:
> > > >
> > > > 0 0.000000000000000E+000 1.00000000000000
> > > > 1 1.00000000000000 1.00000000000000
> > > > 2 1.00000000000000 1.00000000000000
> > > > 3 1.00000000000000 1.00000000000000
> > > > 4 1.00000000000000 1.00000000000000
> > > > 5 1.00000000000000 1.00000000000000
> > > > 6 1.00000000000000 1.00000000000000
> > > > 7 1.00000000000000 1.00000000000000
> > > > 8 1.00000000000000 1.00000000000000
> > > > 9 1.00000000000000 1.00000000000000
> > > > 10 1.00000000000000 1.996650376645798E-314
> > > >
> > > >
> > > > As you can see, for component a, there is a 0 for i=0, then the
> values are correct. For component b, correct values go from i=1 to 9.There
> is garbage in second component for i=10 . I checked that if you define a
> third component c, its values go from i=-1 to n-2. It's like if values of
> second component started at the end of first component, and same thing for
> third component.
> > > >
> > > > Then, instead of using VecSet(), I tried to assign values directly
> to each component of the vector with
> > > >
> > > > call VecGetArrayMyStruct(x,xarray,ierr)
> > > > do i = 0 , n-1
> > > > xarray(i)%a = 2.0
> > > > xarray(i)%b = 3.0
> > > > end do
> > > > call VecRestoreArrayMyStruct(x,xarray,ierr)
> > > >
> > > > Here I checked that indices actually start at 0 and not at 1. With a
> loop from i=1 to n I got a Memory corruption message.
> > > >
> > > > and I checked that the values are correctly assigned with
> > > >
> > > > call VecGetArrayMyStruct(x,xarray,ierr)
> > > > do i = 0 , n-1
> > > > write(*,*) i, xarray(i)%a, xarray(i)%b
> > > > end do
> > > > call VecRestoreArrayMyStruct(x,xarray,ierr)
> > > >
> > > >
> > > >
> > > > Then, I obtained:
> > > >
> > > > 0 2.00000000000000 2.00000000000000
> > > > 1 2.00000000000000 2.00000000000000
> > > > 2 2.00000000000000 2.00000000000000
> > > > 3 2.00000000000000 2.00000000000000
> > > > 4 2.00000000000000 2.00000000000000
> > > > 5 2.00000000000000 2.00000000000000
> > > > 6 2.00000000000000 2.00000000000000
> > > > 7 2.00000000000000 2.00000000000000
> > > > 8 2.00000000000000 2.00000000000000
> > > > 9 2.00000000000000 3.00000000000000
> > > >
> > > >
> > > > Here the problem seems more severe. Values are not correctly
> assigned to the second component. There should be 3.0 in the second column.
> It seems values of the first component are copied to the second one. Only
> for i=10 the value of xarray(i)%b is correct (3.0).
> > > >
> > > > Any idea where it could come from ?
> > > > I guess it needs some fixes here and there but I think your idea is
> good and that it could work.
> > > >
> > > > Christophe
> > > >
> > > >
> > > >
> > > > On Thu, Sep 26, 2013 at 5:45 PM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> > > >
> > > > I just put it with the Fortran source code and compile it with
> the rest of the application code; here is the makefile I used
> > > >
> > > >
> > > >
> > > >
> > > > On Sep 26, 2013, at 10:14 AM, Christophe Ortiz <
> christophe.ortiz at ciemat.es> wrote:
> > > >
> > > > > By the way, what should I do with the small .c code ? Where should
> I put it ?
> > > > >
> > > > > Christophe
> > > > >
> > > > >
> > > > >
> > > > > On Thu, Sep 26, 2013 at 4:09 PM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> > > > >
> > > > > Christophe,
> > > > >
> > > > > Despite my LinkIn Endorsement for expertise in Fortran :-) I
> cannot pretend to be an expert in FortranXX but I have cooked up an example
> demonstrating accessing the Vec entries as if they are in an array of
> derived types. I've attached the example code; there needs to be a small C
> stub that defines the functions for your specific derived type name.
> > > > > Note that it will only work I think if your N is a compile time
> constant.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > It worked with
> > > > > ~/Downloads$ gfortran --version
> > > > > GNU Fortran (GCC) 4.8.1 20130404 (prerelease)
> > > > >
> > > > >
> > > > > I do not understand exactly why it works since it uses
> F90Array1dCreate(fa,PETSC_SCALAR,1,len,ptr PETSC_F90_2PTR_PARAM(ptrd));
> which has a single PETSC_SCALAR as a building block but … I hope it works
> for you. If it doesn't, let us know the compiler you are using and we may
> be able to get it working for that compiler.
> > > > >
> > > > > Barry
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Sep 26, 2013, at 4:41 AM, Christophe Ortiz <
> christophe.ortiz at ciemat.es> wrote:
> > > > >
> > > > > > Hi all,
> > > > > >
> > > > > > Me again !
> > > > > >
> > > > > > I have read in previous posts that it is hard in Fortran to
> declare something similar to a typedef struct in C to manage a
> multicomponent problem.
> > > > > >
> > > > > > Is it still the case ? Has the problem been solved ?
> > > > > >
> > > > > > I am asking because my plan is to implement a multicomponent
> problem (in 1D), with many components that will be organized in arrays of
> two dimensions. In C I could define
> > > > > >
> > > > > > typedef struct{
> > > > > > PetscScalar U;
> > > > > > PetscScalar V;
> > > > > > PetscScalar A[N][N];
> > > > > > } Field;
> > > > > >
> > > > > > and then I could calculate the residual function with
> > > > > >
> > > > > > F[i].U = ...
> > > > > > F[i].V = ...
> > > > > > F[i].A[k][n] = ...
> > > > > >
> > > > > > which is quite convenient.
> > > > > >
> > > > > > If in Fortran it is not possible to use a struct as in C, I am
> afraid I'll have to deal with
> > > > > >
> > > > > > F(jdof,i) = ...
> > > > > >
> > > > > > where I will have only jdof to address U, V and A[ ][ ], which
> can be difficult and not very convenient I guess. Before I move all my code
> to C, does anyone have an alternative idea to manage this
> multi(many)component problem in Fortran ?
> > > > > >
> > > > > > Many thanks in advance for your help and suggestion !
> > > > > >
> > > > > > Christophe
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
> >
>
>
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