[petsc-users] Back to struct in Fortran to represent field with dof > 1
Christophe Ortiz
christophe.ortiz at ciemat.es
Mon Sep 30 03:01:20 CDT 2013
Hi Barry,
It works ! Great job ! Here is the output:
Vector Object: 1 MPI processes
type: seq
1
100
10000
2
200
20000
3
300
30000
4
400
40000
5
500
50000
6
600
60000
7
700
70000
8
800
80000
9
900
90000
10
1000
100000
1.00000000000000 100.000000000000 10000.0000000000
2.00000000000000 200.000000000000 20000.0000000000
3.00000000000000 300.000000000000 30000.0000000000
4.00000000000000 400.000000000000 40000.0000000000
5.00000000000000 500.000000000000 50000.0000000000
6.00000000000000 600.000000000000 60000.0000000000
7.00000000000000 700.000000000000 70000.0000000000
8.00000000000000 800.000000000000 80000.0000000000
9.00000000000000 900.000000000000 90000.0000000000
10.0000000000000 1000.00000000000 100000.000000000
Components have the right values.
Do you think it can be adapted to work with DMDAVecGetArrayF90(da,...) /
DMDAVecRestoreArrayF90(da,...) in order to work with distributed arrays ?
Best regards,
Christophe
2013/9/29 Barry Smith <bsmith at mcs.anl.gov>
>
>
> Sorry, that is what I get for having a ex1.F and ex1F90.F in the same
> directory.
>
> Barry
>
> On Sep 29, 2013, at 6:16 AM, Christophe Ortiz <christophe.ortiz at ciemat.es>
> wrote:
>
> > 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
> > Edificio 2 - Planta 0 - Despacho 28m
> > Avenida Complutense 40,
> > 28040 Madrid, Spain
> > Tel: +34 91496 2582
> > Fax: +34 91346 6442
> >
> > --
> > Q
> > Por favor, piense en el medio ambiente antes de imprimir este mensaje.
> > Please consider the environment before printing this email.
> >
> >
> > 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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