Hi Barry, Thanks for the piece of code. I will try to implement it. My problem is 1D, so should be ok. If I have some pb I'll let you know.
If this work, do you plan to include it in next version of PETSc ? Christophe On Mon, Sep 30, 2013 at 2:04 PM, Barry Smith <[email protected]> wrote: > > On Sep 30, 2013, at 3:01 AM, Christophe Ortiz <[email protected]> > wrote: > > > Hi Barry, > > > > It works ! Great job ! Here is the output: > > > > > > 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 ? > > What dimension do you need? For one dimension, which I think you > mentioned before it is almost identical to what I sent you > > PETSC_EXTERN void PETSC_STDCALL dmdavecgetarrayf901_(DM *da,Vec > *v,F90Array1d *a,PetscErrorCode *ierr PETSC_F90_2PTR_PROTO(ptrd)) > { > PetscInt xs,ys,zs,xm,ym,zm,gxs,gys,gzs,gxm,gym,gzm,N,dim,dof; > PetscScalar *aa; > > *ierr = DMDAGetCorners(*da,&xs,&ys,&zs,&xm,&ym,&zm);if (*ierr) return; > *ierr = DMDAGetGhostCorners(*da,&gxs,&gys,&gzs,&gxm,&gym,&gzm);if > (*ierr) return; > *ierr = DMDAGetInfo(*da,&dim,0,0,0,0,0,0,&dof,0,0,0,0,0);if (*ierr) > return; > > /* Handle case where user passes in global vector as opposed to local */ > *ierr = VecGetLocalSize(*v,&N);if (*ierr) return; > if (N == xm*ym*zm*dof) { > gxm = xm; > gym = ym; > gzm = zm; > gxs = xs; > gys = ys; > gzs = zs; > } else if (N != gxm*gym*gzm*dof) { > *ierr = PETSC_ERR_ARG_INCOMP; > } > *ierr = VecGetArray(*v,&aa);if (*ierr) return; > *ierr = F90Array1dCreate(aa,PETSC_SCALAR,gxs,gxm,a > PETSC_F90_2PTR_PARAM(ptrd));if (*ierr) return; > } > > > except it (1) handles both the local vector or global vector version (the > if above) and (2) handles that start index at gxs instead of 0. All you > should have to do is rename the beast above, provide an FORTRAN 90 > interface for it, have it call the specialized version of F90Array1dCreate > I already provided. Two and three dimensions are a bit more involved > since you need to copy over and modify more functions but I don't think > there are any tricky things. > > > Barry > > > > > > Best regards, > > Christophe > > > > > > 2013/9/29 Barry Smith <[email protected]> > > > > > > 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 < > [email protected]> 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 <[email protected]> > > > > > > On Sep 27, 2013, at 3:06 PM, Christophe Ortiz < > [email protected]> wrote: > > > > > > > The files were not attached. Could you please send them again ? > > > > > > > > Thanks. > > > > Christophe > > > > > > > > El 27/09/2013 21:28, "Barry Smith" <[email protected]> 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 < > [email protected]> 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 <[email protected]> > 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 < > [email protected]> 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 <[email protected]> > 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 < > [email protected]> 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 < > [email protected]> 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 < > [email protected]> 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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
