Hello Barry, I have tried to follow the debugger but I got lost. I have run my code in this way:
./NSE -start_in_debugger noxterm then after getting some output I get gdb() Then I type *break vecsetvalues_ * and a break point is generated Breakpoint 1 at 0x2ae97eda5827: file /scratch/home0/pmatteo/research/lib_src/petsc/src/vec/vec/interface/ftn-auto/rvectorf.c, line 239. I keep typing *n* and it goes on. It shows me every time vectsetvalues is called but it never goes inside vectsetvalues. I have tested the VecSetValues with just two elements and it does not work. It sets correctly the values both in serial and in parallel if I set one value at the time. Thanks ** On Tue, Apr 30, 2013 at 8:35 AM, Barry Smith <[email protected]> wrote: > > On Apr 30, 2013, at 7:21 AM, Matteo Parsani <[email protected]> > wrote: > > > Hello Barry, > > it does not work also if m is not so large. > > Then you need to run in the debugger. You can use the command line > options > > -start_in_debugger noxterm > > in the debugger put a break point in vecsetvalues_ (yes lower case > followed by an underscore) then when it > gets to that point print the size of the array and the values in the > integer and double array to see if they match, then step into the > VecSetValues() function that is called by vecsetvalues_() and look at the > array values ago, continue to step along and it will go into > VecSetValues_Seq() and start actually putting the values into the Vec array. > > Barry > > > > > Thanks again. > > > > > > > > > > > > > > On Fri, Apr 26, 2013 at 3:23 PM, Barry Smith <[email protected]> wrote: > > > > Shouldn't matter that it is called from Fortran we do it all the time. > > > > Does it work if the final m is not very large? > > > > You may need to run in the debugger and follow the values through the > code to see why they don't get to where they belong. > > > > > > Barry > > > > Could also be a buggy fortran compiler. > > > > > > On Apr 26, 2013, at 2:06 PM, Matteo Parsani <[email protected]> > wrote: > > > > > Hello Barry, > > > sorry I modified few things just before to write the mail. > > > The correct loop with the correct name of the variables is the > following > > > > > > ! Number of DOFs owned by this process > > > len_local = (elem_high-elem_low+1)*nodesperelem*nequations > > > > > > ! Allocate memory for x_vec_local and index_list > > > allocate(x_vec_local(len_local)) > > > allocate(index_list(len_local)) > > > > > > > > > m = 1 > > > ! Loop over all elements > > > do ielem = elem_low, elem_high > > > ! Loop over all nodes in the element > > > do inode = 1, nodesperelem > > > !Loop over all equations > > > do ieq = 1, nequations > > > ! Add element to x_vec_local > > > x_vec_local(m) = ug(ieq,inode,ielem) > > > ! Add element to index list > > > index_list(m) = > (elem_low-1)*nodesperelem*nequations+m-1 > > > ! Update m index > > > m = m+1 > > > end do > > > end do > > > end do > > > > > > ! HERE I HAVE PRINTED x_vec_local, ug and index_list > > > > > > ! Set values in the portion of the vector owned by the process > > > call > VecSetValues(x_vec_in,m-1,index_list,x_vec_local,INSERT_VALUES,& > > > & ierr_local) > > > > > > ! Assemble initial guess > > > call VecAssemblyBegin(x_vec_in,ierr_local) > > > call VecAssemblyEnd(x_vec_in,ierr_local) > > > > > > > > > > > > I have printed the values and the indices I want to pass to > VecSetValues() and they are correct. > > > > > > I also printed the values after VecSetValues() has been called and > they are wrong. > > > > > > The attachment shows that. > > > > > > > > > Could it be a problem of VecSetValues() + F90 when more than 1 > elements is set? > > > > > > I order to debug my the code I am running just with 1 processor. Thus > the process owns all the DOFs. > > > > > > Thank you. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Fri, Apr 26, 2013 at 2:39 PM, Barry Smith <[email protected]> > wrote: > > > > > > On Apr 26, 2013, at 10:20 AM, Matteo Parsani <[email protected]> > wrote: > > > > > > > Hello, > > > > I have some problem when I try to set multiple values to a PETSc > vector that I will use later on with SNES. I am using Fortran 90. > > > > Here the problem and two fixes that however are not so good for > performances reasons. The code is very simple. > > > > > > > > Standard approach that does not work correctly: (I am probably doing > something wrong) > > > > > > > > m = 1 > > > > ! Loop over all elements > > > > do ielem = elem_low, elem_high > > > > ! Loop over all nodes in the element > > > > do inode = 1, nodesperelem > > > > !Loop over all equations > > > > do ieq = 1, nequations > > > > ! Add element to x_vec_local > > > > x_vec_local(m) = ug(ieq,inode,ielem) > > > > ! Add element to index list > > > > ind(m) = (elem_low-1)*nodesperelem*nequations+m-1 > > > > ! Update m index > > > > m = m+1 > > > > end do > > > > end do > > > > end do > > > > > > > > ! Set values in the portion of the vector owned by the process > > > > call > VecSetValues(x_vec_in,len_local,index_list,x_vec_local,INSERT_VALUES,& > > > > > > What is len_local and index_list? They do not appear in the loop > above. Shouldn't you be passing m-1 for the length and ind for the indices? > > > > > > I would first print out the all the values in your input to > VecSetValues() and make sure they are correct. > > > > > > Barry > > > > > > > & ierr_local) > > > > > > > > ! Assemble initial guess > > > > call VecAssemblyBegin(x_vec_in,ierr_local) > > > > call VecAssemblyEnd(x_vec_in,ierr_local) > > > > > > > > Then I print my expected values and the values contained in the > PETSc vector to a file. See attachment. I am running in serial for the > moment BUT strangely if you look at the file I have attached the first 79 > DOFs values have a wrong ordering and the remaining 80 are zero. > > > > > > > > > > > > 1st approach: set just one value at the time inside the loop. > > > > m = 1 > > > > ! Loop over all elements > > > > do ielem = elem_low, elem_high > > > > ! Loop over all nodes in the element > > > > do inode = 1, nodesperelem > > > > !Loop over all equations > > > > do ieq = 1, nequations > > > > ! Add element to x_vec_local > > > > value = ug(ieq,inode,ielem) > > > > ! Add element to index list > > > > ind = (elem_low-1)*nodesperelem*nequations+m-1 > > > > call > VecSetValues(x_vec_in,1,ind,value,INSERT_VALUES,& > > > > & ierr_local) > > > > ! Update m index > > > > m = m+1 > > > > end do > > > > end do > > > > end do > > > > > > > > > > > > This works fine. As you can see I am using the same expression used > in the previous loop to compute the index of the element that I have to add > in the x_vec_in, i.e. > > > > ind = (elem_low-1)*nodesperelem*nequations+m-1 > > > > > > > > Thus I cannot see which is the problem. > > > > > > > > 2nd approach: get the pointer to the local part of the global vector > and use it to set the values in the global vector > > > > > > > > m = 1 > > > > ! Loop over all elements > > > > do ielem = elem_low, elem_high > > > > ! Loop over all nodes in the element > > > > do inode = 1, nodesperelem > > > > !Loop over all equations > > > > do ieq = 1, nequations > > > > ! Add element to x_vec_local > > > > tmp(m) = ug(ieq,inode,ielem) > > > > ! Update m index > > > > m = m+1 > > > > end do > > > > end do > > > > end do > > > > > > > > > > > > This works fine too. > > > > > > > > > > > > Jut to be complete. I use the following two approaches to view the > vector: > > > > > > > > call VecView(x_vec_in,PETSC_VIEWER_STDOUT_WORLD,ierr_local) > > > > > > > > > > > > and > > > > > > > > call VecGetArrayF90(x_vec_in,tmp,ierr_local) > > > > > > > > > > > > m = 1 > > > > ! Loop over all elements > > > > do ielem = elem_low, elem_high > > > > ! Loop over all nodes in the element > > > > do inode = 1, nodesperelem > > > > !Loop over all equations > > > > do ieq = 1, nequations > > > > write(*,*) m,index_list(m),x_vec_local(m),tmp(m) > > > > ! Update m index > > > > m = m+1 > > > > end do > > > > end do > > > > end do > > > > > > > > > > > > Thank you. > > > > > > > > > > > > -- > > > > Matteo > > > > <values.txt> > > > > > > > > > > > > > > > -- > > > Matteo > > > <comparison.txt> > > > > > > > > > > -- > > Matteo > > -- Matteo
