[petsc-users] unexpected ordering when VecSetValues set multiples values
Matteo Parsani
parsani.matteo at gmail.com
Mon Jun 10 10:53:15 CDT 2013
Thanks Barry and Satish.
As you said I have a wrong flag in my makefile.
Best Regards
On Fri, Jun 7, 2013 at 4:14 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> On Fri, 7 Jun 2013, Barry Smith wrote:
>
> >
> > How large is your integer on the Fortran side and the C side?
> >
> > Normally a PetscInt is a C int and a Fortran integer*4 which are
> each 4 bytes long.
> >
> > If PETSc is configured with --with-64-bit-indices then PetscInt is a
> C long long int and Fortran integer*8 both 8 bytes long.
> >
> > It looks like you are using 8 byte Fortran integers but have not
> compiled PETSc with --with-64-bit-indices Possibly you are using come
> fortran compile time flag that "promotes" float to double and integer*4 to
> integer*8 in Fortran.
> >
> > 1) we recommend never using any fortran compiler flag that promotes
> types automatically.
>
> If Petsc datatypes are used in fortran code [i.e declare variable as
> PetscInt - and not integer for functions that expect PetscInt] - then
> the code [from PETSc part] would be resiliant to -i8 type options.
>
> Satish
>
> >
> > 2) likely you just want to use 4 byte integers in fortran. If you want
> to use 8 bytes then configure PETSc with --with-64-bit-indices
> >
> > Barry
> >
> >
> >
> >
> > On Jun 7, 2013, at 2:57 PM, Matteo Parsani <parsani.matteo at gmail.com>
> wrote:
> >
> > > Hello Barry,
> > > I have tried to pass to VectSetValues two values
> > >
> > > call
> VecSetValues(x_vec_in,2,index_list(1:2),x_vec_local(1:2),INSERT_VALUES,ierr_local)
> > >
> > > By looking at the values of index_list and x_vec_local with gdb I see
> the correct numbers:
> > >
> > > (gdb) print x_vec_local(1)
> > > $1 = 0.9394877605834675
> > > (gdb) print x_vec_local(2)
> > > $2 = 0.55294328167143081
> > >
> > > (gdb) print index_list(1)
> > > $3 = 0
> > > (gdb) print index_list(2)
> > > $4 = 1
> > >
> > > Now, when I ask gdb to print the values of ni, ix and y in
> > >
> > > PetscErrorCode VecSetValues_Seq(Vec xin,PetscInt ni,const PetscInt
> ix[],const PetscScalar y[],InsertMode m)
> > >
> > >
> > > I get
> > >
> > > (gdb) print ni
> > > $5 = 2
> > >
> > > (gdb) print ix[0]
> > > $6 = 0
> > > (gdb) print ix[1]
> > > $7 = 0
> > >
> > >
> > > print y[0]
> > > $13 = 0.9394877605834675
> > > (gdb) print y[1]
> > > $14 = 0.55294328167143081
> > >
> > >
> > > The values of y match with the values I am passing in, i.e.
> x_vec_local. However the index ix is wrong because the first two components
> of it are zero. Thus, when i = 1 in the VecSetValues_Seq for loop, the
> first element that was placed correctly is replaced by the second element.
> This is also waht I see if I use
> > >
> > > call VecView(x_vec_in,PETSC_VIEWER_STDOUT_WORLD,ierr_local)
> > >
> > > Now if I keep printing ix in gdb I see the following pattern:
> > >
> > > (gdb) print ix[0]
> > > $18 = 0
> > > (gdb) print ix[1]
> > > $19 = 0
> > > (gdb) print ix[2]
> > > $20 = 1
> > > (gdb) print ix[3]
> > > $21 = 0
> > > (gdb) print ix[4]
> > > $22 = 2
> > > (gdb) print ix[5]
> > > $23 = 0
> > > (gdb) print ix[6]
> > > $24 = 3
> > >
> > >
> > > which I think is strange since I ix should be a vector of length 2
> because I am calling VecSetValues as
> > >
> > >
> > > call
> VecSetValues(x_vec_in,2,index_list(1:2),x_vec_local(1:2),INSERT_VALUES,ierr_local)
> > >
> > > Am I doing something wrong?
> > >
> > > Thank you in advance.
> > >
> > >
> > >
> > >
> > >
> > > On Fri, Jun 7, 2013 at 3:03 PM, Matteo Parsani <
> parsani.matteo at gmail.com> wrote:
> > > Yes, they are correct. When asked, the debugger prints the right
> values for bot the vector of the index and the vector of the values.
> > >
> > > Sorry, how can I set a break point in VecSetValues_Seq() and
> VecSetValues_MPI()?
> > > If I type
> > >
> > > break VecSetValues_Seq()
> > >
> > > or
> > >
> > > break VecSetValues_MPI()
> > >
> > > or
> > >
> > >
> /home0/pmatteo/research/lib_src/petsc/src/vec/vec/impls/seq/bvec2.c:1050
> > >
> > > I get
> > >
> > > Function "vecsetvalues_seq" not defined.
> > >
> > > or
> > >
> > > Function "vecsetvalues_mpi" not defined.
> > >
> > >
> > > Thanks
> > >
> > >
> > >
> > > On Fri, Jun 7, 2013 at 2:32 PM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> > >
> > > Are, seemingly the correct values getting into the vecsetvalues_
> call?
> > >
> > > Put a break point also in VecSetValues_Seq() and VecSetValues_MPI()
> when it gets into either of those routines you can do step in the debugger
> and watch it take the values passed in and attempt to put them in the
> appropriate places in the vector's array.
> > >
> > > Barry
> > >
> > > On Jun 7, 2013, at 1:20 PM, Matteo Parsani <parsani.matteo at gmail.com>
> wrote:
> > >
> > > > 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 <bsmith at mcs.anl.gov>
> wrote:
> > > >
> > > > On Apr 30, 2013, at 7:21 AM, Matteo Parsani <
> parsani.matteo at gmail.com> 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 <bsmith at mcs.anl.gov>
> 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 <
> parsani.matteo at gmail.com> 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 <bsmith at mcs.anl.gov>
> wrote:
> > > > > >
> > > > > > On Apr 26, 2013, at 10:20 AM, Matteo Parsani <
> parsani.matteo at gmail.com> 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
> > >
> > >
> > >
> > >
> > > --
> > > Matteo
> > >
> > >
> > >
> > > --
> > > Matteo
> >
> >
>
>
--
Matteo
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