> On Oct 27, 2015, at 9:42 PM, Sang pham van wrote:
>
> Hi Barry,
>
> In the original MatMPIAIJSetPreallocation(), PETSc determines column index
> when preallocating the matrix: cols[cnt++] = l + nc*(slot + ii + gnx*jj +
> gnx*gny*kk); If I understand correctly, while PETSc allocates the mat
Hi Barry,
In the original MatMPIAIJSetPreallocation(), PETSc determines column index
when preallocating the matrix: cols[cnt++] = l + nc*(slot + ii + gnx*jj +
gnx*gny*kk); If I understand correctly, while PETSc allocates the matrix
the value of cnt is important, entries value of the cols[] array i
> On Oct 27, 2015, at 8:55 PM, Sang pham van wrote:
>
> Hi Matt,
>
> Can you please answer my second question about the way PESCs understand the
> column indies? :
>
> One more question I have is that, when preallocating for a node, as you can
> see in my below code (based on original PETSc
Hi Matt,
Can you please answer my second question about the way PESCs understand the
column indies? :
One more question I have is that, when preallocating for a node, as you can
see in my below code (based on original PETSc code), since I have 3
equations, I preallocated 3 rows (in rows[l] array)
On Tue, Oct 27, 2015 at 8:18 PM, Sang pham van wrote:
> Hi Barry,
>
> I made my function for preallocating the DM matrix. I am using immersed
> boundary method to solve a problem of solid mechanics (3D, linear
> elasticity).
> At every solid nodes, I have 3 unknowns for displacement in 3 directio
I did a quick test:
1) ilu with any shift type does not converge
2) gmres/4 bjacobi/ilu + shift_type nonzero does not converge
3) mpiexec -n 4 ./ex10 -f0 $D/mat.bin -rhs 0 -ksp_monitor -sub_pc_type lu
-sub_pc_factor_shift_type nonzero
...
0 KSP Residual norm 3.284826093129e+03
1 KSP Residual norm
Denis,
I use Homebrew to manage petsc and all related dependencies on OSX which
uses .dylib for shared libs instead of .so. However, I have not had any
issues linking against them just the usual way by passing -L/path/to/lib
-lwhatever (you need to pass -Wl,-rpath,/path/to/lib as well if lib is no
> On Oct 27, 2015, at 12:40 PM, Hong wrote:
>
> Here is the reason why it does not converge:
> ./ex10 -f0 $D/mat.bin -rhs 0 -ksp_monitor_true_residual -ksp_view
> -ksp_converged_reason
> Linear solve did not converge due to DIVERGED_NANORINF iterations 0
This means it found a zero pivot eit
Here is the reason why it does not converge:
./ex10 -f0 $D/mat.bin -rhs 0 -ksp_monitor_true_residual -ksp_view
-ksp_converged_reason
Linear solve did not converge due to DIVERGED_NANORINF iterations 0
KSP Object: 1 MPI processes
type: gmres
GMRES: restart=30, using Classical (unmodified) Gra
On Tue, Oct 27, 2015 at 12:36 PM, Hong wrote:
> Matt:
>
>> On Tue, Oct 27, 2015 at 11:13 AM, Hong wrote:
>>
>>> Gary :
>>> I tested your mat.bin using
>>> petsc/src/ksp/ksp/examples/tutorials/ex10.c
>>> ./ex10 -f0 $D/mat.bin -rhs 0 -ksp_monitor_true_residual -ksp_view
>>> ...
>>> Mat Object:
Matt:
> On Tue, Oct 27, 2015 at 11:13 AM, Hong wrote:
>
>> Gary :
>> I tested your mat.bin using
>> petsc/src/ksp/ksp/examples/tutorials/ex10.c
>> ./ex10 -f0 $D/mat.bin -rhs 0 -ksp_monitor_true_residual -ksp_view
>> ...
>> Mat Object: 1 MPI processes
>> type: seqaij
>> rows=588, cols=
On Fri, Oct 23, 2015 at 2:21 PM, Marcelo Xavier Guterres <
m.guter...@gmail.com> wrote:
> Dear friends,
>
> I need to read a matrix from a text file (txt).
>
> This matrix has a high dimension (2000 X 2000) .
>
> Example: date.txt - provision in the text file:
>
> 1 2 3 5
> 5 5 7 8
> 5 6 8 9
>
>
>
On Tue, Oct 27, 2015 at 11:13 AM, Hong wrote:
> Gary :
> I tested your mat.bin using
> petsc/src/ksp/ksp/examples/tutorials/ex10.c
> ./ex10 -f0 $D/mat.bin -rhs 0 -ksp_monitor_true_residual -ksp_view
> ...
> Mat Object: 1 MPI processes
> type: seqaij
> rows=588, cols=588
> total: n
Dear developers,
It seems that the compiled PETSc library does not have a soname
(-Wl,-install_name=xyz.dylib in OS-X).
I compile PETSc/SLEPc using Homebrew both on OS-X and Linux and judging from
ldd/otool there is indeed a difference:
Linux (soname is there):
$ ldd .linuxbrew_openblas/opt/sle
Gary :
I tested your mat.bin using
petsc/src/ksp/ksp/examples/tutorials/ex10.c
./ex10 -f0 $D/mat.bin -rhs 0 -ksp_monitor_true_residual -ksp_view
...
Mat Object: 1 MPI processes
type: seqaij
rows=588, cols=588
total: nonzeros=11274, allocated nonzeros=11274
total number of malloc
Thanks Jose and Hong for the prompt reply.
I will let you know if I encounter any issues due to calling function in
different order.
Kind regards,
Denis
> On 27 Oct 2015, at 15:39, Jose E. Roman wrote:
>
> Yes, in principle you can set options in any order. Let us know if anything
> does no
Yes, in principle you can set options in any order. Let us know if anything
does not work for you.
Jose
> El 27/10/2015, a las 9:15, Denis Davydov escribió:
>
> Dear developers,
>
> I wonder if there are any restriction (apart from obvious) on the calling
> order of EPS functions?
> Is the
Denis:
Your code looks fine to me. There are examples under
slepc/src/eps/examples/tutorials
using ST with SHELL, e.g., ex10.c
Hong
Dear developers,
>
> I wonder if there are any restriction (apart from obvious) on the calling
> order of EPS functions?
> Is the following logic correct:
>
> once I
On Tue, Oct 27, 2015 at 9:10 AM, Matthew Knepley wrote:
> On Tue, Oct 27, 2015 at 9:06 AM, Gary Rebt wrote:
>
>> Dear petsc-users,
>>
>> While using the FEniCS package to Solve a simple Stokes' flow problem, I
>> have run into problems with PETSc preconditioners. In particular, I would
>> like t
Dear petsc-users,
While using the FEniCS package to Solve a simple Stokes' flow problem, I have
run into problems with PETSc preconditioners. In particular, I would like to
use ILU (no parallel version) along with GMRES to solve my linear system but
the solver just hangs indefinitely at MatLUF
On Tue, Oct 27, 2015 at 9:06 AM, Gary Rebt wrote:
> Dear petsc-users,
>
> While using the FEniCS package to Solve a simple Stokes' flow problem, I
> have run into problems with PETSc preconditioners. In particular, I would
> like to use ILU (no parallel version) along with GMRES to solve my linea
Dear petsc-users,
While using the FEniCS package to Solve a simple Stokes' flow problem, I have run into problems with PETSc preconditioners. In particular, I would like to use ILU (no parallel version) along with GMRES to solve my linear system but the solver just hangs indefinitely at MatLUFa
Dear developers,
I wonder if there are any restriction (apart from obvious) on the calling order
of EPS functions?
Is the following logic correct:
once I create EPS object (and specified it’s type)
ierr = EPSCreate (mpi_communicator, eps);
ierr = EPSSetType (eps, const_cast(EPSKRYLOVSCHUR)
On Mon, Oct 26, 2015 at 10:03 PM, Adrian Croucher wrote:
> hi
>
> When I read the HDF5 file back in again using PetscViewerHDF5Open() and
> VecLoad(), is there any easy way to navigate to the last time step in the
> results?
>
> Or, equivalently, to find how many timesteps there are in there, so
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