There is another sparse direct solver that PETSc supports: PaStix. You
can try it by --download-pastix.
Xiangdong
On Tue, May 15, 2012 at 5:34 AM, Anton Popov wrote:
> On 5/15/12 9:25 AM, Thomas Witkowski wrote:
>>
>> I made some comparisons of using umfpack, superlu, superlu_dist and mumps
>>
On Wed, Mar 14, 2012 at 4:17 PM, Matthew Knepley wrote:
> On Wed, Mar 14, 2012 at 1:33 PM, Xiangdong Liang wrote:
>>
>> On Tue, Mar 13, 2012 at 5:57 PM, Matthew Knepley
>> wrote:
>> > On Tue, Mar 13, 2012 at 4:39 PM, Xiangdong Liang
>> > wrote:
>
On Tue, Mar 13, 2012 at 5:57 PM, Matthew Knepley wrote:
> On Tue, Mar 13, 2012 at 4:39 PM, Xiangdong Liang wrote:
>>
>> Hello everyone,
>>
>> Can someone provide me advice on using OpenMP in PETSc? I am solving a
>> problem like this:
>>
>> int main
Hello everyone,
Can someone provide me advice on using OpenMP in PETSc? I am solving a
problem like this:
int main()
{
vec vsum;
for(i=0; i< N; i++)
{
vec vi;
fcomputev(i, vi);
VecAXPY(vsum, 1.0, vi); // vsum +=vi;
}
}
Can I use OpenMP "omp parallel for" to do the
PM, Xiangdong Liang wrote:
>>
>> Hello everyone,
>>
>> I am solving complex Ax=b with PaStix on 20 processors successfully
>> but failed on 24 processors. The relatively error indicated by
>> mat_pastix_verbose becomes "nan" ?for 24 processors. Where cou
Hello everyone,
I am solving complex Ax=b with PaStix on 20 processors successfully
but failed on 24 processors. The relatively error indicated by
mat_pastix_verbose becomes "nan" for 24 processors. Where could be
wrong? Can someone give me some hints on how I can debug? Thanks.
Xiangdong
On Tue, Dec 13, 2011 at 11:24 AM, Matthew Knepley wrote:
> On Tue, Dec 13, 2011 at 10:19 AM, Xiangdong Liang
> wrote:
>>
>> On Tue, Dec 13, 2011 at 11:14 AM, Matthew Knepley
>> wrote:
>> > On Tue, Dec 13, 2011 at 10:13 AM, Xiangdong Liang
>> > wrote:
On Tue, Dec 13, 2011 at 11:14 AM, Matthew Knepley wrote:
> On Tue, Dec 13, 2011 at 10:13 AM, Xiangdong Liang
> wrote:
>>
>> Hello everyone,
>>
>> I am using PetscPrintf(PETSC_COMM_WORLD,.) to print out some
>> information. When I run the program on m
Hello everyone,
I am using PetscPrintf(PETSC_COMM_WORLD,.) to print out some
information. When I run the program on multiple processors, some of
these calls are printed out multiple times, while other calls are
printed out once. Should it be printed only once if I use
PETSC_COMM_WORLD? Thanks.
Hi Alexander,
I am just curious how other sparse direct solver (eg. PaStiX) works on
your problem. Right now, I only have single RHS, but I will need
multi-RHS soon. For my single RHS problem, PaStiX works better for my
sparse matrix pattern (helmholtz like). If you tried PaStiX, I would
be happy
hints on where to modify? Thanks.
Xiangdong
On Sun, Dec 11, 2011 at 12:49 PM, Barry Smith wrote:
>
> ?Looks like Pastix is running with different options hence different
> performance.
>
> ? Barry
>
> On Dec 11, 2011, at 10:08 AM, Xiangdong Liang wrote:
>
>> On Sun, De
On Sun, Dec 11, 2011 at 9:04 AM, Matthew Knepley wrote:
> On Sun, Dec 11, 2011 at 12:05 AM, Xiangdong Liang
> wrote:
>>
>> Hello PETSc team,
>>
>> I was using PaStiX within petsc 3.1-p8. Today, I am trying PaStiX
>> within petsc-dev. However, For the same cod
Hello PETSc team,
I was using PaStiX within petsc 3.1-p8. Today, I am trying PaStiX
within petsc-dev. However, For the same code, solving the same linear
system takes longer time (120s vs 90s) in petsc-dev. Both are compiled
with debugging mode off. Is it possible that the newer PaStiX is
slower t
Hello everyone,
I am solving a complex linear system C x = d, where C= A+ iB (A, B are
real), in sparse-direct solver. So far, I use the real formulation by
solving the linear system [A, -B; B,A]. The reason we chose this
approach is to use the property of that the imaginary part B in our
problem
On Fri, Dec 9, 2011 at 11:02 PM, Satish Balay wrote:
> On Fri, 9 Dec 2011, Xiangdong Liang wrote:
>
>> Another quick question, when I use mat_view_draw command line option,
>> how can I make the figure X window larger? I think petsc
>> PetscDrawOpenX can do this job, bu
On Fri, Dec 9, 2011 at 7:23 PM, Matthew Knepley wrote:
> On Fri, Dec 9, 2011 at 6:15 PM, Xiangdong Liang wrote:
>>
>> If I use MAT_IGNORE_ZERO_ENTRIES option, is it possible that I still
>> see some zeros in the sparse matrix? In my problem, when I use this
>
>
&
wrote:
> No, a different ordering will be computed, and the ordering with the sparser
> matrix could even lead to more fill.
>
> On Dec 9, 2011 4:13 PM, "Xiangdong Liang" wrote:
>>
>> On Fri, Dec 9, 2011 at 7:02 PM, Barry Smith wrote:
>> >
>> &g
If I use MAT_IGNORE_ZERO_ENTRIES option, is it possible that I still
see some zeros in the sparse matrix? In my problem, when I use this
ignore_zero options, the number of nonzeros is significantly reduced
(from mat_view_info) but still larger than the number of nonzeros
counting from matlab. When
On Fri, Dec 9, 2011 at 7:02 PM, Barry Smith wrote:
>
> On Dec 9, 2011, at 5:55 PM, Xiangdong Liang wrote:
>
>> Hello everyone,
>>
>> I am solving Ax=b with sparse direct solver Pastix. I have two
>> equivalent A's (upto these zero entries): A1 and A2. A1 i
Hello everyone,
I am solving Ax=b with sparse direct solver Pastix. I have two
equivalent A's (upto these zero entries): A1 and A2. A1 is generated
with ignor_zero_entries and A2 is without this option. For example A1
has 9 millions nonzeros, while A2 has 10 millions zeros. When I solve
them with
Hello everyone,
When I use mat_view_draw for a matrix, I see different colors ( red ,
blue, and etc) in the drawing. What does these colors mean? Thanks.
Best,
Xiangdong
Hello everyone,
I am trying to compile petsc-3.2 on cray. However, when I specify blas
and lapack library
--with-blas-lapack-lib=[/opt/acml/4.4.0/pgi64/lib/libacml.a,
libacml_mv.a], petsc complains like this:
===
Hello everyone,
I am using mat_view_info to see the matrix information in ksp/ksp/ex2.c:
http://www.mcs.anl.gov/petsc/petsc-current/src/ksp/ksp/examples/tutorials/ex2.c.html
When I use single processor, I see two matrix-objects. One is the
operator A, but what's the other one? It seems that the o
On Wed, Dec 7, 2011 at 12:07 PM, Satish Balay wrote:
> On Wed, 7 Dec 2011, Xiangdong Liang wrote:
>
>> >> >> Matrix Object:
>> >> >> type=mpiaij, rows=10, cols=10
>> >> >> total: nonzeros=20, allocated nonzeros=40
>> >> &g
On Wed, Dec 7, 2011 at 4:44 AM, Matthew Knepley wrote:
> On Tue, Dec 6, 2011 at 11:39 PM, Xiangdong Liang wrote:
>>
>> On Wed, Dec 7, 2011 at 12:11 AM, Barry Smith wrote:
>> >
>> > On Dec 6, 2011, at 10:26 PM, Xiangdong Liang wrote:
>> >
>> >&
On Wed, Dec 7, 2011 at 11:53 AM, Satish Balay wrote:
> On Wed, 7 Dec 2011, Xiangdong Liang wrote:
>
>> I think I did have 10 zeros entries. In my script, I have inserted
>> zeros by MatSetValue(A,i, (i+1)%N, 0.0, ADD_VALUES); Why doesn't that
>> option matter in
On Wed, Dec 7, 2011 at 9:28 AM, Barry Smith wrote:
>
> On Dec 6, 2011, at 11:39 PM, Xiangdong Liang wrote:
>
>> On Wed, Dec 7, 2011 at 12:11 AM, Barry Smith wrote:
>>>
>>> On Dec 6, 2011, at 10:26 PM, Xiangdong Liang wrote:
>>>
>>>> Hel
On Wed, Dec 7, 2011 at 12:11 AM, Barry Smith wrote:
>
> On Dec 6, 2011, at 10:26 PM, Xiangdong Liang wrote:
>
>> Hello everyone,
>>
>> Can anyone help on the usage of MAT_IGNORE_ZERO_ENTRIES? Suppose I
>> want to have a 10-by-10 sparse matrix, where each row has
might change in successive
>> iterations, that might not be a good idea since the memory reallocation
>> could be very slow, but for a lot of cases which a constant matrix, that
>> could be simply helpful.
>>
>> Best,
>> Mohamad
>>
>>
>>
>
Thanks. If this is the case, will the option MAT_IGNORE_ZERO_ENTRIES be helpful?
Xiangdong
On Thu, Dec 1, 2011 at 8:00 PM, Barry Smith wrote:
>
> On Dec 1, 2011, at 6:44 PM, Xiangdong Liang wrote:
>
>> Hello everyone,
>>
>> I have a question about whether zeros wil
Hello everyone,
I have a question about whether zeros will change the sparse pattern.
Suppose I am generating two sparse matrices A and B. A is generated
with exactly number of nonzeros, say 10 nnz per row. When I generate
matrix B, I specify 12 nonzeros, but two of them are given zero values
by M
Great. Thanks a lot, Barry!
Xiangdong
On Sun, Nov 27, 2011 at 6:34 PM, Barry Smith wrote:
>
> ? I have fixed the command line parsing in petsc-dev so you will no longer
> get messages about nonexistent arguments like this.
>
> ? Barry
>
> On Nov 23, 2011, at 10:26 PM,
Thanks, Barry! Yes, I do have my own command line arguments -1 and 1.
Good to know that it's safe to ignore the warning.
Xiangdong
On Wed, Nov 23, 2011 at 11:30 PM, Barry Smith wrote:
>
> On Nov 23, 2011, at 10:26 PM, Xiangdong Liang wrote:
>
>> Hello everyone,
>>
&g
Hello everyone,
When I compile my program with debug mode and ran it, I got
WARNING! There are options you set that were not used!
WARNING! could be spelling mistake, etc!
Option left: name:-1 value: -1
I even got the warning if I do not provide any options. What's the option left?
However, su
Hello everyone,
I have a question about the default values set by PETSc. For example,
KSPSetTolerances(ksp,1.e-5,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT);
What's the atol and maxits set by PETSC_DEAULT? Is there a way to
print them out? Thanks.
Xiangdong
ompiled library will heavily affect the
performance. Thanks.
Best,
Xiangdong
On Sun, Oct 30, 2011 at 9:47 PM, Barry Smith wrote:
>
> ? You can install petsc-dev on the system yourself and use whatever solver
> you chose.
>
> ? Barry
>
> On Oct 30, 2011, at 8:43 PM, Xiangd
Hello everyone,
I am trying to solve linear system with sparse-direct solver on Kraken
Cray XT5 system. As I tested on our own small cluster, PaStiX works
better than superlu_dist and mumps.
However, PaStix was not installed on Kraken, while superlu_dist and
mumps are installed as part of PETSc.
Thanks for helping me check the code.
I agree that moving the KSPSetOperators(ksp,M,M,SAME_NONZERO_PATTERN)
outside the iteration loop lifted the crash of superlu_dist. However,
I have the following concerns:
1) If we only call KSPSetOperators once outside the loop, the ksp
solver would be the
Thanks, Hong. I tried the runtime option -mat_superlu_dist_equil NO.
However, the problem is still there.
I've upload my short codes here:
http://math.mit.edu/~xdliang/superlu_dist_test.zip
In this code, I first generate my sparse matrix M with dimension
N-by-N, then solve Mx=J for a few times. E
Hello everyone,
I had some problem in using superlu_dist with same_nonzero_pattern.
Sometimes superlu_dist solver halts there and never finishes. However,
when I switched to different_nonzero_pattern or other solvers, the
program works nicely. ?Ding had reported this problem a few months
ago:
?htt
to what is a reasonable approach. Accessing diagonals is not a
> natural operation for sparse matrices stored by rows or columns.
>
> ? Barry
>
>
>
> On May 6, 2011, at 3:56 PM, Xiangdong Liang wrote:
>
>> Hello everyone,
>>
>> I am wondering whether ther
Hello everyone,
I am wondering whether there is some function like MatGetDiagonal to
get the k-th diagonal (above or below the main diagonal) of the matrix
A. If I have to write my own function, what built-in function should I
use to get a particular element of A? It seems that MatGetValues
return
Hello everyone,
I am trying to create a sparse matrix A, which depends on a parallel
vector v. For example, my function looks like this: Mat
myfun(MPI_Comm comm, Vec v, other parameters). When I set the value
A(i,j) = v[k], v[k] may not be obtained by VecGetValues since that
operation can only ge
Hello everyone,
I have a problem with creating a new large vector via combining existing
small vectors. Suppose I have two vectors v1 and v2 (size n-by-1) already. I
want to have a new vector vout (size 2n-by-1) with vout(1:n) = v1 and
vout(n+1:2*n) = v2. Is there any quick way to create vout with
On Wed, Apr 27, 2011 at 12:03 PM, Jed Brown wrote:
> On Wed, Apr 27, 2011 at 17:57, Xiangdong Liang wrote:
>
>> I am a novice to Petsc and parallel computing. I have created a mpi sparse
>> matrix A (size n-by-n) and a parallel vector b (size n-by-1). Now I want to
>>
Hello everyone,
I am a novice to Petsc and parallel computing. I have created a mpi sparse
matrix A (size n-by-n) and a parallel vector b (size n-by-1). Now I want to
modify the diagonal of A by adding the values of vector b. Namely, A(i,i) =
A(i,i) + b(i) and all the off-diagonal elements remains
Hello everyone,
I am wondering what function in petsc computes the pointwise product of two
vectors. For example, vin1=[1,2], vin2=[3,4]; I need a function to output
vout= vin1.*vin2 = [3,8]. I can write my own function, but I am worrying
whether the vin1 and vin2 are known by all the processors (
Hi everyone,
I am wondering how I can run the direct solver in parallel. I can run
my program in a single processor with direct linear solver by
./foo.out -ksp_type preonly -pc_type lu -pc_factor_mat_solver_package spooles
However, when I try to run it with mpi:
mpirun.openmpi -np 2 ./foo.out
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