How to copy global data to local ?
OK. It worksThank you --- 09?12?1, ming zhu foolishzhu at yahoo.com.cn ??? ???: ming zhu foolishzhu at yahoo.com.cn ??: Re: How to copy global data to local ? ???: PETSc users list petsc-users at mcs.anl.gov ??: 2009?12?1?,??,??10:29 It seems that MatGetSubMatrix() only get the local matrix for the processor? If U is global(PETSC_COMM_WORLD), the local matrix may not store the column or row I wanted. For example, if U is 4*4, and there are 4 processors, processors one has local matrix 2*2, but i need the third row, Then,MatGetSubmatrix() may not work --- 09?12?1, Barry Smith bsmith at mcs.anl.gov ??? ???: Barry Smith bsmith at mcs.anl.gov ??: Re: How to copy global data to local ? ???: PETSc users list petsc-users at mcs.anl.gov ??: 2009?12?1?,??,??10:23 On Nov 30, 2009, at 11:21 PM, ming zhu wrote: Hi I have a huge matrix U for all processors (PETSC_COMM_WORLD). I only want to copy only two rows (i,j) for each local processor. i,j is different for each processor and not related to rank.? I was trying to use a vector filter (like, 001). However, if the vector is PETSC_COMM_WORLD, it will be changed by different processor. So, how to make it ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???^ ???I do not understand what this means. To do the multiply you can and should use a vector of PETSC_COMM_WORLD. ???Also multiplying by a vector will not give you back rows of a matrix. Do you truly want the entire row of nonzeros of the matrix or something else. If you want the entire row or part of a row then you can use MatGetSubMatrix(). ???Barry Thank you My original code is Vec filter VecCreate(PETSC_COMM_WORLD,filter); VecSetsizes(filter,PETSC_DECIDE,m); VecSetFromOptions(filter); Vecset(filter,0); VecSetValue(filter,i,1,INSERT_VALUES); ... MatMult(U, filter,ui); If I create filter with PETSC_COMM_SELF, it is impossible for U and filter to multiply. ? ? ___ ? http://card.mail.cn.yahoo.com/ -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20091202/bd7a0f30/attachment.htm
how to run petsc on different machine
?With?--download-mpich=1,Petsc install mpi. However, since I want to run my Petsc program on different machines and mpiexec -machinefile machineifle does not work.?It complains:invalid mpiexec argument -machinefile. Do I have to install mpi for this?? Or do other way? Thank you ___ ? http://card.mail.cn.yahoo.com/ -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20091202/980951ec/attachment.htm
How to copy global data to local ?
HiI tried?MatGetSubMatrix() but I am a little confused by the column parameter. For exampleMy matrix is U (m * n). I want to get i,j rows to local.my code is? PetscInt* rowindex,colindex;PetscMalloc...for (k= 0; k n; k++)?? colindex[k] = k; rowindex[0] = i;rowindex[1] = j; MatGetSubMatrixRaw(U,1,i,n,indices,n,MAT_INITIAL_MATRIX,newmat); What I hope is newmat is 2 * n matrix. But I failed. Thank you --- 09?12?1, Barry Smith bsmith at mcs.anl.gov ??? ???: Barry Smith bsmith at mcs.anl.gov ??: Re: How to copy global data to local ? ???: PETSc users list petsc-users at mcs.anl.gov ??: 2009?12?1?,??,??10:35 ???You misunderstand the usage of MatGetSubMatrix(). Any process can request ANY row, including rows that are not originally owned by that process. ???Barry On Dec 1, 2009, at 8:29 AM, ming zhu wrote: It seems that MatGetSubMatrix() only get the local matrix for the processor? If U is global(PETSC_COMM_WORLD), the local matrix may not store the column or row I wanted. For example, if U is 4*4, and there are 4 processors, processors one has local matrix 2*2, but i need the third row, Then,MatGetSubmatrix() may not work --- 09?12?1, Barry Smith bsmith at mcs.anl.gov ??? ???: Barry Smith bsmith at mcs.anl.gov ??: Re: How to copy global data to local ? ???: PETSc users list petsc-users at mcs.anl.gov ??: 2009?12?1?,??,??10:23 On Nov 30, 2009, at 11:21 PM, ming zhu wrote: Hi I have a huge matrix U for all processors (PETSC_COMM_WORLD). I only want to copy only two rows (i,j) for each local processor. i,j is different for each processor and not related to rank.? I was trying to use a vector filter (like, 001). However, if the vector is PETSC_COMM_WORLD, it will be changed by different processor. So, how to make it ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ^ ? ? I do not understand what this means. To do the multiply you can and should use a vector of PETSC_COMM_WORLD. ? ? Also multiplying by a vector will not give you back rows of a matrix. Do you truly want the entire row of nonzeros of the matrix or something else. If you want the entire row or part of a row then you can use MatGetSubMatrix(). ? ? Barry Thank you My original code is Vec filter VecCreate(PETSC_COMM_WORLD,filter); VecSetsizes(filter,PETSC_DECIDE,m); VecSetFromOptions(filter); Vecset(filter,0); VecSetValue(filter,i,1,INSERT_VALUES); ... MatMult(U, filter,ui); If I create filter with PETSC_COMM_SELF, it is impossible for U and filter to multiply. ? ? ___ ? http://card.mail.cn.yahoo.com/ -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20091202/37a23483/attachment.htm
How to copy global data to local ?
OK. I am now use MatGetSubMatrix.My code is as follows
? PetscMalloc(n*sizeof(PetscInt),indices);?
? for (j = 0; j n; j++)
? {??
? indices[j] = j;
? }
? ISCreateGeneral(PETSC_COMM_SELF,n,indices,iy); // get all columns
?
?? PetscMalloc(2*sizeof(PetscInt),indices);?
??? indices[0] = i;
??? indices[1] = j;
??? ISCreateGeneral(PETSC_COMM_SELF,2,indices,ix); // only get i,j rows
??? Mat ui,uj;
// I am not sure how to set the third parameter : how many local columns..
Since I want all columns, I set it to n
ierr = MatGetSubMatrix(U,ix,iy,n, MAT_INITIAL_MATRIX,ui);CHKERRQ(ierr);
What I really hope is to
??? for (i = 0; i n; i++)
{
? ? PetscInt row = 0;
? MatGetValues(ui,1,row,1,i,u_ik);
}
It does not work. I tried to change the n to PETSC_DECIDE, it still does not
work
So, I really doubt that whether I can get the entire row of the matrix.
BTW, the matrix is created as follows:
?MatCreateMPIDense(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,m,n,PETSC_NULL,U)
THank you
--- 09?12?2, Barry Smith bsmith at mcs.anl.gov ???
???: Barry Smith bsmith at mcs.anl.gov
??: Re: How to copy global data to local ?
???: PETSc users list petsc-users at mcs.anl.gov
??: 2009?12?2?,??,??1:46
???Don't know what MatGetSubMatrixRaw() is, but based on the calling sequence
you are asking for the ith row whatever that is, and n columns in the array
indices
???For MatGetSubMatrix() each process can ask for any rows it wants, but all
the processors have to ask for the same columns that are wanted.
???Barry
On Dec 1, 2009, at 9:59 PM, ming zhu wrote:
Hi
I tried MatGetSubMatrix() but I am a little confused by the column parameter.
For example
My matrix is U (m * n). I want to get i,j rows to local.
my code is
PetscInt* rowindex,colindex;
PetscMalloc...
for (k= 0; k n; k++)
? ? colindex[k] = k;
rowindex[0] = i;
rowindex[1] = j;
MatGetSubMatrixRaw(U,1,i,n,indices,n,MAT_INITIAL_MATRIX,newmat);
What I hope is newmat is 2 * n matrix. But I failed.
Thank you
--- 09?12?1, Barry Smith bsmith at mcs.anl.gov ???
???: Barry Smith bsmith at mcs.anl.gov
??: Re: How to copy global data to local ?
???: PETSc users list petsc-users at mcs.anl.gov
??: 2009?12?1?,??,??10:35
? ? You misunderstand the usage of MatGetSubMatrix(). Any process can request
ANY row, including rows that are not originally owned by that process.
? ? Barry
On Dec 1, 2009, at 8:29 AM, ming zhu wrote:
It seems that MatGetSubMatrix() only get the local matrix for the
processor? If U is global(PETSC_COMM_WORLD), the local matrix may not store
the column or row I wanted. For example, if U is 4*4, and there are 4
processors, processors one has local matrix 2*2, but i need the third row,
Then,MatGetSubmatrix() may not work
--- 09?12?1, Barry Smith bsmith at mcs.anl.gov ???
???: Barry Smith bsmith at mcs.anl.gov
??: Re: How to copy global data to local ?
???: PETSc users list petsc-users at mcs.anl.gov
??: 2009?12?1?,??,??10:23
On Nov 30, 2009, at 11:21 PM, ming zhu wrote:
Hi
I have a huge matrix U for all processors (PETSC_COMM_WORLD). I only want
to copy only two rows (i,j) for each local processor. i,j is different
for each processor and not related to rank.? I was trying to use a vector
filter (like, 001). However, if the vector is PETSC_COMM_WORLD,
it will be changed by different processor. So, how to make it ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ^
? ? I do not understand what this means. To do the multiply you can and
should use a vector of PETSC_COMM_WORLD.
? ? Also multiplying by a vector will not give you back rows of a matrix.
Do you truly want the entire row of nonzeros of the matrix or something
else. If you want the entire row or part of a row then you can use
MatGetSubMatrix().
? ? Barry
Thank you
My original code is
Vec filter
VecCreate(PETSC_COMM_WORLD,filter);
VecSetsizes(filter,PETSC_DECIDE,m);
VecSetFromOptions(filter);
Vecset(filter,0);
VecSetValue(filter,i,1,INSERT_VALUES);
...
MatMult(U, filter,ui);
If I create filter with PETSC_COMM_SELF, it is impossible for U and
filter to multiply.
?
?
?
___
?
http://card.mail.cn.yahoo.com/
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How to copy global data to local ?
Let's move this over to petsc-maint at mcs.anl.gov to cut the traffic
on petsc-users See below.
On Dec 2, 2009, at 12:33 AM, ming zhu wrote:
OK. I am now use MatGetSubMatrix.My code is as follows
PetscMalloc(n*sizeof(PetscInt),indices);
for (j = 0; j n; j++)
{
indices[j] = j;
}
ISCreateGeneral(PETSC_COMM_SELF,n,indices,iy); // get all columns
.
PetscMalloc(2*sizeof(PetscInt),indices);
indices[0] = i;
indices[1] = j;
ISCreateGeneral(PETSC_COMM_SELF,2,indices,ix); // only get
i,j rows
Mat ui,uj;
// I am not sure how to set the third parameter : how many local
columns. Since I want all columns, I set it to n
ierr = MatGetSubMatrix(U,ix,iy,n,
MAT_INITIAL_MATRIX,ui);CHKERRQ(ierr);
What I really hope is to
for (i = 0; i n; i++)
{
PetscInt row = 0;
MatGetValues(ui,1,row,1,i,u_ik);
}
It does not work. I tried to change the n to PETSC_DECIDE, it still
does not work
^
^
^
^
^
^
^
^
^
^
^
^
^
^
^
^
Saying it does not work is extremely uninformative and makes it
difficult for us to know what happened and thus make useful
suggestions. Please say exactly what goes wrong and cut and paste all
error messages. At this point we would be totally guessing what is
happening.
Barry
So, I really doubt that whether I can get the entire row of the
matrix.
BTW, the matrix is created as follows:
MatCreateMPIDense
(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,m,n,PETSC_NULL,U)
THank you
--- 09?12?2, Barry Smith bsmith at mcs.anl.gov ?
??
???: Barry Smith bsmith at mcs.anl.gov
??: Re: How to copy global data to local ?
???: PETSc users list petsc-users at mcs.anl.gov
??: 2009?12?2?,??,??1:46
Don't know what MatGetSubMatrixRaw() is, but based on the calling
sequence you are asking for the ith row whatever that is, and n
columns in the array indices
For MatGetSubMatrix() each process can ask for any rows it wants,
but all the processors have to ask for the same columns that are
wanted.
Barry
On Dec 1, 2009, at 9:59 PM, ming zhu wrote:
Hi
I tried MatGetSubMatrix() but I am a little confused by the column
parameter. For example
My matrix is U (m * n). I want to get i,j rows to local.
my code is
PetscInt* rowindex,colindex;
PetscMalloc...
for (k= 0; k n; k++)
colindex[k] = k;
rowindex[0] = i;
rowindex[1] = j;
MatGetSubMatrixRaw(U,1,i,n,indices,n,MAT_INITIAL_MATRIX,newmat);
What I hope is newmat is 2 * n matrix. But I failed.
Thank you
--- 09?12?1, Barry Smith bsmith at mcs.anl.gov ?
??
???: Barry Smith bsmith at mcs.anl.gov
??: Re: How to copy global data to local ?
???: PETSc users list petsc-users at mcs.anl.gov
??: 2009?12?1?,??,??10:35
You misunderstand the usage of MatGetSubMatrix(). Any process
can request ANY row, including rows that are not originally owned by
that process.
Barry
On Dec 1, 2009, at 8:29 AM, ming zhu wrote:
It seems that MatGetSubMatrix() only get the local matrix for
the processor If U is global(PETSC_COMM_WORLD), the local matrix
may not store the column or row I wanted. For example, if U is 4*4,
and there are 4 processors, processors one has local matrix 2*2, but
i need the third row, Then,MatGetSubmatrix() may not work
--- 09?12?1, Barry Smith bsmith at mcs.anl.gov ?
??
???: Barry Smith bsmith at mcs.anl.gov
??: Re: How to copy global data to local ?
???: PETSc users list petsc-users at mcs.anl.gov
??: 2009?12?1?,??,??10:23
On Nov 30, 2009, at 11:21 PM, ming zhu wrote:
Hi
I have a huge matrix U for all processors (PETSC_COMM_WORLD).
I only want to copy only two rows (i,j) for each local processor.
i,j is different for each processor and not related to rank. I was
trying to use a vector filter (like, 001). However, if the
vector is PETSC_COMM_WORLD, it will be changed by different
processor. So, how to make it ?
^
I do not understand what this means. To do the multiply you
can and should use a vector of PETSC_COMM_WORLD.
Also multiplying by a vector will not give you back rows of
a matrix. Do you truly want the entire row of nonzeros of the matrix
or something else. If you want the entire row or part of a row then
you can use MatGetSubMatrix().
Barry
Thank you
My original code is
Vec filter
VecCreate(PETSC_COMM_WORLD,filter);
VecSetsizes(filter,PETSC_DECIDE,m);
VecSetFromOptions(filter);
Vecset(filter,0);
optimized complex number kernel
Hi, The Petsc 3 manual (pdf)mentions using an optimized fortran kernel for complex numbers, that somehow uses the same C interface. It refers to a document on how to build these kernels, but that document does not appear to be in the tarball (or on the anl.gov website). Furthermore, the FAQ on the website only mentions C and C++ in the section on complex number performance... If someone could clarify what was possible, and where to look for more information, that would be great! thanks, Craig
optimized complex number kernel
The performance difference between c/c++ kernels and fortran kernels - or c-complex/c++-complex can be compiler specific. You can build all relavent versions [each with a different PETSC_ARCH] and see if it makes a difference for you code. The relavent configure options are: --with-fortran-kernels=generic [default 'none'] --with-clanguage=cxx [or default 'c'] --with-scalar-type=complex [default 'real'] Satish On Wed, 2 Dec 2009, Craig Tanis wrote: Hi, The Petsc 3 manual (pdf)mentions using an optimized fortran kernel for complex numbers, that somehow uses the same C interface. It refers to a document on how to build these kernels, but that document does not appear to be in the tarball (or on the anl.gov website). Furthermore, the FAQ on the website only mentions C and C++ in the section on complex number performance... If someone could clarify what was possible, and where to look for more information, that would be great! thanks, Craig
optimized complex number kernel
Craig, Thanks for pointing this out. I have updated the manual and installation.html in PETSc-dev to explicitly provide this information. Barry On Dec 2, 2009, at 11:09 AM, Satish Balay wrote: The performance difference between c/c++ kernels and fortran kernels - or c-complex/c++-complex can be compiler specific. You can build all relavent versions [each with a different PETSC_ARCH] and see if it makes a difference for you code. The relavent configure options are: --with-fortran-kernels=generic [default 'none'] --with-clanguage=cxx [or default 'c'] --with-scalar-type=complex [default 'real'] Satish On Wed, 2 Dec 2009, Craig Tanis wrote: Hi, The Petsc 3 manual (pdf)mentions using an optimized fortran kernel for complex numbers, that somehow uses the same C interface. It refers to a document on how to build these kernels, but that document does not appear to be in the tarball (or on the anl.gov website). Furthermore, the FAQ on the website only mentions C and C++ in the section on complex number performance... If someone could clarify what was possible, and where to look for more information, that would be great! thanks, Craig
