General matrix interative solver

[Julian]

Ok, so this is what I am doing now... And I still get the same result. It goes very slowly till the 200th MAT_FLUSH_ASSEMBLY call and then just stays there... The output that I gave u earlier is the complete output its been giving for the following code:

	Mat		mat; 
	PetscInitialize(0,0,"petscOptions.txt",0);
	int i;
	int *nnz;
	nnz=new int[L];
	for(i=0;i<L;i++){
		nnz[i]=row[i].getNum();
	}

	MatCreateSeqSBAIJ(PETSC_COMM_SELF, 1, L, L, PETSC_DEFAULT, nnz, &mat);
	delete [] nnz;

Maybe it is not giving the output you are requiring because the program never gets to the point where MAT_FINAL_ASSEMBLY is called.

Now, when I do a MAT_FINAL_ASSEMBLY call right after the preallocation, then I get a different output

	Mat		mat; 
	PetscInitialize(0,0,"petscOptions.txt",0);
	int i;
	int *nnz;
	nnz=new int[L];
	for(i=0;i<L;i++){
		nnz[i]=row[i].getNum();
	}

	MatCreateSeqSBAIJ(PETSC_COMM_SELF, 1, L, L, PETSC_DEFAULT, nnz, &mat);

	MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);	// <-----------------
	MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);		// <-----------------

	delete [] nnz;

This is what I get :
[0] PetscInitializePETSc successfully started: number of processors = 1
[0] PetscGetHostNameRejecting domainname, likely is NIS ALPHA2.☺0☺
[0] PetscInitializeRunning on machine: ALPHA2
[0] PetscCommDuplicateDuplicating a communicator 1 1 max tags = 100000000
[0] MatAssemblyEnd_SeqSBAIJMatrix size: 14883 X 14883, block size 1; storage spa
ce: 1040055 unneeded, 0 used
[0] MatAssemblyEnd_SeqSBAIJNumber of mallocs during MatSetValues is 0
[0] MatAssemblyEnd_SeqSBAIJMost nonzeros blocks in any row is 0

In this case, the assembly goes very fast TILL the 200th MAT_FLUSH_ASSEMBLY call and THEN gets stuck!



> -----Original Message-----
> From: owner-petsc-users at mcs.anl.gov 
> [mailto:owner-petsc-users at mcs.anl.gov] On Behalf Of Satish Balay
> Sent: Thursday, October 12, 2006 6:46 PM
> To: petsc-users at mcs.anl.gov
> Subject: RE: General matrix interative solver
> 
> On Thu, 12 Oct 2006, Julian wrote:
> 
> > I am now using MatCreateSeqSBAIJ() - I am assuming the second 
> > parameter bs=1 in my case because I am using one processor. Is that 
> > correct ?
> 
> No - it refers to a blocksize. The matrix could have a block 
> structure.  In this case - the correct blocksize can be 
> specified. The matrix operations will exploit this block 
> structure for better performance.
> 
> bs=1 is a fine [This is the equivalent of AIJ type in the 
> block notation]
> 
> > The method of creating a matrix I used was taken from Pavel Solin's 
> > book 'Partial Differential Equations and the finite Element 
> Method'. 
> > Is there any particular reason why is should follow this
> > method:
> > mat = (double*)malloc(sizeof(Mat))
> > MatCreateSeqSBAIJ(PETSC_COMM_SELF, 1, L, L, PETSC_DEFAULT, nnz, 
> > (Mat*)mat); In the examples that I have seen in the petsc website I 
> > don't see this statement where memory is allocated.
> 
> No - you should just use PETSc example codes a guidelines. i.e
> 
>    Mat mat;
>    MatCreateSeqSBAIJ(PETSC_COMM_SELF, 1, L, L, PETSC_DEFAULT, 
> nnz, &mat);
> 
> Mat is just a pointer - and all the memory allocation 
> required is done inside XXXCreate() routines.
> 
> > Anyway, I changed my code to the following:
> > 	PetscInitialize(0,0,"petscOptions.txt",0);
> > 
> > 	int i;
> > 	int *nnz;
> > 	nnz=new int[L];
> > 	for(i=0;i<L;i++){
> > 		nnz[i]=row[i].getNum();
> > 	}
> > 
> > 	Assert( mat = (double*)malloc(sizeof(Mat)) );
> > 	MatCreateSeqSBAIJ(PETSC_COMM_SELF, 1, L, L, 
> PETSC_DEFAULT, nnz, (Mat*)mat);
> > 	delete [] nnz;
> 
> > And I'm still getting stuck at the same place... There is a 
> difference 
> > though.. Now the assembly process is even slower than before (when 
> > there was no preallocation) I noticed that it is getting 
> stuck around 
> > the 200th MAT_FLUSH_ASSEMBLY call.. I don't know if that is 
> > significant.Is there some limit on how many times 
> MAT_FLUSH_ASSEMBLY 
> > can be called ?
> 
> MAT_FLUSH_ASSEMBLY is cheap - in sequential mode - but 
> expensive in parallel mode [becasue of parallel 
> syncronization]. However ...
> 
> > This is the petsc output I get:
> > [0] PetscInitializePETSc successfully started: number of 
> processors = 
> > 1 [0] PetscGetHostNameRejecting domainname, likely is NIS 
> ALPHA2.ÿÿ0ÿÿ 
> > [0] PetscInitializeRunning on machine: ALPHA2 [0] 
> > PetscCommDuplicateDuplicating a communicator 1 1 max tags = 
> 100000000
> 
> The above log is incomplete. You should be looking for lines 
> with the string 'malloc'
> 
> Satish
> 
> > 
> > I also tried this :
> > 	mat = new Mat;
> > 	MatCreateSeqSBAIJ(PETSC_COMM_SELF, 1, L, L, 
> PETSC_DEFAULT, nnz, mat);
> > 
> > And got the same performance.
>