> On Nov 21, 2014, at 1:46 PM, Abhyankar, Shrirang G. <[email protected]> > wrote: > > I think this may have to do with the matrix reodering scheme. I think > CHOLMOD, used by MATLAB backslash operator, uses AMD (approximate min. > degree) ordering scheme by default. PETSc's default reordering scheme is > nested dissection. For PETSc + MATLAB, use the option > -pc_factor_mat_ordering_type qmd
This is possible and definitely worth trying with different orders, but I checked the nonzeros in the matrix and the L factor for both approaches and they are very similar PETSc call: Common.fl 1.81877e+10 (flop count from most recent analysis) Common.lnz 4.46748e+07 (fundamental nz in L) MatLab call: flop count: 1.8188e+10 nnz(L): 4.4675e+07 Unless I am misunderstanding something both factors likely look very similar. Barry > > Shri > > On Nov 21, 2014, at 11:23 AM, "Victor Magri" <[email protected]> > wrote: > >> Hi, >> >> I'm solving a linear system which comes from the discretization of an >> elliptic equation. The mesh has 1 million control volumes and there are two >> more constraints for the system. >> >> First, I've solved it in MATLAB using backslash command, which in turn calls >> CHOLMOD once the matrix is SPD. Using tic and toc funtions, I could see that >> it takes about 2s for the system to be solved (See attached for more >> details). >> >> I wrote both matrix and rhs in PETSc binary format and solved the linear >> system using the example problem defined in ksp/examples/tutorials/ex10.c. >> The command line options were: >> >> mpiexec -n -1 ./ex10 -f A1mi.dat -rhs rhs1mi.dat -log_summary -ksp_monitos >> -ksp_view -ksp_type preonly -pc_type cholesky -pc_factor_mat_solver_package >> cholmod >> >> The configuration parameters for CHOLMOD in PETSc and MATLAB seems the same, >> so I was expecting a similar computation time, but it took about 13s to >> solve in PETSc. (See attached for more details). >> >> Why does CHOLMOD solution time differs between them? >> >> If someone wants to try for yourself, here are the binaries for the matrix >> and the rhs, respectively. >> https://www.dropbox.com/s/q9s6mlrmv1qdxon/A1mi.dat?dl=0 >> https://www.dropbox.com/s/2zadcbjg5d9bycy/rhs1mi.dat?dl=0 >> >> >> >> <PetscOutput.dat> >> <MatlabOutput.dat>
