Dear all, Sorry for the delay on this topic.
Thank you Gaetan for your suggestion. I had thought about doing that originally, but I had left it out since I thought that a rank owned the entire row of the matrix (and not only the sub-diagonal part). I will certainly give it a try. I still need the MatSolveTranspose since I need the ability to reuse the residual jacobian matrix from the flow (a 1st order approximation of it), which is assembled in a non-transposed format. This way the adjoint system is solved in a pseudo-time step manner, where the product of the exact jacobian matrix and the adjoint vector is used as a source term in the rhs. Hong, do you have an estimation of the time required to implement it in superlu_dist? Best, Antoine -----Message d'origine----- De : Hong [mailto:[email protected]] Envoyé : Friday, August 29, 2014 9:14 PM À : Gaetan Kenway Cc : Antoine De Blois; [email protected] Objet : Re: [petsc-users] superlu_dist and MatSolveTranspose We can add MatSolveTranspose() to the petsc interface with superlu_dist. Jed, Are you working on it? If not, I can work on it. Hong On Fri, Aug 29, 2014 at 6:14 PM, Gaetan Kenway <[email protected]> wrote: > Hi Antoine > > We are also using PETSc for solving adjoint systems resulting from > CFD. To get around the matSolveTranspose issue we just assemble the > transpose matrix directly and then call KSPSolve(). If this is > possible in your application I think it is probably the best approach > > Gaetan > > > On Fri, Aug 29, 2014 at 3:58 PM, Antoine De Blois > <[email protected]> wrote: >> >> Hello Jed, >> >> Thank you for your quick response. So I spent some time to dig deeper >> into my problem. I coded a shell script that passes through a bunch >> of ksp_type, pc_type and sub_pc_type. So please disregard the comment >> about the "does not converge properly for transpose". I had taken >> that conclusion from my own code (and not from the ex10 and extracted >> matrix), and a KSPSetFromOptions was missing. Apologies for that. >> >> What remains is the performance issue. The MatSolveTranspose takes a >> very long time to converge. For a matrix of 3 million rows, >> MatSolveTranspose takes roughly 5 minutes on 64 cpus, whereas the >> MatSolve is almost instantaneous!. When I gdb my code, petsc seems to >> be stalled in the MatLUFactorNumeric_SeqAIJ_Inode () for a long time. >> I also did a top on the compute node to check the RAM usage. It was >> hovering over 2 gig, so memory usage does not seem to be an issue here. >> >> #0 0x00002afe8dfebd08 in MatLUFactorNumeric_SeqAIJ_Inode () >> from >> /gpfs/fs2/aero/SOFTWARE/FLOW_SOLVERS/FANSC/EXT_LIB/petsc-3.5.1/lib/li >> bpetsc.so.3.5 >> #1 0x00002afe8e07f15c in MatLUFactorNumeric () >> from >> /gpfs/fs2/aero/SOFTWARE/FLOW_SOLVERS/FANSC/EXT_LIB/petsc-3.5.1/lib/li >> bpetsc.so.3.5 >> #2 0x00002afe8e2afa99 in PCSetUp_ILU () >> from >> /gpfs/fs2/aero/SOFTWARE/FLOW_SOLVERS/FANSC/EXT_LIB/petsc-3.5.1/lib/li >> bpetsc.so.3.5 >> #3 0x00002afe8e337c0d in PCSetUp () >> from >> /gpfs/fs2/aero/SOFTWARE/FLOW_SOLVERS/FANSC/EXT_LIB/petsc-3.5.1/lib/li >> bpetsc.so.3.5 >> #4 0x00002afe8e39d643 in KSPSetUp () >> from >> /gpfs/fs2/aero/SOFTWARE/FLOW_SOLVERS/FANSC/EXT_LIB/petsc-3.5.1/lib/li >> bpetsc.so.3.5 >> #5 0x00002afe8e39e3ee in KSPSolveTranspose () >> from >> /gpfs/fs2/aero/SOFTWARE/FLOW_SOLVERS/FANSC/EXT_LIB/petsc-3.5.1/lib/li >> bpetsc.so.3.5 >> #6 0x00002afe8e300f8c in PCApplyTranspose_ASM () >> from >> /gpfs/fs2/aero/SOFTWARE/FLOW_SOLVERS/FANSC/EXT_LIB/petsc-3.5.1/lib/li >> bpetsc.so.3.5 >> #7 0x00002afe8e338c13 in PCApplyTranspose () >> from >> /gpfs/fs2/aero/SOFTWARE/FLOW_SOLVERS/FANSC/EXT_LIB/petsc-3.5.1/lib/li >> bpetsc.so.3.5 >> #8 0x00002afe8e3a8a84 in KSPInitialResidual () >> from >> /gpfs/fs2/aero/SOFTWARE/FLOW_SOLVERS/FANSC/EXT_LIB/petsc-3.5.1/lib/li >> bpetsc.so.3.5 >> #9 0x00002afe8e376c32 in KSPSolve_GMRES () >> from >> /gpfs/fs2/aero/SOFTWARE/FLOW_SOLVERS/FANSC/EXT_LIB/petsc-3.5.1/lib/li >> bpetsc.so.3.5 >> #10 0x00002afe8e39e425 in KSPSolveTranspose () >> >> For that particular application, I was using: >> ksp_type: gmres >> pc_type: asm >> sub_pc_type: ilu >> adj_sub_pc_factor_levels 1 >> >> For small matrices, the MatSolveTranspose computing time is very >> similar to the simple MatSolve. >> >> And if I want to revert to a MatTranspose followed by the MatSolve, >> then the MatTranspose takes forever to finish... For a matrix of 3 >> million rows, MatTranspose takes 30 minutes on 64 cpus!! >> >> So thank you for implementing the transpose solve in superlu_dist. It >> would also be nice to have it with hypre. >> Let me know what you think and ideas on how to improve my >> computational time, Regards, Antoine >> >> -----Message d'origine----- >> De : Jed Brown [mailto:[email protected]] Envoyé : Thursday, August >> 28, 2014 5:01 PM À : Antoine De Blois; '[email protected]' >> Objet : Re: [petsc-users] superlu_dist and MatSolveTranspose >> >> Antoine De Blois <[email protected]> writes: >> >> > Hello everyone, >> > >> > I am trying to solve a A^T x = b system. For my applications, I had >> > realized that the MatSolveTranspose does not converge properly. >> >> What do you mean "does not converge properly"? Can you send a test >> case where the transpose solve should be equivalent, but is not? We >> have only a few tests for transpose solve and not all preconditioners >> support it, but where it is supported, we want to ensure that it is correct. >> >> > Therefore, I had implemented a MatTranspose followed by a MatSolve. >> > This proved to converge perfectly (which is strange since the >> > transposed matrix has the same eigenvalues as the untransposed...). >> > The problem is that for bigger matrices, the MatTranspose is very >> > costly and thus cannot be used. >> >> Costly in terms of memory? (I want you to be able to use >> KSPSolveTranspose, but I'm curious what you're experiencing.) >> >> > I tried using the superlu_dist package. Although it the package >> > works perfectly for the MatSolve, I get the an "No support for this >> > operation for this object type" error with MatSolveTransopse. I >> > reproduced the error using the MatView an ex10 tutorial. I can >> > provide the matrix and rhs upon request. My command line was: >> > >> > ex10 -f0 A_and_rhs.bin -pc_type lu -pc_factor_mat_solver_package >> > superlu_dist -trans >> > >> > So it there an additional parameter I need to use for the >> > transposed solve? >> > >> > [0]PETSC ERROR: --------------------- Error Message >> > -------------------------------------------------------------- >> > [0]PETSC ERROR: No support for this operation for this object type >> > [0]PETSC ERROR: Matrix type mpiaij >> >> This is easy to add. I'll do it now. >> >> > [0]PETSC ERROR: See >> > http://www.mcs.anl.gov/petsc/documentation/faq.html >> > for trouble shooting. >> > [0]PETSC ERROR: Petsc Release Version 3.5.1, unknown [0]PETSC ERROR: >> > /gpfs/fs1/aero/SOFTWARE/TOOLS/PROGRAMMING/petsc/src/ksp/ksp/example >> > s/t >> > utorials/ex10 on a ARGUS_impi_opt named hpc-user11 by ad007804 Thu >> > Aug >> > 28 16:41:15 2014 [0]PETSC ERROR: Configure options --CFLAGS="-xHost >> > -axAVX" --download-hypre --download-metis --download-ml >> > --download-parmetis --download-scalapack --download-superlu_dist >> > --download-mumps --with-c2html=0 --with-cc=mpiicc >> > --with-fc=mpiifort --with-cxx=mpiicpc --with-debugging=yes >> > --prefix=/gpfs/fs1/aero/SOFTWARE/TOOLS/PROGRAMMING/petsc/petsc-3.5. >> > 1 >> > --with-cmake=/gpfs/fs1/aero/SOFTWARE/TOOLS/CMAKE/cmake-2.8.7/bin/cm >> > ake >> > --with-valgrind=/gpfs/fs1/aero/SOFTWARE/TOOLS/PROGRAMMING/valgrind- >> > 3.9 .0/bin/valgrind --with-shared-libraries=0 [0]PETSC ERROR: #1 >> > MatSolveTranspose() line 3473 in >> > /gpfs/fs2/aero/SOFTWARE/TOOLS/PROGRAMMING/petsc/src/mat/interface/m >> > atr ix.c [0]PETSC ERROR: #2 PCApplyTranspose_LU() line 214 in >> > /gpfs/fs2/aero/SOFTWARE/TOOLS/PROGRAMMING/petsc/src/ksp/pc/impls/fa >> > cto r/lu/lu.c [0]PETSC ERROR: #3 PCApplyTranspose() line 573 in >> > /gpfs/fs2/aero/SOFTWARE/TOOLS/PROGRAMMING/petsc/src/ksp/pc/interfac >> > e/p recon.c [0]PETSC ERROR: #4 KSP_PCApply() line 233 in >> > /gpfs/fs2/aero/SOFTWARE/TOOLS/PROGRAMMING/petsc/include/petsc-priva >> > te/ kspimpl.h [0]PETSC ERROR: #5 KSPInitialResidual() line 63 in >> > /gpfs/fs2/aero/SOFTWARE/TOOLS/PROGRAMMING/petsc/src/ksp/ksp/interfa >> > ce/ itres.c [0]PETSC ERROR: #6 KSPSolve_GMRES() line 234 in >> > /gpfs/fs2/aero/SOFTWARE/TOOLS/PROGRAMMING/petsc/src/ksp/ksp/impls/g >> > mre s/gmres.c [0]PETSC ERROR: #7 KSPSolveTranspose() line 704 in >> > /gpfs/fs2/aero/SOFTWARE/TOOLS/PROGRAMMING/petsc/src/ksp/ksp/interfa >> > ce/ itfunc.c [0]PETSC ERROR: #8 main() line 324 in >> > /gpfs/fs1/aero/SOFTWARE/TOOLS/PROGRAMMING/petsc/src/ksp/ksp/example >> > s/t >> > utorials/ex10.c >> > >> > FYI, the transpose solve is a typical application for adjoint >> > optimization. There should be a big adjoint community of developers >> > that try to solve the transposed matrix. >> > >> > Any help is much appreciated, >> > Best, >> > Antoine >> > >> > >> > Antoine DeBlois >> > Specialiste ingenierie, MDO lead / Engineering Specialist, MDO lead >> > Aéronautique / Aerospace 514-855-5001, x 50862 >> > [email protected]<mailto:[email protected] >> > bar >> > dier.com> >> > >> > 2351 Blvd Alfred-Nobel >> > Montreal, Qc >> > H4S 1A9 >> > >> > [Description : Description : >> > http://signatures.ca.aero.bombardier.net/eom_logo_164x39_fr.jpg] >> > CONFIDENTIALITY NOTICE - This communication may contain privileged >> > or confidential information. >> > If you are not the intended recipient or received this >> > communication by error, please notify the sender and delete the >> > message without copying > >
