You are doing a spectrum slicing run (EPSSetInterval) with “size” partitions (EPSKrylovSchurSetPartitions), so every single process will be in charge of computing a subinterval. Each subcommunicator needs a redundant copy of the matrix, and in this case this copy is SeqAIJ since subcommunicators consist in just one process. You will probably need to share this memory across a set of processes and use MUMPS for the factorization. Try setting e.g. size/8 partitions.
Jose > El 29/8/2015, a las 1:14, Barry Smith <[email protected]> escribió: > > > It is using a SeqAIJ matrix, not a parallel matrix. Increasing the number of > cores won't affect the size of a sequential matrix since it must be stored > entirely on one process. Perhaps you need to use parallel matrices? > > > [1]PETSC ERROR: #4 MatDuplicate_SeqAIJ() line 4103 in > /home1/apps/intel15/mvapich2_2_1/petsc/3.6/src/mat/impls/aij/seq/aij.c > [1]PETSC ERROR: #5 MatDuplicate() line 4252 in > /home1/apps/intel15/mvapich2_2_1/petsc/3.6/src/mat/interface/matrix.c > > >> On Aug 28, 2015, at 4:13 PM, Hank Lamm <[email protected]> wrote: >> >> Hi All, >> >> I am having a problem running Petsc3.6 and Slepc3.6 on Stampede. My code >> should be a simple eigenvalue solver, but when I attempt to solve large >> problems (8488x8488 matrices) I get errors: >> >> --------------------- Error Message >> -------------------------------------------------------------- >> [1]Total space allocated 1736835920 bytes >> [1]PETSC ERROR: Out of memory. This could be due to allocating >> [1]PETSC ERROR: too large an object or bleeding by not properly >> [1]PETSC ERROR: destroying unneeded objects. >> [1]PETSC ERROR: Memory allocated 1736835920 Memory used by process 1769742336 >> [1]PETSC ERROR: [0]PETSC ERROR: Memory requested 864587796 >> [1]PETSC ERROR: [0]PETSC ERROR: See >> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. >> [1]PETSC ERROR: #8 STSetUp() line 305 in >> /work/03324/hlammiv/slepc-3.6.0/src/sys/classes/st/interface/stsolve.c >> [1]PETSC ERROR: [0]PETSC ERROR: #1 MatDuplicateNoCreate_SeqAIJ() line 4030 >> in /home1/apps/intel15/mvapich2_2_1/petsc/3.6/src/mat/impls/aij/seq/aij.c >> [1]PETSC ERROR: #2 PetscTrMallocDefault() line 188 in >> /home1/apps/intel15/mvapich2_2_1/petsc/3.6/src/sys/memory/mtr.c >> [1]PETSC ERROR: #4 MatDuplicate_SeqAIJ() line 4103 in >> /home1/apps/intel15/mvapich2_2_1/petsc/3.6/src/mat/impls/aij/seq/aij.c >> [1]PETSC ERROR: #5 MatDuplicate() line 4252 in >> /home1/apps/intel15/mvapich2_2_1/petsc/3.6/src/mat/interface/matrix.c >> [1]PETSC ERROR: #6 STMatMAXPY_Private() line 379 in >> /work/03324/hlammiv/slepc-3.6.0/src/sys/classes/st/interface/stsolve.c >> [1]PETSC ERROR: #7 STSetUp_Sinvert() line 131 in >> /work/03324/hlammiv/slepc-3.6.0/src/sys/classes/st/impls/sinvert/sinvert.c >> [1]PETSC ERROR: #8 STSetUp() line 305 in >> /work/03324/hlammiv/slepc-3.6.0/src/sys/classes/st/interface/stsolve.c >> [1]PETSC ERROR: #9 EPSSliceGetInertia() line 295 in >> /work/03324/hlammiv/slepc-3.6.0/src/eps/impls/krylov/krylovschur/ks-slice.c >> [1]PETSC ERROR: #10 EPSSetUp_KrylovSchur_Slice() line 425 in >> /work/03324/hlammiv/slepc-3.6.0/src/eps/impls/krylov/krylovschur/ks-slice.c >> [1]PETSC ERROR: #11 EPSSetUp_KrylovSchur() line 89 in >> /work/03324/hlammiv/slepc-3.6.0/src/eps/impls/krylov/krylovschur/krylovschur.c >> [1]PETSC ERROR: #12 EPSSetUp() line 121 in >> /work/03324/hlammiv/slepc-3.6.0/src/eps/interface/epssetup.c >> [1]PETSC ERROR: #13 EPSSliceGetEPS() line 267 in >> /work/03324/hlammiv/slepc-3.6.0/src/eps/impls/krylov/krylovschur/ks-slice.c >> [1]PETSC ERROR: #14 EPSSetUp_KrylovSchur_Slice() line 368 in >> /work/03324/hlammiv/slepc-3.6.0/src/eps/impls/krylov/krylovschur/ks-slice.c >> [1]PETSC ERROR: #15 EPSSetUp_KrylovSchur() line 89 in >> /work/03324/hlammiv/slepc-3.6.0/src/eps/impls/krylov/krylovschur/krylovschur.c >> [1]PETSC ERROR: #16 EPSSetUp() line 121 in >> /work/03324/hlammiv/slepc-3.6.0/src/eps/interface/epssetup.c >> [1]PETSC ERROR: #17 EPSSolve() line 88 in >> /work/03324/hlammiv/slepc-3.6.0/src/eps/interface/epssolve.c >> [1]PETSC ERROR: #18 eigensolver() line 64 in >> /work/03324/hlammiv/TMSWIFT/src/solver.cpp >> [1]Current space PetscMalloc()ed 1.73683e+09, max space PetscMalloced() >> 1.73684e+09 >> [1]Current process memory 1.76979e+09 max process memory 1.76979e+09 >> >> >> The curious thing about this error, is that it seems that if I increase the >> number of nodes, from 32 to 64 to 128, the amount of memory per node doesn't >> decrease. I have used valgrind and it doesn't seem to a memory leak. >> >> The relevant code piece is: >> >> void eigensolver(PetscErrorCode ierr, params *params, Mat &H, int argc, char >> **argv) >> { >> >> >> EPS eps; /* eigenproblem solver context */ >> EPSType type; >> ST st; >> KSP ksp; >> PC pc; >> PetscReal tol,error; >> PetscReal lower,upper; >> //PetscInt nev=dim,maxit,its; >> PetscInt nev,maxit,its,nconv; >> Vec xr,xi; >> PetscScalar kr,ki; >> PetscReal re,im; >> PetscViewer viewer; >> PetscInt rank; >> PetscInt size; >> std::string eig_file_n; >> std::ofstream eig_file; >> char ofile[100]; >> >> MPI_Comm_rank(PETSC_COMM_WORLD,&rank); >> MPI_Comm_size(PETSC_COMM_WORLD,&size); >> >> ierr = PetscPrintf(PETSC_COMM_WORLD,"---Beginning Eigenvalue >> Solver---\n");CHKERRV(ierr); >> ierr = EPSCreate(PETSC_COMM_WORLD,&eps);CHKERRV(ierr); >> >> eig_file_n.append(params->ofile_n); >> eig_file_n.append("_eval"); >> eig_file.open(eig_file_n.c_str(),std::ofstream::trunc); >> >> //Set operators. In this case, it is a standard eigenvalue problem >> ierr = EPSSetOperators(eps,H,NULL);CHKERRV(ierr); >> ierr = EPSSetProblemType(eps,EPS_HEP);CHKERRV(ierr); >> >> ierr = EPSSetType(eps,EPSKRYLOVSCHUR);CHKERRV(ierr); >> >> ierr = EPSGetST(eps,&st);CHKERRV(ierr); >> ierr = STSetType(st,STSINVERT);CHKERRV(ierr); >> >> ierr = STGetKSP(st,&ksp);CHKERRV(ierr); >> ierr = KSPSetType(ksp,KSPPREONLY);CHKERRV(ierr); >> ierr = KSPGetPC(ksp,&pc);CHKERRV(ierr); >> ierr = PCSetType(pc,PCCHOLESKY);CHKERRV(ierr); >> ierr = EPSKrylovSchurSetPartitions(eps,size);CHKERRV(ierr); >> >> for(PetscInt i=0;i<params->nf;i++){ >> >> lower=std::pow(2.0*params->m[i]-params->m[i]*params->alpha*params->alpha,2.0); >> upper=4.0*params->m[i]*params->m[i]; >> ierr = EPSSetInterval(eps,lower,upper); >> ierr = EPSSetWhichEigenpairs(eps,EPS_ALL); >> //Set solver parameters at runtime >> ierr = EPSSetFromOptions(eps);CHKERRV(ierr); >> // ierr = EPSSetWhichEigenpairs(eps,EPS_SMALLEST_REAL); >> >> ierr = MatCreateVecs(H,NULL,&xr);CHKERRV(ierr); >> ierr = MatCreateVecs(H,NULL,&xi);CHKERRV(ierr); >> >> >> ierr = EPSSolve(eps);CHKERRV(ierr); >> >> ierr = EPSGetIterationNumber(eps,&its);CHKERRV(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD," Number of iterations of the >> method: %D\n",its);CHKERRV(ierr); >> >> >> //Optional: Get some information from the solver and display it >> ierr = EPSGetType(eps,&type);CHKERRV(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD," Solution method: >> %s\n\n",type);CHKERRV(ierr); >> ierr = EPSGetDimensions(eps,&nev,NULL,NULL);CHKERRV(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD," Number of requested eigenvalues: >> %D\n",nev);CHKERRV(ierr); >> ierr = EPSGetTolerances(eps,&tol,&maxit);CHKERRV(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD," Stopping condition: tol=%.4g, >> maxit=%D\n",tol,maxit);CHKERRV(ierr); >> >> ierr = EPSGetConverged(eps,&nconv);CHKERRV(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD," Number of converged eigenpairs: >> %D\n\n",nconv);CHKERRV(ierr); >> >> strcpy(ofile,params->ofile_n); >> strcat(ofile,"_evecr"); >> >> ierr = >> PetscViewerASCIIOpen(PETSC_COMM_WORLD,ofile,&viewer);CHKERRV(ierr); >> >> if (nconv>0) >> { >> ierr = PetscPrintf(PETSC_COMM_WORLD, >> " k ||Ax-kx||/||kx||\n" >> " ----------------- ------------------\n");CHKERRV(ierr); >> >> for (PetscInt i=0;i<nconv;i++) >> { >> //Get converged eigenpairs: i-th eigenvalue is stored in kr (real >> part) and ki (imaginary part) >> ierr = EPSGetEigenpair(eps,i,&kr,&ki,xr,xi);CHKERRV(ierr); >> //Compute the relative error associated to each eigenpair >> ierr = >> EPSComputeError(eps,i,EPS_ERROR_RELATIVE,&error);CHKERRV(ierr); >> >> #if defined(PETSC_USE_COMPLEX) >> re = PetscRealPart(kr); >> im = PetscImaginaryPart(kr); >> #else >> re = kr; >> im = ki; >> #endif >> >> if (im!=0.0) >> { >> >> ierr = PetscPrintf(PETSC_COMM_WORLD," %9f%+9f j >> %12g\n",re,im,error);CHKERRV(ierr); >> if(rank==0) eig_file << re << " " << im << " " << error << >> std::endl; >> } else >> { >> ierr = PetscPrintf(PETSC_COMM_WORLD," %12f >> %12g\n",re,error);CHKERRV(ierr); >> if(rank==0) eig_file << re << " " << 0 << " " << error << >> std::endl; >> } >> >> ierr = VecView(xr,viewer);CHKERRV(ierr); >> >> } >> ierr = PetscPrintf(PETSC_COMM_WORLD,"\n");CHKERRV(ierr); >> } >> } >> eig_file.close(); >> ierr = EPSDestroy(&eps);CHKERRV(ierr); >> ierr = PetscViewerDestroy(&viewer);CHKERRV(ierr); >> ierr = VecDestroy(&xr);CHKERRV(ierr); >> ierr = VecDestroy(&xi);CHKERRV(ierr); >> >> ierr = PetscPrintf(PETSC_COMM_WORLD,"---Finishing Eigenvalue >> Solver---\n");CHKERRV(ierr); >> } >> >> >> >> Thanks, >> Hank >
