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
