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
