###################=- Blues Job 1386940.bmgt1.lcrc.anl.gov -=##################### Job ID: 1386940.bmgt1.lcrc.anl.gov User ID: zhaox Group ID: collab Job Name: ex01_validation_test Resources: neednodes=1:ppn=16,nodes=1:ppn=16,size=16,walltime=02:00:00 Queue: msd Account: nano-soft-assembly ########################################################## ------------------------------------------------------------------ ----------------------- Iterative solver ------------------------- --------------------------------------------------------------------- The program starts. The current date/time is: Tue Jun 7 15:22:01 2016 --------------------------------------------------------------------- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### The mesh and geometric info: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nx_mesh = 60, Lx = 30, hx = 0.5 ny_mesh = 60, Ly = 30, hy = 0.5 nz_mesh = 60, Lz = 30, hz = 0.5 fluid mesh size: hmin = 0.5, hmax = 0.5 the smoothing parameter in GGEM alpha = 1.2 alpha*hmax = 0.6 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### The Stokes solver info: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Stokes solver type = field_split FieldSplit Schur Complement Reduction Solver schur_pc_type = SMp user defined KSP is used for Schur Complement! KSP rel tolerance for Schur Complement solver is = 1e-09 KSP abs tolerance for Schur Complement solver is = 1e-06 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### The physical parameters in the simulation: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - viscosity mu = 4.33e-14 (cP = N*s/um^2) kBT = 4.1e-15 (N*um = N*um) number of springs Ns = 20 number of beads Nb = 21 Kuhn length bk = 0.106 (um) # of Kuhn segment per spring Nks = 19.8 Radius of the bead a = 0.077 (um) maximum spring length q0 = 2.0988 (um) chain length of polymer Lc = 41.976 (um) bead diffusivity Db = 0.0652385 (um^2/s) chain diffusivity Dc = 0.0031066 (um^2/s) Ss2 = 0.0370788 (um^2) HI Drag coefficient zeta = 6*PI*mu*a = 6.28463e-14 (N*s/um) ksi = sqrt(PI)/(3a) = 7.67296 Excluded volume parameter ev = 0.0012 (um^3) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### The characteristic variables: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - characteristic time = 0.0908819 (s) characteristic velocity = 0.847254 (m/s) characteristic force = 5.32468e-14 (N) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### The non-dimensional variables: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - non-dimensional bead radius a0 = 1 non-dimensional Kuhn length bk/a = 1.37662 non-dimensional spring length q0/a = 27.2571 non-dimensional contour length Lc/a = 545.143 non-dimensional Ss/a = sqrt(Ss2/a^2) = 2.50076 non-dimensional ksi = sqrt(PI)/(3a0) = 0.590818 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### Create finite element mesh: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Mesh Information: elem_dimensions()={3} spatial_dimension()=3 n_nodes()=896761 n_local_nodes()=116667 n_elem()=216000 n_local_elem()=27000 n_active_elem()=216000 n_subdomains()=1 n_partitions()=8 n_processors()=8 n_threads()=1 processor_id()=0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### Create periodic box, Polymer chain(s) and point-mesh: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ###point data filename = random_points_file.txt Reading point data from random_points_file.txt is completed! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### The point-mesh info: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Total number of particles: 100 search_radius_p = 3.33333, search_radius_e = 3.58333 Periodic BC in x-y-z directions: FALSE FALSE FALSE ###Equation systems are initialized: EquationSystems n_systems()=1 System #0, "Stokes" Type "LinearImplicit" Variables={ "u" "v" "w" } "p" Finite Element Types="LAGRANGE", "JACOBI_20_00" "LAGRANGE", "JACOBI_20_00" Infinite Element Mapping="CARTESIAN" "CARTESIAN" Approximation Orders="SECOND", "THIRD" "FIRST", "THIRD" n_dofs()=2917264 n_local_dofs()=379922 n_constrained_dofs()=0 n_local_constrained_dofs()=0 n_vectors()=1 n_matrices()=2 DofMap Sparsity Average On-Processor Bandwidth <= 192.246 Average Off-Processor Bandwidth <= 6.10606 Maximum On-Processor Bandwidth <= 332 Maximum Off-Processor Bandwidth <= 263 DofMap Constraints Number of DoF Constraints = 0 Number of Node Constraints = 0 System has: 216000 elements, 896761 nodes, 2917264 degrees of freedom. 2917264 active degrees of freedom. 100 point particles. --------------------------------------------------------------------- --->TEST reinit particle mesh: --------------------------------------------------------------------- --------------------------------------------------------------------- --->reinit_system(): step 1: reinit the PointMesh object --------------------------------------------------------------------- --------------------------------------------------------------------- --->reinit_system(): step 2: reinit the ForceField object --------------------------------------------------------------------- --------------------------------------------------------------------- --->test in PMLinearImplicitSystem::test_velocity_profile(): --------------------------------------------------------------------- --------------------------------------------------------------------- --->reinit_system(): step 1: reinit the PointMesh object --------------------------------------------------------------------- --------------------------------------------------------------------- --->reinit_system(): step 2: reinit the ForceField object --------------------------------------------------------------------- assemble_global_K(): Start to assemble the global matrix K ... --->test in PMLinearImplicitSystem::assemble_matrix(): Initialize the preconditioning matrix (all zeros) *** Warning, This code is deprecated, and likely to be removed in future library versions! /home/zhaox/software/libmesh/libmesh-dbg-3.7/include/libmesh/type_vector.h, line 878, compiled Jun 3 2016 at 14:41:50 *** assemble_matrix_K(): The global matrix K has been assembled ... --->test in StokesSolver::init_ksp_solver(): Start to initialize the PETSc KSP solver... StokesSolver: Indices Sets are built! StokesSolver: Approximate Schur matrix is computed! StokesSolver: PC for Schur complement is set up! --->test in StokesSolver::init_ksp_solver(): the PETSc KSP solver is initialized assemble_global_F(): Start to assemble the global force vector F ... assemble_global_F(): The global RHS vector has been assembled ... --->test in StokesSolver::solve(): Start the KSP solve... =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 23903 RUNNING AT b461 = EXIT CODE: 9 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions ##############=- Blues Job Resource Usage -=############## Job ID: 1386940.bmgt1.lcrc.anl.gov User ID: zhaox Group ID: collab Job Name: ex01_validation_test Session ID: 23801 Resources: neednodes=1:ppn=16,nodes=1:ppn=16,size=16,walltime=02:00:00 Resources Used: cput=00:48:07,mem=9512kb,vmem=76628kb,walltime=00:06:05 Queue: msd Account: nano-soft-assembly ##########################################################