Starting Xolotl Plasma-Surface Interactions Simulator Fri Aug 28 15:52:54 2020 Loaded network of size 12302. -1 -0.5 0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5 5.5 6 6.5 7 7.5 8 8.5 0 TS dt 1e-12 time 0. Time: 0 Helium content = 0 Deuterium content = 0 Tritium content = 0 Vacancy content = 0 Interstitial content = 0 Fluence = 0 1 TS dt 1.87486e-12 time 1e-12 Time: 1e-12 Helium content = 3.998268973002881e-08 Deuterium content = 1.799760296381141e-07 Tritium content = 1.799814376083755e-07 Vacancy content = 5.54221024241515e-86 Interstitial content = 1.076083851388208e-09 Fluence = 4e-07 2 TS dt 9.33506e-12 time 2.87486e-12 Time: 2.874863371692955e-12 Helium content = 1.148621169190103e-07 Deuterium content = 5.172733926277329e-07 Tritium content = 5.173129029911139e-07 Vacancy content = 4.658476854195309e-78 Interstitial content = 2.786274004228506e-09 Fluence = 1.149945348677182e-06 3 TS dt 8.31605e-11 time 1.22099e-11 Time: 1.220992231043647e-11 Helium content = 4.860866926971022e-07 Deuterium content = 2.194127143629604e-06 Tritium content = 2.194804298858191e-06 Vacancy content = 2.239663947526481e-63 Interstitial content = 8.661082643970004e-09 Fluence = 4.883968924174588e-06 4 TS dt 8.31605e-10 time 9.53705e-11 Time: 9.537046352538632e-11 Helium content = 3.678776568415282e-06 Deuterium content = 1.69451969981092e-05 Tritium content = 1.698554014545955e-05 Vacancy content = -3.419344797889238e-49 Interstitial content = 3.117542829612831e-08 Fluence = 3.814818541015453e-05 5 TS dt 8.31605e-09 time 9.26976e-10 Time: 9.269758756748847e-10 Helium content = 2.707166607834261e-05 Deuterium content = 0.0001480748666772199 Tritium content = 0.0001512025198850674 Vacancy content = 1.874072027347334e-35 Interstitial content = 4.784869796591994e-08 Fluence = 0.0003707903502699539 6 TS dt 3.67703e-08 time 9.24303e-09 Time: 9.243029997169868e-09 Helium content = 5.981727029232682e-05 Deuterium content = 0.0006649850032406357 Tritium content = 0.0007604914245556196 Vacancy content = 1.242134501693808e-25 Interstitial content = 4.587227649229742e-08 Fluence = 0.003697211998867947 7 TS dt 1.70705e-07 time 4.60134e-08 Time: 4.601337569781458e-08 Helium content = 5.608141577731466e-05 Deuterium content = 0.0007229862566200205 Tritium content = 0.0008927171367993695 Vacancy content = 8.821578752783583e-23 Interstitial content = 4.592631030278966e-08 Fluence = 0.01840535027912583 8 TS dt 1.27967e-06 time 2.16718e-07 Time: 2.167182119912474e-07 Helium content = 5.636796729822405e-05 Deuterium content = 0.0007159591775982223 Tritium content = 0.0008765901992898002 Vacancy content = 6.163530024811232e-21 Interstitial content = 4.592588203947602e-08 Fluence = 0.08668728479649895 9 TS dt 1.27967e-05 time 1.49639e-06 Time: 1.496391882028352e-06 Helium content = 5.636167377621148e-05 Deuterium content = 0.0007163342298980516 Tritium content = 0.0008775936745554613 Vacancy content = 6.76351397219519e-20 Interstitial content = 4.592586036660697e-08 Fluence = 0.5985567528113409 10 TS dt 0.000127967 time 1.42931e-05 Time: 1.42931285823994e-05 Helium content = 5.636170958070677e-05 Deuterium content = 0.0007163283813925675 Tritium content = 0.0008775743701864409 Vacancy content = 1.378329880888954e-19 Interstitial content = 4.592586130914882e-08 Fluence = 5.717251432959761 ************************************************************************************************************************ *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document *** ************************************************************************************************************************ ---------------------------------------------- PETSc Performance Summary: ---------------------------------------------- Unknown Name on a 20200828 named sophie-Precision-5530 with 4 processors, by sophie Fri Aug 28 16:47:41 2020 Using Petsc Development GIT revision: v3.13.4-851-gde18fec8da GIT Date: 2020-08-28 16:47:50 +0000 Max Max/Min Avg Total Time (sec): 3.091e+03 1.000 3.091e+03 Objects: 9.100e+01 1.000 9.100e+01 Flop: 1.625e+11 1.000 1.625e+11 6.501e+11 Flop/sec: 5.258e+07 1.000 5.258e+07 2.103e+08 MPI Messages: 7.187e+04 2.000 5.390e+04 2.156e+05 MPI Message Lengths: 7.073e+09 2.000 9.842e+04 2.122e+10 MPI Reductions: 7.206e+04 1.000 Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract) e.g., VecAXPY() for real vectors of length N --> 2N flop and VecAXPY() for complex vectors of length N --> 8N flop Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages --- -- Message Lengths -- -- Reductions -- Avg %Total Avg %Total Count %Total Avg %Total Count %Total 0: Main Stage: 3.0909e+03 100.0% 6.5013e+11 100.0% 2.156e+05 100.0% 9.842e+04 100.0% 7.205e+04 100.0% ------------------------------------------------------------------------------------------------------------------------ See the 'Profiling' chapter of the users' manual for details on interpreting output. Phase summary info: Count: number of times phase was executed Time and Flop: Max - maximum over all processors Ratio - ratio of maximum to minimum over all processors Mess: number of messages sent AvgLen: average message length (bytes) Reduct: number of global reductions Global: entire computation Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop(). %T - percent time in this phase %F - percent flop in this phase %M - percent messages in this phase %L - percent message lengths in this phase %R - percent reductions in this phase Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over all processors) ------------------------------------------------------------------------------------------------------------------------ Event Count Time (sec) Flop --- Global --- --- Stage ---- Total Max Ratio Max Ratio Max Ratio Mess AvgLen Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s ------------------------------------------------------------------------------------------------------------------------ --- Event Stage 0: Main Stage BuildTwoSided 1 1.0 1.8411e-05 1.7 0.00e+00 0.0 6.0e+00 4.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 0 SFSetGraph 1 1.0 4.2300e-07 1.8 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 SFSetUp 1 1.0 3.7780e-05 1.2 0.00e+00 0.0 1.2e+01 4.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 0 SFBcastOpBegin 35933 1.0 1.0361e+01 1.4 0.00e+00 0.0 2.2e+05 9.8e+04 0.0e+00 0 0100100 0 0 0100100 0 0 SFBcastOpEnd 35933 1.0 6.3830e+00 3.1 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 SFPack 35933 1.0 1.5615e+00285.6 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 SFUnpack 35933 1.0 1.1998e+00183.6 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecDot 47 1.0 1.9313e+00273.0 5.78e+06 1.0 0.0e+00 0.0e+00 4.7e+01 0 0 0 0 0 0 0 0 0 0 12 VecMDot 34677 1.0 1.5005e+0321.7 6.57e+10 1.0 0.0e+00 0.0e+00 3.5e+04 17 40 0 0 48 17 40 0 0 48 175 VecNorm 37045 1.0 6.0632e+01 8.0 4.56e+09 1.0 0.0e+00 0.0e+00 3.7e+04 1 3 0 0 51 1 3 0 0 51 301 VecScale 107594 1.0 4.0805e+00 1.3 4.41e+09 1.0 0.0e+00 0.0e+00 0.0e+00 0 3 0 0 0 0 3 0 0 0 4324 VecCopy 37244 1.0 1.5880e+00 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecSet 37200 1.0 1.6951e+00 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecAXPY 38137 1.0 3.9457e+00 1.3 4.69e+09 1.0 0.0e+00 0.0e+00 0.0e+00 0 3 0 0 0 0 3 0 0 0 4757 VecAYPX 35933 1.0 3.9184e+00 1.2 2.21e+09 1.0 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 2256 VecAXPBYCZ 35953 1.0 1.4487e+01 1.1 6.63e+09 1.0 0.0e+00 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 1832 VecWAXPY 35893 1.0 1.1341e+01 1.2 4.41e+09 1.0 0.0e+00 0.0e+00 0.0e+00 0 3 0 0 0 0 3 0 0 0 1556 VecMAXPY 35926 1.0 7.5672e+01 1.1 6.99e+10 1.0 0.0e+00 0.0e+00 0.0e+00 2 43 0 0 0 2 43 0 0 0 3697 VecScatterBegin 35933 1.0 1.0453e+01 1.4 0.00e+00 0.0 2.2e+05 9.8e+04 0.0e+00 0 0100100 0 0 0100100 0 0 VecScatterEnd 35933 1.0 6.4492e+00 3.1 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecReduceArith 94 1.0 1.2670e-02 1.1 1.16e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 3651 VecReduceComm 47 1.0 5.5436e-0229.3 0.00e+00 0.0 0.0e+00 0.0e+00 4.7e+01 0 0 0 0 0 0 0 0 0 0 0 VecNormalize 35846 1.0 5.7913e+01 6.1 6.61e+09 1.0 0.0e+00 0.0e+00 3.6e+04 1 4 0 0 50 1 4 0 0 50 457 TSStep 10 1.0 3.0906e+03 1.0 1.63e+11 1.0 2.2e+05 9.8e+04 7.2e+04100100100100100 100100100100100 210 TSFunctionEval 35933 1.0 2.9025e+03 2.0 2.21e+09 1.0 2.2e+05 9.8e+04 0.0e+00 79 1100100 0 79 1100100 0 3 SNESSolve 30 1.0 3.0901e+03 1.0 1.63e+11 1.0 2.2e+05 9.8e+04 7.2e+04100100100100100 100100100100100 210 SNESSetUp 1 1.0 3.0985e-04 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 4.0e+00 0 0 0 0 0 0 0 0 0 0 0 SNESFunctionEval 35923 1.0 2.9163e+03 2.0 8.84e+09 1.0 2.2e+05 9.8e+04 0.0e+00 79 5100100 0 79 5100100 0 12 SNESJacobianEval 47 1.0 7.7553e-03 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 4.0e+00 0 0 0 0 0 0 0 0 0 0 0 SNESLineSearch 47 1.0 7.8849e+00 1.0 6.93e+07 1.0 5.6e+02 9.8e+04 1.9e+02 0 0 0 0 0 0 0 0 0 0 35 MatMult MF 35846 1.0 2.9273e+03 2.0 2.00e+10 1.0 2.2e+05 9.8e+04 1.1e+03 80 12100100 2 80 12100100 2 27 MatMult 35846 1.0 2.9274e+03 2.0 2.00e+10 1.0 2.2e+05 9.8e+04 1.1e+03 80 12100100 2 80 12100100 2 27 MatAssemblyBegin 47 1.0 7.9460e-06 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatAssemblyEnd 47 1.0 7.5770e-03 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 4.0e+00 0 0 0 0 0 0 0 0 0 0 0 KSPSetUp 47 1.0 1.0295e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 1.0e+01 0 0 0 0 0 0 0 0 0 0 0 KSPSolve 47 1.0 3.0794e+03 1.0 1.62e+11 1.0 2.1e+05 9.8e+04 7.2e+04100100100100 99 100100100100 99 211 KSPGMRESOrthog 34677 1.0 1.5676e+0311.2 1.31e+11 1.0 0.0e+00 0.0e+00 3.5e+04 19 81 0 0 48 19 81 0 0 48 335 PCSetUp 47 1.0 1.0055e-05 1.9 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 PCApply 35846 1.0 1.4963e+00 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 ------------------------------------------------------------------------------------------------------------------------ Memory usage is given in bytes: Object Type Creations Destructions Memory Descendants' Mem. Reports information only for process 0. --- Event Stage 0: Main Stage Distributed Mesh 2 2 10636 0. Index Set 4 4 3628 0. IS L to G Mapping 1 1 708 0. Star Forest Graph 5 5 5392 0. Discrete System 2 2 1920 0. Vec Scatter 1 1 816 0. Vector 62 62 28844704 0. TSAdapt 1 1 1272 0. TS 1 1 2480 0. DMTS 1 1 768 0. SNES 1 1 1412 0. DMSNES 3 3 2040 0. SNESLineSearch 1 1 1008 0. Krylov Solver 1 1 18656 0. DMKSP interface 1 1 664 0. MatMFFD 1 1 752 0. Matrix 1 1 3080 0. Preconditioner 1 1 1120 0. Viewer 1 0 0 0. ======================================================================================================================== Average time to get PetscTime(): 4.35e-08 Average time for MPI_Barrier(): 1.3176e-06 Average time for zero size MPI_Send(): 2.5725e-06 #No PETSc Option Table entries Compiled without FORTRAN kernels Compiled with full precision matrices (default) sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 sizeof(PetscScalar) 8 sizeof(PetscInt) 4 Configure options: PETSC_DIR=/home/sophie/Code/petsc PETSC_ARCH=20200828 --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif77 --with-debugging=no --with-shared-libraries ----------------------------------------- Libraries compiled on 2020-08-28 19:04:45 on sophie-Precision-5530 Machine characteristics: Linux-5.4.0-42-generic-x86_64-with-glibc2.29 Using PETSc directory: /home/sophie/Code/petsc Using PETSc arch: 20200828 ----------------------------------------- Using C compiler: mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O Using Fortran compiler: mpif77 -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O ----------------------------------------- Using include paths: -I/home/sophie/Code/petsc/include -I/home/sophie/Code/petsc/20200828/include ----------------------------------------- Using C linker: mpicc Using Fortran linker: mpif77 Using libraries: -Wl,-rpath,/home/sophie/Code/petsc/20200828/lib -L/home/sophie/Code/petsc/20200828/lib -lpetsc -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -llapack -lblas -lX11 -lm -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl ----------------------------------------- Timers: name: Flux process_count: 4 min: 1314.986373829005 max: 2710.160338506994 average: 2269.130352842237 stdev: 564.8118469801432 name: Partial Derivatives process_count: 4 min: 0 max: 0 average: 0 stdev: 0 name: RHSFunctionTimer process_count: 4 min: 1421.154035243007 max: 2898.291923265016 average: 2434.779431158001 stdev: 603.2482947852172 name: RHSJacobianTimer process_count: 4 min: 0 max: 0 average: 0 stdev: 0 name: SolveTimer process_count: 4 min: 3090.769498707 max: 3090.776894364 average: 3090.77344393525 stdev: 0.002733325756942514 name: monitor1D:checkNeg process_count: 4 min: 0 max: 0 average: 0 stdev: 0 name: monitor1D:event process_count: 4 min: 0.000265262 max: 0.000280984 average: 0.00027393375 stdev: 5.619976618056686e-06 name: monitor1D:heRet process_count: 4 min: 0.163278166 max: 0.164602271 average: 0.163611881 stdev: 0.0005718095422132117 name: monitor1D:init process_count: 4 min: 0.000323421 max: 0.00048071 average: 0.000363009 stdev: 6.795505535646326e-05 name: monitor1D:postEvent process_count: 4 min: 0 max: 0 average: 0 stdev: 0 name: monitor1D:scatter process_count: 4 min: 0 max: 0 average: 0 stdev: 0 name: monitor1D:series process_count: 4 min: 0 max: 0 average: 0 stdev: 0 name: monitor1D:startStop process_count: 4 min: 0 max: 0 average: 0 stdev: 0 name: monitor1D:tridyn process_count: 4 min: 0 max: 0 average: 0 stdev: 0 name: monitor1D:xeRet process_count: 4 min: 0 max: 0 average: 0 stdev: 0 Counters: name: Flux process_count: 4 min: 71866 max: 179665 average: 143732 stdev: 44008.75746371397 name: Partial Derivatives process_count: 4 min: 0 max: 0 average: 0 stdev: 0 HardwareCounters: