Starting Xolotl Plasma-Surface Interactions Simulator Fri Aug 28 15:40:46 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 = 3.998453355656088e-08 Deuterium content = 1.799754050011278e-07 Tritium content = 1.799799241815265e-07 Vacancy content = 5.183275479630833e-86 Interstitial content = 1.085277712412299e-09 Fluence = 4e-07 2 TS dt 9.33506e-12 time 2.87486e-12 Time: 2.874863371648933e-12 Helium content = 1.148666308125159e-07 Deuterium content = 5.172716233423786e-07 Tritium content = 5.17309064862937e-07 Vacancy content = 7.529087673238805e-79 Interstitial content = 2.794423493510334e-09 Fluence = 1.149945348659573e-06 3 TS dt 8.31605e-11 time 1.22099e-11 Time: 1.220992231427955e-11 Helium content = 4.860946003548312e-07 Deuterium content = 2.194114458139551e-06 Tritium content = 2.194788782571064e-06 Vacancy content = 5.88846442845581e-68 Interstitial content = 8.661671344256942e-09 Fluence = 4.883968925711822e-06 4 TS dt 8.31605e-10 time 9.53705e-11 Time: 9.537046345911179e-11 Helium content = 3.678429468697813e-06 Deuterium content = 1.694343578854218e-05 Tritium content = 1.698409072971427e-05 Vacancy content = 8.199076747767878e-53 Interstitial content = 3.117599405335611e-08 Fluence = 3.814818538364472e-05 5 TS dt 8.31605e-09 time 9.26976e-10 Time: 9.269758749074341e-10 Helium content = 2.704843186609527e-05 Deuterium content = 0.0001480489510446246 Tritium content = 0.0001511966396747453 Vacancy content = 3.17763401489997e-37 Interstitial content = 4.785787897242143e-08 Fluence = 0.0003707903499629736 6 TS dt 3.67778e-08 time 9.24303e-09 Time: 9.243029989390658e-09 Helium content = 5.981804087746346e-05 Deuterium content = 0.0006649926823889447 Tritium content = 0.0007604993902267464 Vacancy content = -2.440075099058014e-26 Interstitial content = 4.586783835841149e-08 Fluence = 0.003697211995756263 7 TS dt 1.70247e-07 time 4.60208e-08 Time: 4.602082733157514e-08 Helium content = 5.608817965934341e-05 Deuterium content = 0.0007228336282560409 Tritium content = 0.000892435974583055 Vacancy content = 2.800714813815969e-23 Interstitial content = 4.592624813261854e-08 Fluence = 0.01840833093263006 8 TS dt 1.26255e-06 time 2.16268e-07 Time: 2.162675511088579e-07 Helium content = 5.636705290898551e-05 Deuterium content = 0.0007160168831708334 Tritium content = 0.0008767183714606261 Vacancy content = 7.196478669185629e-20 Interstitial content = 4.592583806232926e-08 Fluence = 0.08650702044354315 9 TS dt 1.26255e-05 time 1.47882e-06 Time: 1.47881741173335e-06 Helium content = 5.636169192941323e-05 Deuterium content = 0.0007163310946872647 Tritium content = 0.0008775850103291917 Vacancy content = 5.852389689608021e-17 Interstitial content = 4.59258386244094e-08 Fluence = 0.5915269646933402 10 TS dt 0.000126255 time 1.41043e-05 Time: 1.410431601797827e-05 Helium content = 5.63616933608036e-05 Deuterium content = 0.000716330972295392 Tritium content = 0.0008775829798637923 Vacancy content = 1.928147214843122e-15 Interstitial content = 4.592583862447052e-08 Fluence = 5.641726407191309 ************************************************************************************************************************ *** 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 15:46:04 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): 1.188e+02 1.000 1.188e+02 Objects: 1.410e+02 1.000 1.410e+02 Flop: 1.048e+09 1.049 1.031e+09 4.124e+09 Flop/sec: 8.821e+06 1.049 8.683e+06 3.473e+07 MPI Messages: 8.510e+02 1.522 7.050e+02 2.820e+03 MPI Message Lengths: 2.433e+07 1.947 2.611e+04 7.364e+07 MPI Reductions: 8.000e+02 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: 1.1876e+02 100.0% 4.1244e+09 100.0% 2.820e+03 100.0% 2.611e+04 100.0% 7.930e+02 99.1% ------------------------------------------------------------------------------------------------------------------------ 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 127 1.0 5.4117e+01364.6 0.00e+00 0.0 3.6e+01 4.0e+00 1.3e+02 15 0 1 0 16 15 0 1 0 16 0 BuildTwoSidedF 119 1.0 5.4117e+01364.3 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+02 15 0 0 0 15 15 0 0 0 15 0 DMCreateMat 1 1.0 2.3224e-01 1.0 0.00e+00 0.0 1.2e+01 3.6e+01 8.0e+00 0 0 0 0 1 0 0 0 0 1 0 SFSetGraph 8 1.0 6.0344e-05 1.0 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 8 1.0 9.8374e-04 1.1 0.00e+00 0.0 7.2e+01 7.6e+01 8.0e+00 0 0 3 0 1 0 0 3 0 1 0 SFBcastOpBegin 604 1.0 5.5006e-02 1.1 0.00e+00 0.0 2.7e+03 2.7e+04 0.0e+00 0 0 94 97 0 0 0 94 97 0 0 SFBcastOpEnd 604 1.0 6.1392e-0117.8 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 SFReduceBegin 160 1.0 1.4311e-02 1.3 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 SFReduceEnd 160 1.0 1.6915e-04 1.4 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 764 1.0 9.4400e-0346.5 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 764 1.0 4.2959e-0337.5 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 40 1.0 1.1605e-02 1.2 4.92e+06 1.0 0.0e+00 0.0e+00 4.0e+01 0 0 0 0 5 0 0 0 0 5 1696 VecMDot 40 1.0 1.0304e-02 1.0 4.92e+06 1.0 0.0e+00 0.0e+00 4.0e+01 0 0 0 0 5 0 0 0 0 5 1910 VecNorm 186 1.0 2.9879e+0046.0 2.29e+07 1.0 0.0e+00 0.0e+00 1.9e+02 1 2 0 0 23 1 2 0 0 23 31 VecScale 206 1.0 8.0727e-03 1.7 5.54e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 2747 VecCopy 202 1.0 3.1186e-02 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 542 1.0 1.3831e-02 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 VecAXPY 40 1.0 7.3390e-03 1.8 4.92e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 2682 VecAYPX 80 1.0 8.1422e-03 1.1 4.92e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 2418 VecAXPBYCZ 100 1.0 3.7710e-02 1.3 1.85e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 2 0 0 0 0 2 0 0 0 1958 VecWAXPY 40 1.0 1.1588e-02 1.0 2.46e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 849 VecMAXPY 160 1.0 3.9864e-02 1.1 3.44e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 3 0 0 0 0 3 0 0 0 3457 VecScatterBegin 764 1.0 7.0007e-02 1.1 0.00e+00 0.0 2.7e+03 2.7e+04 0.0e+00 0 0 94 97 0 0 0 94 97 0 0 VecScatterEnd 764 1.0 6.1507e-0117.4 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 80 1.0 1.1059e-02 1.1 9.84e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 3560 VecReduceComm 40 1.0 7.3553e-0323.5 0.00e+00 0.0 0.0e+00 0.0e+00 4.0e+01 0 0 0 0 5 0 0 0 0 5 0 VecNormalize 80 1.0 1.8563e-02 1.1 1.48e+07 1.0 0.0e+00 0.0e+00 8.0e+01 0 1 0 0 10 0 1 0 0 10 3181 TSStep 10 1.0 1.1845e+02 1.0 1.05e+09 1.0 2.8e+03 2.6e+04 6.5e+02100100100100 81 100100100100 82 35 TSFunctionEval 80 1.0 6.4416e+00 1.8 4.92e+06 1.0 4.8e+02 9.8e+04 0.0e+00 5 0 17 64 0 5 0 17 64 0 3 TSJacobianEval 40 1.0 1.0902e+02 1.0 1.67e+08 1.4 2.4e+02 9.8e+04 4.0e+01 92 15 9 32 5 92 15 9 32 5 6 SNESSolve 30 1.0 1.1772e+02 1.0 1.02e+09 1.1 2.7e+03 2.5e+04 6.2e+02 99 97 97 92 78 99 97 97 92 79 34 SNESSetUp 1 1.0 2.3252e-01 1.0 0.00e+00 0.0 1.2e+01 3.6e+01 1.0e+01 0 0 0 0 1 0 0 0 0 1 0 SNESFunctionEval 70 1.0 5.6662e+00 1.8 1.72e+07 1.0 4.2e+02 9.8e+04 0.0e+00 4 2 15 56 0 4 2 15 56 0 12 SNESJacobianEval 40 1.0 1.0902e+02 1.0 1.67e+08 1.4 2.4e+02 9.8e+04 4.0e+01 92 15 9 32 5 92 15 9 32 5 6 SNESLineSearch 40 1.0 3.5682e+00 1.0 1.99e+08 1.0 4.8e+02 4.9e+04 1.6e+02 3 19 17 32 20 3 19 17 32 20 223 MatMult 160 1.0 8.6618e-01 1.2 4.22e+08 1.0 9.6e+02 1.4e+02 0.0e+00 1 41 34 0 0 1 41 34 0 0 1949 MatSolve 80 1.0 2.4229e-03 1.0 2.17e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 3581 MatSOR 80 1.0 1.1120e+00 1.1 3.32e+08 1.0 0.0e+00 0.0e+00 0.0e+00 1 32 0 0 0 1 32 0 0 0 1193 MatLUFactorSym 1 1.0 2.1282e-04 1.0 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 MatLUFactorNum 40 1.0 1.1040e-02 1.1 1.14e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 4124 MatCopy 39 1.0 1.2534e-04 1.3 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 MatConvert 1 1.0 1.9312e-05 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 MatScale 40 1.0 3.2254e-01 1.0 8.23e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 8 0 0 0 0 8 0 0 0 1021 MatAssemblyBegin 324 1.0 5.4119e+01360.6 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+02 15 0 0 0 15 15 0 0 0 15 0 MatAssemblyEnd 324 1.0 5.3798e-03 1.0 0.00e+00 0.0 3.6e+01 3.6e+01 1.5e+01 0 0 1 0 2 0 0 1 0 2 0 MatGetRowIJ 1 1.0 1.4130e-05 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 MatCreateSubMats 40 1.0 1.0297e-02 5.3 0.00e+00 0.0 0.0e+00 0.0e+00 4.3e+01 0 0 0 0 5 0 0 0 0 5 0 MatCreateSubMat 80 1.0 5.8790e-01 1.0 0.00e+00 0.0 4.8e+01 8.6e+01 1.0e+02 0 0 2 0 13 0 0 2 0 13 0 MatGetOrdering 1 1.0 1.1928e-04 1.0 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 MatZeroEntries 40 1.0 1.5298e-01 1.0 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 MatRedundantMat 40 1.0 1.0710e-02 4.5 0.00e+00 0.0 0.0e+00 0.0e+00 4.3e+01 0 0 0 0 5 0 0 0 0 5 0 MatMPIConcateSeq 40 1.0 1.7883e-04 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 KSPSetUp 160 1.0 6.2801e-04 2.5 0.00e+00 0.0 0.0e+00 0.0e+00 1.0e+01 0 0 0 0 1 0 0 0 0 1 0 KSPSolve 40 1.0 2.2788e+00 1.0 6.39e+08 1.0 1.8e+03 1.5e+03 4.0e+02 2 62 65 4 49 2 62 65 4 50 1123 KSPGMRESOrthog 40 1.0 1.7794e-02 1.1 9.84e+06 1.0 0.0e+00 0.0e+00 4.0e+01 0 1 0 0 5 0 1 0 0 5 2212 PCSetUp 120 1.0 6.2884e-01 1.0 1.14e+07 1.0 1.6e+02 1.3e+04 2.6e+02 1 1 6 3 33 1 1 6 3 33 72 PCApply 80 1.0 1.3403e+00 1.0 4.43e+08 1.0 1.5e+03 4.8e+02 6.3e+01 1 43 54 1 8 1 43 54 1 8 1322 KSPSolve_FS_0 80 1.0 1.1169e+00 1.1 3.32e+08 1.0 0.0e+00 0.0e+00 0.0e+00 1 32 0 0 0 1 32 0 0 0 1188 KSPSolve_FS_1 80 1.0 3.2080e-02 1.5 1.36e+07 1.0 1.0e+03 6.4e+02 6.3e+01 0 1 37 1 8 0 1 37 1 8 1690 ------------------------------------------------------------------------------------------------------------------------ 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 31 31 282924 0. IS L to G Mapping 1 1 708 0. Star Forest Graph 12 12 13344 0. Discrete System 2 2 1920 0. Vec Scatter 8 8 6528 0. Vector 53 53 17028544 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 4 4 22904 0. DMKSP interface 1 1 664 0. Matrix 14 14 36300856 0. Preconditioner 4 4 3960 0. Viewer 1 0 0 0. ======================================================================================================================== Average time to get PetscTime(): 3.99e-08 Average time for MPI_Barrier(): 1.0242e-06 Average time for zero size MPI_Send(): 1.6415e-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: 2.753409014999998 max: 5.608755317999998 average: 4.643186591499999 stdev: 1.16397305514639 name: Partial Derivatives process_count: 4 min: 52.42340589499997 max: 103.594970247 average: 87.42253989125001 stdev: 20.93637460508896 name: RHSFunctionTimer process_count: 4 min: 3.481893305999999 max: 6.432799519 average: 5.486161613249999 stdev: 1.20606437014616 name: RHSJacobianTimer process_count: 4 min: 108.440422635 max: 108.440765729 average: 108.440608359 stdev: 0.0001449835906141654 name: SolveTimer process_count: 4 min: 118.630885263 max: 118.640783686 average: 118.63561294775 stdev: 0.003589092694791343 name: monitor1D:checkNeg process_count: 4 min: 0 max: 0 average: 0 stdev: 0 name: monitor1D:event process_count: 4 min: 0.000238582 max: 0.0002488880000000001 average: 0.0002434565 stdev: 3.909336868317932e-06 name: monitor1D:heRet process_count: 4 min: 0.171773307 max: 0.173038982 average: 0.172093411 stdev: 0.0005459390859497897 name: monitor1D:init process_count: 4 min: 0.000391785 max: 0.00062706 average: 0.00045116375 stdev: 0.0001015550578587178 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: 160 max: 400 average: 320 stdev: 97.97958971132712 name: Partial Derivatives process_count: 4 min: 80 max: 200 average: 160 stdev: 48.98979485566356 HardwareCounters: