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Created May 26, 2014 08:29
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simon@doodson ~/src/da-applications/ohta_kawasaki$ py ohta_kawasaki.py
Passing options to PETSc: -ok_snes_monitor -ok_ksp_converged_reason -ok_ksp_type tfqmr -ok_ksp_monitor -ok_ksp_rtol 1.0e-10 -ok_pc_type fieldsplit -ok_pc_fieldsplit_type schur -ok_pc_fieldsplit_schur_factorization_type lower -ok_pc_fieldsplit_schur_precondition self -ok_fieldsplit_0_ksp_type preonly -ok_fieldsplit_0_ksp_max_it 1 -ok_fieldsplit_0_pc_type ilu -ok_fieldsplit_1_ksp_type richardson -ok_fieldsplit_1_ksp_max_it 1 -ok_fieldsplit_1_pc_type mat -ok_fieldsplit_1_hats_pc_type ilu -ok_fieldsplit_1_hats_pc_mg_log -ok_fieldsplit_1_hats_pc_mg_monitor -ok_fieldsplit_1_hats_ksp_type preonly -ok_fieldsplit_1_hats_ksp_max_it 1 -ok_fieldsplit_0_pc_ml_maxCoarseSize 1024 -ok_fieldsplit_1_hats_pc_ml_maxCoarseSize 1024 -ok_fieldsplit_0_pc_ml_DampingFactor 1.5 -ok_fieldsplit_1_hats_pc_ml_DampingFactor 1.5 -ok_fieldsplit_0_pc_hypre_boomeramg_agg_nl 3 -ok_fieldsplit_1_hats_pc_hypre_boomeramg_agg_nl 3 -ok_fieldsplit_1_hats_pc_hypre_boomeramg_strong_threshold 1.0 -ok_fieldsplit_0_pc_hypre_boomeramg_strong_threshold 1.0
Degrees of freedom: 18818
0 SNES Function norm 3.611689825271e-03
Residual norms for ok_ solve.
0 KSP Residual norm 1.326477161665e+01
1 KSP Residual norm 9.249130055509e+00
1 KSP Residual norm 1.053006656777e+01
2 KSP Residual norm 3.405998246119e+00
2 KSP Residual norm 1.563476323264e+00
3 KSP Residual norm 5.368958878041e-01
3 KSP Residual norm 3.911824500664e-01
4 KSP Residual norm 1.478419243839e-01
4 KSP Residual norm 1.128659306022e-01
5 KSP Residual norm 2.400350589409e-02
5 KSP Residual norm 9.103062076229e-03
6 KSP Residual norm 6.046125411097e-03
6 KSP Residual norm 8.479070929962e-03
7 KSP Residual norm 3.026186753032e-03
7 KSP Residual norm 3.724853372024e-04
8 KSP Residual norm 6.434533589289e-05
8 KSP Residual norm 2.280076807845e-05
9 KSP Residual norm 8.687335358618e-06
9 KSP Residual norm 7.276435828839e-06
10 KSP Residual norm 1.708842116445e-06
10 KSP Residual norm 6.960866955402e-07
11 KSP Residual norm 4.139047283282e-07
11 KSP Residual norm 5.501002665778e-07
12 KSP Residual norm 2.178727305753e-07
12 KSP Residual norm 8.278851000855e-08
13 KSP Residual norm 1.112359094420e-08
13 KSP Residual norm 2.934658183403e-09
14 KSP Residual norm 9.417385920097e-10
Linear solve converged due to CONVERGED_RTOL iterations 14
1 SNES Function norm 1.110517424500e-12
0 SNES Function norm 3.346382533808e-05
Residual norms for ok_ solve.
0 KSP Residual norm 5.048267087623e-01
1 KSP Residual norm 2.225279527182e-01
1 KSP Residual norm 1.510470785917e-01
2 KSP Residual norm 3.060546290394e-02
2 KSP Residual norm 1.143301726421e-02
3 KSP Residual norm 2.489384048203e-03
3 KSP Residual norm 1.097514750052e-03
4 KSP Residual norm 4.509230309178e-04
4 KSP Residual norm 4.082869632580e-04
5 KSP Residual norm 1.006922162578e-04
5 KSP Residual norm 4.154554458570e-05
6 KSP Residual norm 8.514707650667e-06
6 KSP Residual norm 3.488217716686e-06
7 KSP Residual norm 1.371378776314e-06
7 KSP Residual norm 1.183482701641e-06
8 KSP Residual norm 2.460704855933e-07
8 KSP Residual norm 8.598672386071e-08
9 KSP Residual norm 3.259022462420e-08
9 KSP Residual norm 2.714488449112e-08
10 KSP Residual norm 5.201242100107e-09
10 KSP Residual norm 1.691892343573e-09
11 KSP Residual norm 7.232516417000e-10
11 KSP Residual norm 6.954429691973e-10
12 KSP Residual norm 1.589694106888e-10
12 KSP Residual norm 5.753066861860e-11
13 KSP Residual norm 2.733950253509e-11
Linear solve converged due to CONVERGED_RTOL iterations 13
1 SNES Function norm 2.721861652329e-14
0 SNES Function norm 4.277311650969e-06
Residual norms for ok_ solve.
0 KSP Residual norm 3.752684670038e-02
1 KSP Residual norm 1.499433510008e-02
1 KSP Residual norm 9.105610787717e-03
2 KSP Residual norm 2.292354961402e-03
2 KSP Residual norm 1.120168155518e-03
3 KSP Residual norm 5.228468047094e-04
3 KSP Residual norm 5.466190320661e-04
4 KSP Residual norm 9.093968964901e-05
4 KSP Residual norm 2.127394455873e-05
5 KSP Residual norm 1.501159983518e-05
5 KSP Residual norm 2.122941808224e-05
6 KSP Residual norm 1.407687833831e-05
6 KSP Residual norm 6.543263044051e-07
7 KSP Residual norm 4.313436449491e-07
7 KSP Residual norm 6.040833443462e-07
8 KSP Residual norm 1.845332599648e-07
8 KSP Residual norm 1.922564074386e-08
9 KSP Residual norm 1.170107231356e-08
9 KSP Residual norm 1.584150126828e-08
10 KSP Residual norm 3.336570240955e-09
10 KSP Residual norm 4.438266818144e-10
11 KSP Residual norm 2.340743479808e-10
11 KSP Residual norm 2.841657303079e-10
12 KSP Residual norm 5.589082916809e-11
12 KSP Residual norm 1.207936624283e-11
13 KSP Residual norm 5.099765868671e-12
13 KSP Residual norm 4.874163757336e-12
14 KSP Residual norm 1.104874110165e-12
Linear solve converged due to CONVERGED_RTOL iterations 14
1 SNES Function norm 2.134230205036e-15
Summary of timings | Average time Total time Reps
------------------------------------------------------------------
Apply (PETScMatrix) | 0.00028129 0.0016878 6
Apply (PETScVector) | 6.7438e-06 0.00014162 21
Assemble cells | 0.0081341 0.10574 13
Build mesh number mesh entities | 2.3842e-07 9.5367e-07 4
Build sparsity | 0.0048287 0.019315 4
Delete sparsity | 2.3842e-07 9.5367e-07 4
HDF5: reorder vertex values | 0.00056493 0.0011299 2
HDF5: write mesh to file | 0.022324 0.022324 1
Init PETSc | 6.8903e-05 6.8903e-05 1
Init dof vector | 0.00011051 0.00022101 2
Init dofmap | 0.0073786 0.014757 2
Init dofmap from UFC dofmap | 0.0014535 0.0058141 4
Init tensor | 0.00021625 0.00086498 4
Nonlinear solver | 0.079767 0.2393 3
SCOTCH graph ordering | 0.00074446 0.0014889 2
SNES solver init | 0.038136 0.038136 1
************************************************************************************************************************
*** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document ***
************************************************************************************************************************
---------------------------------------------- PETSc Performance Summary: ----------------------------------------------
ohta_kawasaki.py on a linux-gnu-c-opt named doodson with 1 processor, by simon Mon May 26 10:28:31 2014
Using Petsc Development GIT revision: v3.4.4-4222-g1475bf8 GIT Date: 2014-05-17 20:34:47 -0500
Max Max/Min Avg Total
Time (sec): 1.024e+00 1.00000 1.024e+00
Objects: 4.560e+02 1.00000 4.560e+02
Flops: 1.924e+08 1.00000 1.924e+08 1.924e+08
Flops/sec: 1.878e+08 1.00000 1.878e+08 1.878e+08
MPI Messages: 0.000e+00 0.00000 0.000e+00 0.000e+00
MPI Message Lengths: 6.000e+00 1.00000 0.000e+00 6.000e+00
MPI Reductions: 2.000e+00 1.00000
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 flops
and VecAXPY() for complex vectors of length N --> 8N flops
Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages --- -- Message Lengths -- -- Reductions --
Avg %Total Avg %Total counts %Total Avg %Total counts %Total
0: Main Stage: 1.0241e+00 100.0% 1.9238e+08 100.0% 0.000e+00 0.0% 0.000e+00 100.0% 2.000e+00 100.0%
------------------------------------------------------------------------------------------------------------------------
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 Flops: Max - maximum over all processors
Ratio - ratio of maximum to minimum over all processors
Mess: number of messages sent
Avg. len: 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 flops 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 flops over all processors)/(max time over all processors)
------------------------------------------------------------------------------------------------------------------------
Event Count Time (sec) Flops --- Global --- --- Stage --- Total
Max Ratio Max Ratio Max Ratio Mess Avg len Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s
------------------------------------------------------------------------------------------------------------------------
--- Event Stage 0: Main Stage
VecDot 82 1.0 1.5438e-03 1.0 3.09e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 2 0 0 0 0 2 0 0 0 1999
VecNorm 217 1.0 2.0602e-03 1.0 4.97e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 3 0 0 0 0 3 0 0 0 2411
VecScale 170 1.0 6.5279e-04 1.0 1.60e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 2450
VecCopy 109 1.0 8.5068e-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
VecSet 963 1.0 3.8204e-03 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
VecAXPY 243 1.0 2.8632e-03 1.0 7.55e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 2636
VecAYPX 164 1.0 2.7502e-03 1.0 3.66e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 2 0 0 0 0 2 0 0 0 1331
VecWAXPY 161 1.0 3.3581e-03 1.0 5.23e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 3 0 0 0 0 3 0 0 0 1558
VecAssemblyBegin 21 1.0 5.5552e-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
VecAssemblyEnd 21 1.0 1.1206e-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
VecScatterBegin 361 1.0 3.6452e-03 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
VecReduceArith 9 1.0 1.3709e-04 1.0 3.39e+05 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 2471
VecReduceComm 3 1.0 9.5367e-07 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
MatMult 422 1.0 1.1538e-01 1.0 1.56e+08 1.0 0.0e+00 0.0e+00 0.0e+00 11 81 0 0 0 11 81 0 0 0 1349
MatMultAdd 85 1.0 5.7476e-03 1.0 1.11e+07 1.0 0.0e+00 0.0e+00 0.0e+00 1 6 0 0 0 1 6 0 0 0 1925
MatSolve 510 1.0 4.9381e-02 1.0 6.16e+07 1.0 0.0e+00 0.0e+00 0.0e+00 5 32 0 0 0 5 32 0 0 0 1247
MatLUFactorNum 4 1.0 2.1012e-03 1.0 8.13e+05 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 387
MatILUFactorSym 2 1.0 6.3992e-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
MatAssemblyBegin 20 1.0 6.6757e-06 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
MatAssemblyEnd 20 1.0 3.2511e-03 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
MatGetRowIJ 2 1.0 9.5367e-07 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
MatGetSubMatrice 14 1.0 6.7933e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0
MatGetOrdering 2 1.0 9.5844e-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
MatZeroEntries 6 1.0 1.3545e-03 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
PCSetUp 8 1.0 1.5697e-02 1.0 8.13e+05 1.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 52
PCApply 85 1.0 1.1876e-01 1.0 1.32e+08 1.0 0.0e+00 0.0e+00 0.0e+00 12 69 0 0 0 12 69 0 0 0 1110
KSPSetUp 10 1.0 2.2483e-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
KSPSolve 3 1.0 1.6266e-01 1.0 1.92e+08 1.0 0.0e+00 0.0e+00 0.0e+00 16100 0 0 0 16100 0 0 0 1178
SNESSolve 3 1.0 2.3882e-01 1.0 1.92e+08 1.0 0.0e+00 0.0e+00 0.0e+00 23100 0 0 0 23100 0 0 0 805
SNESFunctionEval 6 1.0 3.1412e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 3 0 0 0 0 3 0 0 0 0 0
SNESJacobianEval 3 1.0 4.3391e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 4 0 0 0 0 4 0 0 0 0 0
SNESLineSearch 3 1.0 1.6145e-02 1.0 3.95e+05 1.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 24
------------------------------------------------------------------------------------------------------------------------
Memory usage is given in bytes:
Object Type Creations Destructions Memory Descendants' Mem.
Reports information only for process 0.
--- Event Stage 0: Main Stage
Viewer 1 0 0 0
Index Set 24 24 320096 0
IS L to G Mapping 3 3 1788 0
Vector 385 385 29625944 0
Vector Scatter 5 5 3260 0
Matrix 13 13 17763332 0
Preconditioner 6 6 5896 0
Krylov Solver 6 6 7312 0
DMKSP interface 1 1 664 0
SNES 1 1 1348 0
SNESLineSearch 1 1 872 0
DMSNES 1 1 680 0
Distributed Mesh 3 3 13392 0
Star Forest Bipartite Graph 6 6 4896 0
========================================================================================================================
Average time to get PetscTime(): 9.53674e-08
#PETSc Option Table entries:
-log_summary
-ok_fieldsplit_0_ksp_max_it 1
-ok_fieldsplit_0_ksp_type preonly
-ok_fieldsplit_0_pc_hypre_boomeramg_agg_nl 3
-ok_fieldsplit_0_pc_hypre_boomeramg_strong_threshold 1.0
-ok_fieldsplit_0_pc_ml_DampingFactor 1.5
-ok_fieldsplit_0_pc_ml_maxCoarseSize 1024
-ok_fieldsplit_0_pc_type ilu
-ok_fieldsplit_1_hats_ksp_max_it 1
-ok_fieldsplit_1_hats_ksp_type preonly
-ok_fieldsplit_1_hats_pc_hypre_boomeramg_agg_nl 3
-ok_fieldsplit_1_hats_pc_hypre_boomeramg_strong_threshold 1.0
-ok_fieldsplit_1_hats_pc_mg_log
-ok_fieldsplit_1_hats_pc_mg_monitor
-ok_fieldsplit_1_hats_pc_ml_DampingFactor 1.5
-ok_fieldsplit_1_hats_pc_ml_maxCoarseSize 1024
-ok_fieldsplit_1_hats_pc_type ilu
-ok_fieldsplit_1_ksp_max_it 1
-ok_fieldsplit_1_ksp_type richardson
-ok_fieldsplit_1_pc_type mat
-ok_ksp_converged_reason
-ok_ksp_monitor
-ok_ksp_rtol 1.0e-10
-ok_ksp_type tfqmr
-ok_pc_fieldsplit_schur_factorization_type lower
-ok_pc_fieldsplit_schur_precondition self
-ok_pc_fieldsplit_type schur
-ok_pc_type fieldsplit
-ok_snes_monitor
#End of 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: --CXX_LINKER_FLAGS=-Wl,--no-as-needed --useThreads --with-blacs-include=/usr/include --with-blacs-lib="[/usr/lib/libblacsCinit-openmpi.so,/usr/lib/libblacs-openmpi.so]" --with-blacs=1 --with-blas-lib=-lblas --with-c-support --with-suitesparse=0 --with-clanguage=C++ --with-debugging=0 --with-fftw-include=/usr/include --with-fftw-lib="[/usr/lib/x86_64-linux-gnu/libfftw3.so,/usr/lib/x86_64-linux-gnu/libfftw3_mpi.so]" --with-fftw=1 --with-fortran-interfaces=1 --with-hdf5-dir=/usr --with-hdf5=1 --with-hypre=0 --with-lapack-lib=-llapack --with-ml=0 --with-mpi-dir=/usr/lib/openmpi --with-mumps-include=/usr/include --with-mumps-lib="[/usr/lib/libdmumps.so,/usr/lib/libzmumps.so,/usr/lib/libsmumps.so,/usr/lib/libcmumps.so,/usr/lib/libmumps_common.so,/usr/lib/libpord.so]" --with-mumps=1 --with-ptscotch-include=/usr/include/scotch --with-ptscotch-lib="[/usr/lib/libptesmumps.so,/usr/lib/libptscotch.so,/usr/lib/libptscotcherr.so]" --with-ptscotch=1 --with-scalapack-include=/usr/include --with-scalapack-lib=/usr/lib/libscalapack-openmpi.so --with-scalapack=1 --with-shared-libraries --with-spooles-include=/usr/include/spooles --with-spooles-lib=/usr/lib/libspooles.so --with-spooles=1 --with-vtk-include=/usr/include/vtk-5.8 --with-vtk=1 PETSC_ARCH=linux-gnu-c-opt --with-spai=1 --download-spai=yes --with-log=1
-----------------------------------------
Libraries compiled on Sat May 24 13:29:40 2014 on doodson
Machine characteristics: Linux-3.13.0-24-generic-x86_64-with-Ubuntu-14.04-trusty
Using PETSc directory: /home/simon/src/fenics/petsc_trunk
Using PETSc arch: linux-gnu-c-opt
-----------------------------------------
Using C compiler: mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O -fPIC ${COPTFLAGS} ${CFLAGS}
Using Fortran compiler: mpif90 -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -O ${FOPTFLAGS} ${FFLAGS}
-----------------------------------------
Using include paths: -I/home/simon/src/fenics/petsc_trunk/linux-gnu-c-opt/include -I/home/simon/src/fenics/petsc_trunk/include -I/home/simon/src/fenics/petsc_trunk/include -I/home/simon/src/fenics/petsc_trunk/linux-gnu-c-opt/include -I/usr/include -I/usr/include/scotch -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi
-----------------------------------------
Using C linker: mpicxx
Using Fortran linker: mpif90
Using libraries: -Wl,-rpath,/home/simon/src/fenics/petsc_trunk/linux-gnu-c-opt/lib -L/home/simon/src/fenics/petsc_trunk/linux-gnu-c-opt/lib -lpetsc -Wl,-rpath,/usr/lib -L/usr/lib -ldmumps -lzmumps -lsmumps -lcmumps -lmumps_common -lpord -lscalapack-openmpi -Wl,-rpath,/home/simon/src/fenics/petsc_trunk/linux-gnu-c-opt/lib -L/home/simon/src/fenics/petsc_trunk/linux-gnu-c-opt/lib -lspai -llapack -lblas -lX11 -lpthread -lptesmumps -lptscotch -lptscotcherr -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -lfftw3 -lfftw3_mpi -lssl -lcrypto -lhdf5_fortran -lhdf5_hl -lhdf5 -lm -Wl,-rpath,/usr/lib/openmpi/lib -L/usr/lib/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lmpi_f90 -lmpi_f77 -lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpi_cxx -lstdc++ -ldl -lmpi -lhwloc -lgcc_s -lpthread -ldl
---------------------------------------
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