[petsc-users] Recommended solver and preconditioner to solve Poisson eqn on win7
Zhenglun (Alan) Wei
zhenglun.wei at gmail.com
Fri Sep 14 18:08:37 CDT 2012
I'm sorry about that. I attached the output files here with '
-ksp_monitor -ksp_view -log_summary'. They are named after the grid size
and pc-type.
cheers,
Alan
On 9/14/2012 5:51 PM, Jed Brown wrote:
> On Fri, Sep 14, 2012 at 5:49 PM, Matthew Knepley <knepley at gmail.com
> <mailto:knepley at gmail.com>> wrote:
>
> On Fri, Sep 14, 2012 at 5:40 PM, Zhenglun (Alan) Wei
> <zhenglun.wei at gmail.com <mailto:zhenglun.wei at gmail.com>> wrote:
>
> Dear folks,
> I did some test with -pc_type gamg with
> /src/ksp/ksp/example/tutorial/ex45.c. It is not as good as
> default -pc_type when my mesh (Cartisian) is 100*50*50; while
> it is a little bit better than the default one when the mesh
> is 200*100*100. Therefore, I guess this type of pc is good for
> larger problem. Is that ture? or is there any rule of thumb
> for this type of preconditioner? BTW, I tested it with 8
> processes.
>
>
> When asking questions about convergence, always always ALWAYS send
> the output of -ksp_monitor -ksp_view. If
> you don't, we are just guessing blindly.
>
>
> And -log_summary because this is about performance.
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0 KSP Residual norm 1.669256249193e+02
1 KSP Residual norm 3.874064408589e+01
2 KSP Residual norm 1.954600014030e+01
3 KSP Residual norm 1.244345922145e+01
4 KSP Residual norm 9.064420170785e+00
5 KSP Residual norm 7.275278824753e+00
6 KSP Residual norm 5.782414175300e+00
7 KSP Residual norm 4.677087789418e+00
8 KSP Residual norm 3.946201128884e+00
9 KSP Residual norm 3.420632944675e+00
10 KSP Residual norm 2.955422198070e+00
11 KSP Residual norm 2.592490394060e+00
12 KSP Residual norm 2.303387891861e+00
13 KSP Residual norm 2.056577525302e+00
14 KSP Residual norm 1.857163034085e+00
15 KSP Residual norm 1.677130693211e+00
16 KSP Residual norm 1.512895894610e+00
17 KSP Residual norm 1.372371861084e+00
18 KSP Residual norm 1.253935781302e+00
19 KSP Residual norm 1.147442107353e+00
20 KSP Residual norm 1.053519715486e+00
21 KSP Residual norm 9.698850093905e-01
22 KSP Residual norm 8.845629782375e-01
23 KSP Residual norm 7.865775890900e-01
24 KSP Residual norm 6.898777348204e-01
25 KSP Residual norm 6.049168916000e-01
26 KSP Residual norm 5.207655781898e-01
27 KSP Residual norm 4.358566752368e-01
28 KSP Residual norm 3.606652037110e-01
29 KSP Residual norm 2.945720874157e-01
30 KSP Residual norm 2.381008300123e-01
31 KSP Residual norm 2.101595975863e-01
32 KSP Residual norm 1.766392142763e-01
33 KSP Residual norm 1.458305208202e-01
34 KSP Residual norm 1.202168443895e-01
35 KSP Residual norm 9.934133007087e-02
36 KSP Residual norm 8.352384804046e-02
37 KSP Residual norm 7.134843832394e-02
38 KSP Residual norm 6.342135745158e-02
39 KSP Residual norm 5.838796270013e-02
40 KSP Residual norm 5.467571802684e-02
41 KSP Residual norm 5.125401049798e-02
42 KSP Residual norm 4.794972060697e-02
43 KSP Residual norm 4.492615630663e-02
44 KSP Residual norm 4.196741113595e-02
45 KSP Residual norm 3.892472635334e-02
46 KSP Residual norm 3.550920516488e-02
47 KSP Residual norm 3.195558023701e-02
48 KSP Residual norm 2.868405521348e-02
49 KSP Residual norm 2.587274813660e-02
50 KSP Residual norm 2.328392008646e-02
51 KSP Residual norm 2.107487668110e-02
52 KSP Residual norm 1.893796101150e-02
53 KSP Residual norm 1.648168199594e-02
54 KSP Residual norm 1.390814960805e-02
55 KSP Residual norm 1.135250892417e-02
56 KSP Residual norm 8.795176079893e-03
57 KSP Residual norm 6.603350000225e-03
58 KSP Residual norm 4.793743880387e-03
59 KSP Residual norm 3.160719306137e-03
60 KSP Residual norm 1.977784164249e-03
61 KSP Residual norm 1.468666200316e-03
62 KSP Residual norm 1.083389354485e-03
63 KSP Residual norm 8.520500282120e-04
64 KSP Residual norm 6.518964823622e-04
65 KSP Residual norm 5.138109780444e-04
66 KSP Residual norm 4.115277543760e-04
67 KSP Residual norm 3.361506034186e-04
68 KSP Residual norm 2.797128704246e-04
69 KSP Residual norm 2.415674178545e-04
70 KSP Residual norm 2.159180377331e-04
71 KSP Residual norm 1.977197186285e-04
72 KSP Residual norm 1.827136280528e-04
73 KSP Residual norm 1.669270522643e-04
74 KSP Residual norm 1.506437271409e-04
75 KSP Residual norm 1.353521734114e-04
76 KSP Residual norm 1.204344753199e-04
77 KSP Residual norm 1.070648089746e-04
78 KSP Residual norm 9.624021696680e-05
79 KSP Residual norm 8.762931970435e-05
80 KSP Residual norm 8.027844190242e-05
81 KSP Residual norm 7.405766359992e-05
82 KSP Residual norm 6.789476644149e-05
83 KSP Residual norm 6.150052082511e-05
84 KSP Residual norm 5.461716716910e-05
85 KSP Residual norm 4.773931323050e-05
86 KSP Residual norm 4.134556977071e-05
87 KSP Residual norm 3.578449180759e-05
88 KSP Residual norm 3.150018194966e-05
89 KSP Residual norm 2.810040239809e-05
90 KSP Residual norm 2.557532547531e-05
91 KSP Residual norm 2.381861052813e-05
92 KSP Residual norm 2.205833402284e-05
93 KSP Residual norm 2.030591797591e-05
94 KSP Residual norm 1.832395951111e-05
95 KSP Residual norm 1.628084367638e-05
KSP Object: 8 MPI processes
type: gmres
GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement
GMRES: happy breakdown tolerance 1e-30
maximum iterations=10000
tolerances: relative=1e-07, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using PRECONDITIONED norm type for convergence test
PC Object: 8 MPI processes
type: bjacobi
block Jacobi: number of blocks = 8
Local solve is same for all blocks, in the following KSP and PC objects:
KSP Object: (sub_) 1 MPI processes
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: (sub_) 1 MPI processes
type: ilu
ILU: out-of-place factorization
0 levels of fill
tolerance for zero pivot 2.22045e-14
using diagonal shift to prevent zero pivot
matrix ordering: natural
factor fill ratio given 1, needed 1
Factored matrix follows:
Matrix Object: 1 MPI processes
type: seqaij
rows=31250, cols=31250
package used to perform factorization: petsc
total: nonzeros=212500, allocated nonzeros=212500
total number of mallocs used during MatSetValues calls =0
not using I-node routines
linear system matrix = precond matrix:
Matrix Object: 1 MPI processes
type: seqaij
rows=31250, cols=31250
total: nonzeros=212500, allocated nonzeros=212500
total number of mallocs used during MatSetValues calls =0
not using I-node routines
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=250000, cols=250000
total: nonzeros=1725000, allocated nonzeros=1725000
total number of mallocs used during MatSetValues calls =0
Residual norm 4.4807e-07
************************************************************************************************************************
*** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document ***
************************************************************************************************************************
---------------------------------------------- PETSc Performance Summary: ----------------------------------------------
./ex45 on a arch-linux2-c-debug named compute-5-2.local with 8 processors, by zlwei Fri Sep 14 18:03:35 2012
Using Petsc Development HG revision: 98bf11863c3be31b7c2af504314a500bc64d88c9 HG Date: Wed Aug 29 13:51:08 2012 -0500
Max Max/Min Avg Total
Time (sec): 3.476e+00 1.00009 3.476e+00
Objects: 7.400e+01 1.00000 7.400e+01
Flops: 2.712e+08 1.00003 2.712e+08 2.170e+09
Flops/sec: 7.803e+07 1.00009 7.802e+07 6.242e+08
Memory: 1.770e+07 1.00000 1.416e+08
MPI Messages: 3.160e+02 1.01935 3.108e+02 2.486e+03
MPI Message Lengths: 2.500e+06 1.00001 8.045e+03 2.000e+07
MPI Reductions: 2.078e+03 1.00096
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: 3.4761e+00 100.0% 2.1698e+09 100.0% 2.486e+03 100.0% 8.045e+03 100.0% 2.075e+03 99.9%
------------------------------------------------------------------------------------------------------------------------
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
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)
------------------------------------------------------------------------------------------------------------------------
##########################################################
# #
# WARNING!!! #
# #
# This code was compiled with a debugging option, #
# To get timing results run ./configure #
# using --with-debugging=no, the performance will #
# be generally two or three times faster. #
# #
##########################################################
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
KSPGMRESOrthog 95 1.0 1.0751e+00 1.0 1.76e+08 1.0 0.0e+00 0.0e+00 1.5e+03 30 65 0 0 72 30 65 0 0 73 1312
KSPSetUp 2 1.0 7.6380e-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 1 1.0 3.4126e+00 1.0 2.71e+08 1.0 2.4e+03 8.2e+03 2.0e+03 98100 97 98 98 98100 97 98 98 635
VecMDot 95 1.0 4.9396e-01 1.1 8.81e+07 1.0 0.0e+00 0.0e+00 9.5e+01 14 32 0 0 5 14 32 0 0 5 1427
VecNorm 100 1.0 3.0509e-02 1.1 6.25e+06 1.0 0.0e+00 0.0e+00 1.0e+02 1 2 0 0 5 1 2 0 0 5 1639
VecScale 99 1.0 1.4340e-02 1.3 3.09e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 1726
VecCopy 4 1.0 2.5320e-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
VecSet 105 1.0 2.6484e-02 1.3 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
VecAXPY 8 1.0 2.3842e-03 1.0 5.00e+05 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 1678
VecMAXPY 99 1.0 4.3568e-01 1.0 9.41e+07 1.0 0.0e+00 0.0e+00 0.0e+00 12 35 0 0 0 12 35 0 0 0 1727
VecScatterBegin 99 1.0 1.7329e-02 1.4 0.00e+00 0.0 2.4e+03 8.3e+03 0.0e+00 0 0 96 99 0 0 0 96 99 0 0
VecScatterEnd 99 1.0 1.8952e-02 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
VecNormalize 99 1.0 4.7056e-02 1.1 9.28e+06 1.0 0.0e+00 0.0e+00 9.9e+01 1 3 0 0 5 1 3 0 0 5 1578
MatMult 99 1.0 5.4279e-01 1.0 3.96e+07 1.0 2.4e+03 8.3e+03 0.0e+00 15 15 96 99 0 15 15 96 99 0 584
MatSolve 99 1.0 3.6140e-01 1.0 3.90e+07 1.0 0.0e+00 0.0e+00 0.0e+00 10 14 0 0 0 10 14 0 0 0 863
MatLUFactorNum 1 1.0 1.4360e-02 1.0 6.12e+05 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 339
MatILUFactorSym 1 1.0 1.3215e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 0
MatAssemblyBegin 2 1.0 5.4438e-03 3.9 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
MatAssemblyEnd 2 1.0 1.1969e-02 1.0 0.00e+00 0.0 4.8e+01 2.1e+03 2.3e+01 0 0 2 1 1 0 0 2 1 1 0
MatGetRowIJ 1 1.0 7.1526e-06 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
MatGetOrdering 1 1.0 4.9279e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 2.0e+00 0 0 0 0 0 0 0 0 0 0 0
MatView 3 3.0 5.5695e-04 2.8 0.00e+00 0.0 0.0e+00 0.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 0
PCSetUp 2 1.0 3.4658e-02 1.0 6.12e+05 1.0 0.0e+00 0.0e+00 8.0e+00 1 0 0 0 0 1 0 0 0 0 140
PCSetUpOnBlocks 1 1.0 3.3920e-02 1.0 6.12e+05 1.0 0.0e+00 0.0e+00 4.0e+00 1 0 0 0 0 1 0 0 0 0 143
PCApply 99 1.0 5.7720e-01 1.0 3.90e+07 1.0 0.0e+00 0.0e+00 2.0e+02 16 14 0 0 10 16 14 0 0 10 540
------------------------------------------------------------------------------------------------------------------------
Memory usage is given in bytes:
Object Type Creations Destructions Memory Descendants' Mem.
Reports information only for process 0.
--- Event Stage 0: Main Stage
Container 1 1 548 0
Krylov Solver 2 2 19360 0
Vector 43 43 9339072 0
Vector Scatter 3 3 3108 0
Matrix 4 4 6660212 0
Distributed Mesh 2 2 285240 0
Bipartite Graph 4 4 2736 0
Index Set 10 10 282424 0
IS L to G Mapping 1 1 138468 0
Preconditioner 2 2 1784 0
Viewer 2 1 712 0
========================================================================================================================
Average time to get PetscTime(): 6.91414e-07
Average time for MPI_Barrier(): 0.000108814
Average time for zero size MPI_Send(): 2.01166e-05
#PETSc Option Table entries:
-ksp_monitor
-ksp_rtol 1.0e-7
-ksp_view
-log_summary
#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 run at: Wed Aug 29 14:54:25 2012
Configure options: --prefix=/work/zlwei/PETSc --with-cc=gcc --with-fc=gfortran --download-f-blas-lapack --download-mpich
-----------------------------------------
Libraries compiled on Wed Aug 29 14:54:25 2012 on firefox.bioinfo.ittc.ku.edu
Machine characteristics: Linux-2.6.18-92.1.13.el5-x86_64-with-redhat-5.2-Final
Using PETSc directory: /nfs/work/zlwei/PETSc/petsc-dev
Using PETSc arch: arch-linux2-c-debug
-----------------------------------------
Using C compiler: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -fno-inline -O0 ${COPTFLAGS} ${CFLAGS}
Using Fortran compiler: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpif90 -Wall -Wno-unused-variable -g ${FOPTFLAGS} ${FFLAGS}
-----------------------------------------
Using include paths: -I/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/include -I/nfs/work/zlwei/PETSc/petsc-dev/include -I/nfs/work/zlwei/PETSc/petsc-dev/include -I/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/include
-----------------------------------------
Using C linker: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpicc
Using Fortran linker: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpif90
Using libraries: -Wl,-rpath,/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -L/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -lpetsc -lX11 -lpthread -Wl,-rpath,/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -L/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -lflapack -lfblas -lm -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -lmpichf90 -lgfortran -lm -lm -ldl -lmpich -lopa -lmpl -lrt -lgcc_s -ldl
-----------------------------------------
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0 KSP Residual norm 1.875294504732e+02
1 KSP Residual norm 6.461816762057e+01
2 KSP Residual norm 3.470907566660e+01
3 KSP Residual norm 2.099089429528e+01
4 KSP Residual norm 1.437522110067e+01
5 KSP Residual norm 9.245678477105e+00
6 KSP Residual norm 5.901095748255e+00
7 KSP Residual norm 3.667568893250e+00
8 KSP Residual norm 2.100454200874e+00
9 KSP Residual norm 1.151109746641e+00
10 KSP Residual norm 6.512533958321e-01
11 KSP Residual norm 3.268299134386e-01
12 KSP Residual norm 1.338085587322e-01
13 KSP Residual norm 6.206661527722e-02
14 KSP Residual norm 3.045503185174e-02
15 KSP Residual norm 1.336637007228e-02
16 KSP Residual norm 5.597304881397e-03
17 KSP Residual norm 2.926115919013e-03
18 KSP Residual norm 1.931646953591e-03
19 KSP Residual norm 1.181176745071e-03
20 KSP Residual norm 6.854711612750e-04
21 KSP Residual norm 3.242234399228e-04
22 KSP Residual norm 1.402658814864e-04
23 KSP Residual norm 6.074816600231e-05
24 KSP Residual norm 3.055482416759e-05
25 KSP Residual norm 1.566477423228e-05
KSP Object: 8 MPI processes
type: gmres
GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement
GMRES: happy breakdown tolerance 1e-30
maximum iterations=10000
tolerances: relative=1e-07, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using PRECONDITIONED norm type for convergence test
PC Object: 8 MPI processes
type: gamg
MG: type is MULTIPLICATIVE, levels=5 cycles=v
Cycles per PCApply=1
Using Galerkin computed coarse grid matrices
Coarse grid solver -- level -------------------------------
KSP Object: (mg_coarse_) 8 MPI processes
type: gmres
GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement
GMRES: happy breakdown tolerance 1e-30
maximum iterations=1, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: (mg_coarse_) 8 MPI processes
type: bjacobi
block Jacobi: number of blocks = 8
Local solve info for each block is in the following KSP and PC objects:
[0] number of local blocks = 1, first local block number = 0
KSP Object: KSP Object: (mg_coarse_sub_) KSP Object: (mg_coarse_sub_) 1 MPI processes
type: preonly
[0] local block number 0
(mg_coarse_sub_) 1 MPI processes
type: preonly
1 MPI processes
maximum iterations=10000, initial guess is zero
KSP Object: (mg_coarse_sub_) 1 MPI processes
KSP Object: (mg_coarse_sub_) 1 MPI processes
type: preonly
KSP Object: (mg_coarse_sub_) 1 MPI processes
type: preonly
maximum iterations=10000, initial guess is zero
maximum iterations=10000, initial guess is zero
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: (mg_coarse_sub_) type: preonly
maximum iterations=10000, initial guess is zero
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: 1 MPI processes
type: lu
LU: out-of-place factorization
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: left preconditioning
using NONE norm type for convergence test
PC Object: (mg_coarse_sub_) (mg_coarse_sub_) 1 MPI processes
type: lu
LU: out-of-place factorization
(mg_coarse_sub_) 1 MPI processes
type: lu
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
factor fill ratio given 5, needed 0
Factored matrix follows:
(mg_coarse_sub_) 1 MPI processes
type: lu
1 MPI processes
type: lu
LU: out-of-place factorization
PC Object: (mg_coarse_sub_) 1 MPI processes
type: lu
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
factor fill ratio given 5, needed 0
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
Factored matrix follows:
factor fill ratio given 5, needed 0
Factored matrix follows:
Matrix Object: 1 MPI processes
type: seqaij
rows=0, cols=0
matrix ordering: nd
factor fill ratio given 5, needed 0
Factored matrix follows:
factor fill ratio given 5, needed 0
Factored matrix follows:
factor fill ratio given 5, needed 0
Factored matrix follows:
Matrix Object: Matrix Object: 1 MPI processes
type: seqaij
Matrix Object: 1 MPI processes
package used to perform factorization: petsc
Matrix Object: 1 MPI processes
Matrix Object: 1 MPI processes
1 MPI processes
type: seqaij
rows=0, cols=0
rows=0, cols=0
type: seqaij
rows=0, cols=0
total: nonzeros=1, allocated nonzeros=1
total number of mallocs used during MatSetValues calls =0
type: seqaij
rows=0, cols=0
type: seqaij
rows=0, cols=0
package used to perform factorization: petsc
total: nonzeros=1, allocated nonzeros=1
package used to perform factorization: petsc
total: nonzeros=1, allocated nonzeros=1
not using I-node routines
package used to perform factorization: petsc
total: nonzeros=1, allocated nonzeros=1
total number of mallocs used during MatSetValues calls =0
total number of mallocs used during MatSetValues calls =0
total number of mallocs used during MatSetValues calls =0
linear system matrix = precond matrix:
package used to perform factorization: petsc
total: nonzeros=1, allocated nonzeros=1
total number of mallocs used during MatSetValues calls =0
package used to perform factorization: petsc
total: nonzeros=1, allocated nonzeros=1
total number of mallocs used during MatSetValues calls =0
not using I-node routines
not using I-node routines
Matrix Object: 1 MPI processes
not using I-node routines
type: seqaij
not using I-node routines
not using I-node routines
linear system matrix = precond matrix:
linear system matrix = precond matrix:
rows=0, cols=0
total: nonzeros=0, allocated nonzeros=0
linear system matrix = precond matrix:
Matrix Object: Matrix Object: 1 MPI processes
Matrix Object: 1 MPI processes
total number of mallocs used during MatSetValues calls =0
linear system matrix = precond matrix:
Matrix Object: 1 MPI processes
linear system matrix = precond matrix:
Matrix Object: 1 MPI processes
1 MPI processes
type: seqaij
rows=0, cols=0
type: seqaij
rows=0, cols=0
total: nonzeros=0, allocated nonzeros=0
type: seqaij
rows=0, cols=0
total: nonzeros=0, allocated nonzeros=0
not using I-node routines
type: seqaij
rows=0, cols=0
total: nonzeros=0, allocated nonzeros=0
type: seqaij
rows=0, cols=0
total: nonzeros=0, allocated nonzeros=0
total: nonzeros=0, allocated nonzeros=0
total number of mallocs used during MatSetValues calls =0
not using I-node routines
total number of mallocs used during MatSetValues calls =0
not using I-node routines
total number of mallocs used during MatSetValues calls =0
not using I-node routines
total number of mallocs used during MatSetValues calls =0
not using I-node routines
total number of mallocs used during MatSetValues calls =0
not using I-node routines
KSP Object: KSP Object: (mg_coarse_sub_) 1 MPI processes
(mg_coarse_sub_) type: preonly
maximum iterations=10000, initial guess is zero
1 MPI processes
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
type: preonly
PC Object: maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: (mg_coarse_sub_) (mg_coarse_sub_) 1 MPI processes
type: lu
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
factor fill ratio given 5, needed 2.23871
Factored matrix follows:
1 MPI processes
Matrix Object: 1 MPI processes
type: seqaij
rows=179, cols=179
package used to perform factorization: petsc
type: lu
total: nonzeros=3817, allocated nonzeros=3817
total number of mallocs used during MatSetValues calls =0
not using I-node routines
linear system matrix = precond matrix:
LU: out-of-place factorization
Matrix Object: 1 MPI processes
type: seqaij
rows=179, cols=179
total: nonzeros=1705, allocated nonzeros=1705
total number of mallocs used during MatSetValues calls =0
not using I-node routines
- - - - - - - - - - - - - - - - - -
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
factor fill ratio given 5, needed 0
Factored matrix follows:
Matrix Object: 1 MPI processes
type: seqaij
rows=0, cols=0
package used to perform factorization: petsc
total: nonzeros=1, allocated nonzeros=1
total number of mallocs used during MatSetValues calls =0
not using I-node routines
linear system matrix = precond matrix:
Matrix Object: 1 MPI processes
type: seqaij
rows=0, cols=0
total: nonzeros=0, allocated nonzeros=0
total number of mallocs used during MatSetValues calls =0
not using I-node routines
[1] number of local blocks = 1, first local block number = 1
[1] local block number 0
- - - - - - - - - - - - - - - - - -
[2] number of local blocks = 1, first local block number = 2
[2] local block number 0
- - - - - - - - - - - - - - - - - -
[3] number of local blocks = 1, first local block number = 3
[3] local block number 0
- - - - - - - - - - - - - - - - - -
[4] number of local blocks = 1, first local block number = 4
[4] local block number 0
- - - - - - - - - - - - - - - - - -
[5] number of local blocks = 1, first local block number = 5
[5] local block number 0
- - - - - - - - - - - - - - - - - -
[6] number of local blocks = 1, first local block number = 6
[6] local block number 0
- - - - - - - - - - - - - - - - - -
[7] number of local blocks = 1, first local block number = 7
[7] local block number 0
- - - - - - - - - - - - - - - - - -
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=179, cols=179
total: nonzeros=1705, allocated nonzeros=1705
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Down solver (pre-smoother) on level 1 -------------------------------
KSP Object: (mg_levels_1_) 8 MPI processes
type: chebyshev
Chebyshev: eigenvalue estimates: min = 0.0707274, max = 1.48527
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_1_) 8 MPI processes
type: jacobi
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=958, cols=958
total: nonzeros=7836, allocated nonzeros=7836
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Up solver (post-smoother) same as down solver (pre-smoother)
Down solver (pre-smoother) on level 2 -------------------------------
KSP Object: (mg_levels_2_) 8 MPI processes
type: chebyshev
Chebyshev: eigenvalue estimates: min = 0.0708876, max = 1.48864
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_2_) 8 MPI processes
type: jacobi
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=4973, cols=4973
total: nonzeros=43735, allocated nonzeros=43735
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Up solver (post-smoother) same as down solver (pre-smoother)
Down solver (pre-smoother) on level 3 -------------------------------
KSP Object: (mg_levels_3_) 8 MPI processes
type: chebyshev
Chebyshev: eigenvalue estimates: min = 0.0762465, max = 1.60118
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_3_) 8 MPI processes
type: jacobi
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=33833, cols=33833
total: nonzeros=355743, allocated nonzeros=355743
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Up solver (post-smoother) same as down solver (pre-smoother)
Down solver (pre-smoother) on level 4 -------------------------------
KSP Object: (mg_levels_4_) 8 MPI processes
type: chebyshev
Chebyshev: eigenvalue estimates: min = 0.0975151, max = 2.04782
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_4_) 8 MPI processes
type: jacobi
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=250000, cols=250000
total: nonzeros=1725000, allocated nonzeros=1725000
total number of mallocs used during MatSetValues calls =0
Up solver (post-smoother) same as down solver (pre-smoother)
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=250000, cols=250000
total: nonzeros=1725000, allocated nonzeros=1725000
total number of mallocs used during MatSetValues calls =0
Residual norm 6.64872e-07
************************************************************************************************************************
*** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document ***
************************************************************************************************************************
---------------------------------------------- PETSc Performance Summary: ----------------------------------------------
./ex45 on a arch-linux2-c-debug named compute-5-2.local with 8 processors, by zlwei Fri Sep 14 18:04:45 2012
Using Petsc Development HG revision: 98bf11863c3be31b7c2af504314a500bc64d88c9 HG Date: Wed Aug 29 13:51:08 2012 -0500
Max Max/Min Avg Total
Time (sec): 8.570e+00 1.00005 8.570e+00
Objects: 4.570e+02 1.00000 4.570e+02
Flops: 2.035e+08 1.00383 2.032e+08 1.625e+09
Flops/sec: 2.375e+07 1.00378 2.371e+07 1.896e+08
Memory: 3.716e+07 1.00000 2.973e+08
MPI Messages: 5.506e+03 1.10619 5.194e+03 4.155e+04
MPI Message Lengths: 8.593e+06 1.01613 1.639e+03 6.811e+07
MPI Reductions: 4.630e+03 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: 8.5701e+00 100.0% 1.6252e+09 100.0% 4.155e+04 100.0% 1.639e+03 100.0% 4.629e+03 100.0%
------------------------------------------------------------------------------------------------------------------------
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
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)
------------------------------------------------------------------------------------------------------------------------
##########################################################
# #
# WARNING!!! #
# #
# This code was compiled with a debugging option, #
# To get timing results run ./configure #
# using --with-debugging=no, the performance will #
# be generally two or three times faster. #
# #
##########################################################
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
KSPGMRESOrthog 91 1.0 3.1189e-01 1.0 4.86e+07 1.0 0.0e+00 0.0e+00 6.6e+02 4 24 0 0 14 4 24 0 0 14 1246
KSPSetUp 11 1.0 4.4149e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 2.4e+01 1 0 0 0 1 1 0 0 0 1 0
KSPSolve 1 1.0 8.0593e+00 1.0 2.03e+08 1.0 4.1e+04 1.6e+03 4.6e+03 94100100 99 99 94100100 99 99 201
VecMDot 91 1.0 1.4309e-01 1.0 2.43e+07 1.0 0.0e+00 0.0e+00 9.1e+01 2 12 0 0 2 2 12 0 0 2 1358
VecNorm 123 1.0 2.2507e-02 1.1 2.50e+06 1.0 0.0e+00 0.0e+00 1.2e+02 0 1 0 0 3 0 1 0 0 3 884
VecScale 538 1.0 2.0931e-02 1.1 4.99e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 2 0 0 0 0 2 0 0 0 1903
VecCopy 135 1.0 1.1293e-02 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
VecSet 505 1.0 1.5996e-02 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 864 1.0 7.1485e-02 1.1 1.53e+07 1.0 0.0e+00 0.0e+00 0.0e+00 1 8 0 0 0 1 8 0 0 0 1708
VecAYPX 832 1.0 7.6809e-02 1.1 9.43e+06 1.0 0.0e+00 0.0e+00 0.0e+00 1 5 0 0 0 1 5 0 0 0 981
VecMAXPY 122 1.0 1.0202e-01 1.0 2.66e+07 1.0 0.0e+00 0.0e+00 0.0e+00 1 13 0 0 0 1 13 0 0 0 2085
VecAssemblyBegin 53 1.0 3.2252e-02 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 1.6e+02 0 0 0 0 3 0 0 0 0 3 0
VecAssemblyEnd 53 1.0 4.4584e-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
VecPointwiseMult 668 1.0 1.1690e-01 1.0 6.06e+06 1.0 0.0e+00 0.0e+00 0.0e+00 1 3 0 0 0 1 3 0 0 0 414
VecScatterBegin 981 1.0 8.3254e-02 1.1 0.00e+00 0.0 3.8e+04 1.6e+03 0.0e+00 1 0 91 90 0 1 0 91 90 0 0
VecScatterEnd 981 1.0 6.4690e-02 1.1 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
VecSetRandom 4 1.0 4.8918e-02 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
VecNormalize 122 1.0 2.9767e-02 1.0 3.66e+06 1.0 0.0e+00 0.0e+00 1.2e+02 0 2 0 0 3 0 2 0 0 3 977
MatMult 716 1.0 1.6713e+00 1.0 9.31e+07 1.0 3.0e+04 1.8e+03 0.0e+00 19 46 71 77 0 19 46 71 77 0 445
MatMultAdd 104 1.0 8.3075e-02 1.0 1.88e+06 1.0 2.7e+03 2.7e+02 0.0e+00 1 1 6 1 0 1 1 6 1 0 181
MatMultTranspose 104 1.0 1.0354e-01 1.0 1.88e+06 1.0 2.7e+03 2.7e+02 2.1e+02 1 1 6 1 4 1 1 6 1 4 145
MatSolve 52 0.0 2.3191e-03 0.0 3.88e+05 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 167
MatLUFactorSym 1 1.0 4.6897e-04 4.7 0.00e+00 0.0 0.0e+00 0.0e+00 5.0e+00 0 0 0 0 0 0 0 0 0 0 0
MatLUFactorNum 1 1.0 4.5013e-0418.9 4.21e+04 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 94
MatConvert 4 1.0 2.0307e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 2.4e+01 0 0 0 0 1 0 0 0 0 1 0
MatScale 4 1.0 6.1872e-03 1.0 5.35e+05 1.0 1.7e+02 1.6e+03 0.0e+00 0 0 0 0 0 0 0 0 0 0 689
MatAssemblyBegin 50 1.0 4.0176e-02 1.7 0.00e+00 0.0 3.8e+02 3.5e+02 5.6e+01 0 0 1 0 1 0 0 1 0 1 0
MatAssemblyEnd 50 1.0 1.3871e-01 1.0 0.00e+00 0.0 1.5e+03 3.9e+02 4.0e+02 2 0 4 1 9 2 0 4 1 9 0
MatGetRow 72562 1.0 2.7369e-01 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
MatGetRowIJ 1 0.0 4.1008e-05 0.0 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
MatGetOrdering 1 0.0 4.0412e-04 0.0 0.00e+00 0.0 0.0e+00 0.0e+00 2.5e-01 0 0 0 0 0 0 0 0 0 0 0
MatCoarsen 4 1.0 1.6034e-01 1.0 0.00e+00 0.0 1.3e+03 2.7e+03 1.2e+02 2 0 3 5 3 2 0 3 5 3 0
MatView 8 1.0 4.7970e-03 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 6.0e+00 0 0 0 0 0 0 0 0 0 0 0
MatPtAP 4 1.0 1.4446e-01 1.0 1.63e+06 1.1 1.4e+03 6.3e+02 2.3e+02 2 1 3 1 5 2 1 3 1 5 88
MatPtAPSymbolic 4 1.0 1.0185e-01 1.1 0.00e+00 0.0 1.3e+03 5.6e+02 2.0e+02 1 0 3 1 4 1 0 3 1 4 0
MatPtAPNumeric 4 1.0 4.2606e-02 1.0 1.63e+06 1.1 1.2e+02 1.4e+03 2.4e+01 0 1 0 0 1 0 1 0 0 1 297
MatTrnMatMult 4 1.0 7.4679e-01 1.0 1.54e+07 1.0 1.1e+03 4.8e+03 2.5e+02 9 8 3 8 5 9 8 3 8 5 163
MatGetLocalMat 12 1.0 3.0601e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 3.2e+01 0 0 0 0 1 0 0 0 0 1 0
MatGetBrAoCol 4 1.0 1.4587e-02 1.7 0.00e+00 0.0 5.2e+02 1.1e+03 1.6e+01 0 0 1 1 0 0 0 1 1 0 0
MatGetSymTrans 8 1.0 1.3292e-03 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
PCSetUp 2 1.0 3.9298e+00 1.0 3.29e+07 1.0 8.3e+03 2.0e+03 1.7e+03 46 16 20 25 38 46 16 20 25 38 67
PCSetUpOnBlocks 26 1.0 2.2025e-03 2.0 4.21e+04 0.0 0.0e+00 0.0e+00 8.0e+00 0 0 0 0 0 0 0 0 0 0 19
PCApply 26 1.0 2.9146e+00 1.0 1.15e+08 1.0 3.2e+04 1.4e+03 2.3e+03 34 57 78 67 50 34 57 78 67 50 316
PCGAMGgraph_AGG 4 1.0 1.6139e+00 1.0 5.35e+05 1.0 5.2e+02 7.9e+02 1.9e+02 19 0 1 1 4 19 0 1 1 4 3
PCGAMGcoarse_AGG 4 1.0 1.3659e+00 1.0 1.54e+07 1.0 3.5e+03 3.3e+03 4.7e+02 16 8 8 17 10 16 8 8 17 10 89
PCGAMGProl_AGG 4 1.0 3.1176e-01 1.0 0.00e+00 0.0 1.1e+03 1.2e+03 2.0e+02 4 0 3 2 4 4 0 3 2 4 0
PCGAMGPOpt_AGG 4 1.0 2.5988e-05 1.7 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
Container 1 1 548 0
Krylov Solver 11 11 162856 0
Vector 235 235 18591120 0
Vector Scatter 26 26 26936 0
Matrix 92 92 31827700 0
Matrix Coarsen 4 4 2448 0
Distributed Mesh 2 2 285240 0
Bipartite Graph 4 4 2736 0
Index Set 64 64 256456 0
IS L to G Mapping 1 1 138468 0
Preconditioner 11 11 10092 0
Viewer 2 1 712 0
PetscRandom 4 4 2432 0
========================================================================================================================
Average time to get PetscTime(): 5.00679e-07
Average time for MPI_Barrier(): 0.000130177
Average time for zero size MPI_Send(): 2.22325e-05
#PETSc Option Table entries:
-ksp_monitor
-ksp_rtol 1.0e-7
-ksp_view
-log_summary
-pc_type gamg
#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 run at: Wed Aug 29 14:54:25 2012
Configure options: --prefix=/work/zlwei/PETSc --with-cc=gcc --with-fc=gfortran --download-f-blas-lapack --download-mpich
-----------------------------------------
Libraries compiled on Wed Aug 29 14:54:25 2012 on firefox.bioinfo.ittc.ku.edu
Machine characteristics: Linux-2.6.18-92.1.13.el5-x86_64-with-redhat-5.2-Final
Using PETSc directory: /nfs/work/zlwei/PETSc/petsc-dev
Using PETSc arch: arch-linux2-c-debug
-----------------------------------------
Using C compiler: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -fno-inline -O0 ${COPTFLAGS} ${CFLAGS}
Using Fortran compiler: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpif90 -Wall -Wno-unused-variable -g ${FOPTFLAGS} ${FFLAGS}
-----------------------------------------
Using include paths: -I/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/include -I/nfs/work/zlwei/PETSc/petsc-dev/include -I/nfs/work/zlwei/PETSc/petsc-dev/include -I/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/include
-----------------------------------------
Using C linker: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpicc
Using Fortran linker: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpif90
Using libraries: -Wl,-rpath,/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -L/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -lpetsc -lX11 -lpthread -Wl,-rpath,/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -L/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -lflapack -lfblas -lm -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -lmpichf90 -lgfortran -lm -lm -ldl -lmpich -lopa -lmpl -lrt -lgcc_s -ldl
-----------------------------------------
-------------- next part --------------
0 KSP Residual norm 3.368148596765e+02
1 KSP Residual norm 7.884667648061e+01
2 KSP Residual norm 3.983220874680e+01
3 KSP Residual norm 2.529465334442e+01
4 KSP Residual norm 1.819644017854e+01
5 KSP Residual norm 1.458219316768e+01
6 KSP Residual norm 1.180412704465e+01
7 KSP Residual norm 9.575897241358e+00
8 KSP Residual norm 8.043264261713e+00
9 KSP Residual norm 7.018519352883e+00
10 KSP Residual norm 6.130476554332e+00
11 KSP Residual norm 5.397263048170e+00
12 KSP Residual norm 4.835967632485e+00
13 KSP Residual norm 4.352028777238e+00
14 KSP Residual norm 3.952712102274e+00
15 KSP Residual norm 3.617454495697e+00
16 KSP Residual norm 3.301898504445e+00
17 KSP Residual norm 3.027795288920e+00
18 KSP Residual norm 2.801330506731e+00
19 KSP Residual norm 2.600088323848e+00
20 KSP Residual norm 2.415396607825e+00
21 KSP Residual norm 2.251635941363e+00
22 KSP Residual norm 2.107710728118e+00
23 KSP Residual norm 1.976827356870e+00
24 KSP Residual norm 1.855722787536e+00
25 KSP Residual norm 1.744283789182e+00
26 KSP Residual norm 1.643979116571e+00
27 KSP Residual norm 1.555420193633e+00
28 KSP Residual norm 1.473610804642e+00
29 KSP Residual norm 1.395581630789e+00
30 KSP Residual norm 1.324035740635e+00
31 KSP Residual norm 1.289620876123e+00
32 KSP Residual norm 1.254163025674e+00
33 KSP Residual norm 1.218122418418e+00
34 KSP Residual norm 1.181980463870e+00
35 KSP Residual norm 1.145084266546e+00
36 KSP Residual norm 1.107771307421e+00
37 KSP Residual norm 1.070515918578e+00
38 KSP Residual norm 1.033345073830e+00
39 KSP Residual norm 9.957326457777e-01
40 KSP Residual norm 9.574090681547e-01
41 KSP Residual norm 9.206214332288e-01
42 KSP Residual norm 8.860402343860e-01
43 KSP Residual norm 8.519570071849e-01
44 KSP Residual norm 8.160171689292e-01
45 KSP Residual norm 7.780106459520e-01
46 KSP Residual norm 7.384806314831e-01
47 KSP Residual norm 7.011353257545e-01
48 KSP Residual norm 6.660776428339e-01
49 KSP Residual norm 6.290570146661e-01
50 KSP Residual norm 5.898901582810e-01
51 KSP Residual norm 5.530351127027e-01
52 KSP Residual norm 5.150136349357e-01
53 KSP Residual norm 4.769315717084e-01
54 KSP Residual norm 4.418695812249e-01
55 KSP Residual norm 4.055730558383e-01
56 KSP Residual norm 3.701573952578e-01
57 KSP Residual norm 3.405955774779e-01
58 KSP Residual norm 3.138542961303e-01
59 KSP Residual norm 2.904777931959e-01
60 KSP Residual norm 2.721221568117e-01
61 KSP Residual norm 2.637111203338e-01
62 KSP Residual norm 2.555282288716e-01
63 KSP Residual norm 2.457633020644e-01
64 KSP Residual norm 2.312064551884e-01
65 KSP Residual norm 2.168687024333e-01
66 KSP Residual norm 2.021462808115e-01
67 KSP Residual norm 1.882502502712e-01
68 KSP Residual norm 1.726156627947e-01
69 KSP Residual norm 1.580948063184e-01
70 KSP Residual norm 1.450188243537e-01
71 KSP Residual norm 1.329090943840e-01
72 KSP Residual norm 1.224648275772e-01
73 KSP Residual norm 1.134430099592e-01
74 KSP Residual norm 1.062156089215e-01
75 KSP Residual norm 1.009515456891e-01
76 KSP Residual norm 9.677088026876e-02
77 KSP Residual norm 9.330462638461e-02
78 KSP Residual norm 9.014986471375e-02
79 KSP Residual norm 8.728725736359e-02
80 KSP Residual norm 8.474425436748e-02
81 KSP Residual norm 8.239085729749e-02
82 KSP Residual norm 8.004171069055e-02
83 KSP Residual norm 7.754583057709e-02
84 KSP Residual norm 7.503607926802e-02
85 KSP Residual norm 7.251754709396e-02
86 KSP Residual norm 7.023044020357e-02
87 KSP Residual norm 6.816259549138e-02
88 KSP Residual norm 6.615708630367e-02
89 KSP Residual norm 6.410877480267e-02
90 KSP Residual norm 6.220199693340e-02
91 KSP Residual norm 6.079561000422e-02
92 KSP Residual norm 5.945366054862e-02
93 KSP Residual norm 5.805745558808e-02
94 KSP Residual norm 5.647865842490e-02
95 KSP Residual norm 5.482579066632e-02
96 KSP Residual norm 5.327464699030e-02
97 KSP Residual norm 5.181785368265e-02
98 KSP Residual norm 5.026058189172e-02
99 KSP Residual norm 4.853529822466e-02
100 KSP Residual norm 4.672552830768e-02
101 KSP Residual norm 4.488451706047e-02
102 KSP Residual norm 4.274002202667e-02
103 KSP Residual norm 4.066715145826e-02
104 KSP Residual norm 3.879543017112e-02
105 KSP Residual norm 3.692545546597e-02
106 KSP Residual norm 3.496725881242e-02
107 KSP Residual norm 3.291047034156e-02
108 KSP Residual norm 3.073335561917e-02
109 KSP Residual norm 2.849664394983e-02
110 KSP Residual norm 2.626973767994e-02
111 KSP Residual norm 2.438406681556e-02
112 KSP Residual norm 2.253397732039e-02
113 KSP Residual norm 2.054090707797e-02
114 KSP Residual norm 1.890158567808e-02
115 KSP Residual norm 1.742573595014e-02
116 KSP Residual norm 1.629263326782e-02
117 KSP Residual norm 1.532685125519e-02
118 KSP Residual norm 1.465738126879e-02
119 KSP Residual norm 1.408292302474e-02
120 KSP Residual norm 1.353341128860e-02
121 KSP Residual norm 1.310193200424e-02
122 KSP Residual norm 1.268439577064e-02
123 KSP Residual norm 1.221270299177e-02
124 KSP Residual norm 1.153059978148e-02
125 KSP Residual norm 1.084782525529e-02
126 KSP Residual norm 1.008849505102e-02
127 KSP Residual norm 9.358912388407e-03
128 KSP Residual norm 8.541223977083e-03
129 KSP Residual norm 7.865522556463e-03
130 KSP Residual norm 7.286455417054e-03
131 KSP Residual norm 6.746096551092e-03
132 KSP Residual norm 6.265169639034e-03
133 KSP Residual norm 5.831333351878e-03
134 KSP Residual norm 5.460797382663e-03
135 KSP Residual norm 5.177705767837e-03
136 KSP Residual norm 4.933073975857e-03
137 KSP Residual norm 4.721768175681e-03
138 KSP Residual norm 4.524437438027e-03
139 KSP Residual norm 4.341955963482e-03
140 KSP Residual norm 4.188429974280e-03
141 KSP Residual norm 4.043862515122e-03
142 KSP Residual norm 3.918929706117e-03
143 KSP Residual norm 3.814454962740e-03
144 KSP Residual norm 3.716285727000e-03
145 KSP Residual norm 3.616166834928e-03
146 KSP Residual norm 3.517411257480e-03
147 KSP Residual norm 3.424011069705e-03
148 KSP Residual norm 3.333161789233e-03
149 KSP Residual norm 3.238552146236e-03
150 KSP Residual norm 3.148952887727e-03
151 KSP Residual norm 3.071169436807e-03
152 KSP Residual norm 2.995279685803e-03
153 KSP Residual norm 2.918890614973e-03
154 KSP Residual norm 2.841924652276e-03
155 KSP Residual norm 2.767745676000e-03
156 KSP Residual norm 2.709880325144e-03
157 KSP Residual norm 2.655188186095e-03
158 KSP Residual norm 2.594800880316e-03
159 KSP Residual norm 2.511751585705e-03
160 KSP Residual norm 2.418560169069e-03
161 KSP Residual norm 2.323693463105e-03
162 KSP Residual norm 2.202281878316e-03
163 KSP Residual norm 2.081222945431e-03
164 KSP Residual norm 1.973162638634e-03
165 KSP Residual norm 1.862310198198e-03
166 KSP Residual norm 1.749849970665e-03
167 KSP Residual norm 1.633061071294e-03
168 KSP Residual norm 1.521124032557e-03
169 KSP Residual norm 1.408323314143e-03
170 KSP Residual norm 1.293048175498e-03
171 KSP Residual norm 1.198666442585e-03
172 KSP Residual norm 1.104292340266e-03
173 KSP Residual norm 9.903517641547e-04
174 KSP Residual norm 9.006840819784e-04
175 KSP Residual norm 8.220140598814e-04
176 KSP Residual norm 7.701687567256e-04
177 KSP Residual norm 7.277976116145e-04
178 KSP Residual norm 7.000140296237e-04
179 KSP Residual norm 6.773749425038e-04
180 KSP Residual norm 6.550713166809e-04
181 KSP Residual norm 6.359176664418e-04
182 KSP Residual norm 6.168972906949e-04
183 KSP Residual norm 5.950139987555e-04
184 KSP Residual norm 5.622068365562e-04
185 KSP Residual norm 5.273547552299e-04
186 KSP Residual norm 4.818810755826e-04
187 KSP Residual norm 4.384533123217e-04
188 KSP Residual norm 3.907464303241e-04
189 KSP Residual norm 3.586153163812e-04
190 KSP Residual norm 3.336501378016e-04
191 KSP Residual norm 3.104406491737e-04
192 KSP Residual norm 2.901902786842e-04
193 KSP Residual norm 2.716799088525e-04
194 KSP Residual norm 2.537323499807e-04
195 KSP Residual norm 2.393026806501e-04
196 KSP Residual norm 2.263905103671e-04
197 KSP Residual norm 2.157021715528e-04
198 KSP Residual norm 2.057920256098e-04
199 KSP Residual norm 1.969756726158e-04
200 KSP Residual norm 1.900711849490e-04
201 KSP Residual norm 1.834129243787e-04
202 KSP Residual norm 1.778746265038e-04
203 KSP Residual norm 1.740906692660e-04
204 KSP Residual norm 1.706199678117e-04
205 KSP Residual norm 1.668919206574e-04
206 KSP Residual norm 1.622105706626e-04
207 KSP Residual norm 1.572060039751e-04
208 KSP Residual norm 1.518496090051e-04
209 KSP Residual norm 1.463692706552e-04
210 KSP Residual norm 1.418011930173e-04
211 KSP Residual norm 1.377765629498e-04
212 KSP Residual norm 1.334751880052e-04
213 KSP Residual norm 1.291286531826e-04
214 KSP Residual norm 1.251832711544e-04
215 KSP Residual norm 1.218001179107e-04
216 KSP Residual norm 1.196976772828e-04
217 KSP Residual norm 1.177303742190e-04
218 KSP Residual norm 1.155947299539e-04
219 KSP Residual norm 1.122085992182e-04
220 KSP Residual norm 1.083653641467e-04
221 KSP Residual norm 1.043599353987e-04
222 KSP Residual norm 9.863046990455e-05
223 KSP Residual norm 9.288192270074e-05
224 KSP Residual norm 8.783813676585e-05
225 KSP Residual norm 8.246551518283e-05
226 KSP Residual norm 7.720911064459e-05
227 KSP Residual norm 7.171219551448e-05
228 KSP Residual norm 6.709483001659e-05
229 KSP Residual norm 6.232136142160e-05
230 KSP Residual norm 5.725941336029e-05
231 KSP Residual norm 5.315634584336e-05
232 KSP Residual norm 4.868189668074e-05
233 KSP Residual norm 4.242157170447e-05
234 KSP Residual norm 3.768648100701e-05
235 KSP Residual norm 3.337401865099e-05
KSP Object: 8 MPI processes
type: gmres
GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement
GMRES: happy breakdown tolerance 1e-30
maximum iterations=10000
tolerances: relative=1e-07, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using PRECONDITIONED norm type for convergence test
PC Object: 8 MPI processes
type: bjacobi
block Jacobi: number of blocks = 8
Local solve is same for all blocks, in the following KSP and PC objects:
KSP Object: (sub_) 1 MPI processes
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: (sub_) 1 MPI processes
type: ilu
ILU: out-of-place factorization
0 levels of fill
tolerance for zero pivot 2.22045e-14
using diagonal shift to prevent zero pivot
matrix ordering: natural
factor fill ratio given 1, needed 1
Factored matrix follows:
Matrix Object: 1 MPI processes
type: seqaij
rows=250000, cols=250000
package used to perform factorization: petsc
total: nonzeros=1725000, allocated nonzeros=1725000
total number of mallocs used during MatSetValues calls =0
not using I-node routines
linear system matrix = precond matrix:
Matrix Object: 1 MPI processes
type: seqaij
rows=250000, cols=250000
total: nonzeros=1725000, allocated nonzeros=1725000
total number of mallocs used during MatSetValues calls =0
not using I-node routines
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=2000000, cols=2000000
total: nonzeros=13900000, allocated nonzeros=13900000
total number of mallocs used during MatSetValues calls =0
Residual norm 4.10372e-07
************************************************************************************************************************
*** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document ***
************************************************************************************************************************
---------------------------------------------- PETSc Performance Summary: ----------------------------------------------
./ex45 on a arch-linux2-c-debug named compute-5-2.local with 8 processors, by zlwei Fri Sep 14 18:02:30 2012
Using Petsc Development HG revision: 98bf11863c3be31b7c2af504314a500bc64d88c9 HG Date: Wed Aug 29 13:51:08 2012 -0500
Max Max/Min Avg Total
Time (sec): 6.489e+01 1.00001 6.489e+01
Objects: 7.400e+01 1.00000 7.400e+01
Flops: 5.455e+09 1.00001 5.455e+09 4.364e+10
Flops/sec: 8.407e+07 1.00001 8.407e+07 6.725e+08
Memory: 1.397e+08 1.00000 1.118e+09
MPI Messages: 7.480e+02 1.00809 7.428e+02 5.942e+03
MPI Message Lengths: 2.440e+07 1.00000 3.285e+04 1.952e+08
MPI Reductions: 4.972e+03 1.00040
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: 6.4885e+01 100.0% 4.3638e+10 100.0% 5.942e+03 100.0% 3.285e+04 100.0% 4.969e+03 99.9%
------------------------------------------------------------------------------------------------------------------------
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
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)
------------------------------------------------------------------------------------------------------------------------
##########################################################
# #
# WARNING!!! #
# #
# This code was compiled with a debugging option, #
# To get timing results run ./configure #
# using --with-debugging=no, the performance will #
# be generally two or three times faster. #
# #
##########################################################
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
KSPGMRESOrthog 235 1.0 2.4753e+01 1.0 3.58e+09 1.0 0.0e+00 0.0e+00 3.8e+03 38 66 0 0 77 38 66 0 0 77 1157
KSPSetUp 2 1.0 2.5209e-02 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 1 1.0 6.4022e+01 1.0 5.45e+09 1.0 5.9e+03 3.3e+04 4.9e+03 99100 99 99 99 99100 99 99 99 681
VecMDot 235 1.0 1.1786e+01 1.1 1.79e+09 1.0 0.0e+00 0.0e+00 2.4e+02 18 33 0 0 5 18 33 0 0 5 1215
VecNorm 244 1.0 7.7111e-01 1.4 1.22e+08 1.0 0.0e+00 0.0e+00 2.4e+02 1 2 0 0 5 1 2 0 0 5 1266
VecScale 243 1.0 2.0378e-01 1.0 6.08e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 2385
VecCopy 8 1.0 4.7706e-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 253 1.0 6.1563e-01 1.3 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
VecAXPY 16 1.0 8.1648e-02 1.0 8.00e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 784
VecMAXPY 243 1.0 1.3352e+01 1.0 1.91e+09 1.0 0.0e+00 0.0e+00 0.0e+00 20 35 0 0 0 20 35 0 0 0 1143
VecScatterBegin 243 1.0 1.3329e-01 1.0 0.00e+00 0.0 5.8e+03 3.3e+04 0.0e+00 0 0 98100 0 0 0 98100 0 0
VecScatterEnd 243 1.0 1.6686e-01 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
VecNormalize 243 1.0 9.7965e-01 1.3 1.82e+08 1.0 0.0e+00 0.0e+00 2.4e+02 1 3 0 0 5 1 3 0 0 5 1488
MatMult 243 1.0 1.0068e+01 1.0 7.84e+08 1.0 5.8e+03 3.3e+04 0.0e+00 15 14 98100 0 15 14 98100 0 623
MatSolve 243 1.0 9.0452e+00 1.0 7.78e+08 1.0 0.0e+00 0.0e+00 0.0e+00 14 14 0 0 0 14 14 0 0 0 688
MatLUFactorNum 1 1.0 1.2613e-01 1.0 5.19e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 328
MatILUFactorSym 1 1.0 1.2127e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 0
MatAssemblyBegin 2 1.0 5.0238e-02 6.8 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
MatAssemblyEnd 2 1.0 9.5135e-02 1.0 0.00e+00 0.0 4.8e+01 8.3e+03 2.3e+01 0 0 1 0 0 0 0 1 0 0 0
MatGetRowIJ 1 1.0 7.1526e-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
MatGetOrdering 1 1.0 4.3743e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 2.0e+00 0 0 0 0 0 0 0 0 0 0 0
MatView 3 3.0 5.2476e-04 2.9 0.00e+00 0.0 0.0e+00 0.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 0
PCSetUp 2 1.0 2.9335e-01 1.0 5.19e+06 1.0 0.0e+00 0.0e+00 8.0e+00 0 0 0 0 0 0 0 0 0 0 141
PCSetUpOnBlocks 1 1.0 2.9270e-01 1.0 5.19e+06 1.0 0.0e+00 0.0e+00 4.0e+00 0 0 0 0 0 0 0 0 0 0 141
PCApply 243 1.0 1.3113e+01 1.0 7.78e+08 1.0 0.0e+00 0.0e+00 4.9e+02 20 14 0 0 10 20 14 0 0 10 474
------------------------------------------------------------------------------------------------------------------------
Memory usage is given in bytes:
Object Type Creations Destructions Memory Descendants' Mem.
Reports information only for process 0.
--- Event Stage 0: Main Stage
Container 1 1 548 0
Krylov Solver 2 2 19360 0
Vector 43 43 74164072 0
Vector Scatter 3 3 3108 0
Matrix 4 4 53610212 0
Distributed Mesh 2 2 2111040 0
Bipartite Graph 4 4 2736 0
Index Set 10 10 2107424 0
IS L to G Mapping 1 1 1051368 0
Preconditioner 2 2 1784 0
Viewer 2 1 712 0
========================================================================================================================
Average time to get PetscTime(): 5.96046e-07
Average time for MPI_Barrier(): 0.000142002
Average time for zero size MPI_Send(): 0.00040701
#PETSc Option Table entries:
-ksp_monitor
-ksp_rtol 1.0e-7
-ksp_view
-log_summary
#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 run at: Wed Aug 29 14:54:25 2012
Configure options: --prefix=/work/zlwei/PETSc --with-cc=gcc --with-fc=gfortran --download-f-blas-lapack --download-mpich
-----------------------------------------
Libraries compiled on Wed Aug 29 14:54:25 2012 on firefox.bioinfo.ittc.ku.edu
Machine characteristics: Linux-2.6.18-92.1.13.el5-x86_64-with-redhat-5.2-Final
Using PETSc directory: /nfs/work/zlwei/PETSc/petsc-dev
Using PETSc arch: arch-linux2-c-debug
-----------------------------------------
Using C compiler: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -fno-inline -O0 ${COPTFLAGS} ${CFLAGS}
Using Fortran compiler: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpif90 -Wall -Wno-unused-variable -g ${FOPTFLAGS} ${FFLAGS}
-----------------------------------------
Using include paths: -I/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/include -I/nfs/work/zlwei/PETSc/petsc-dev/include -I/nfs/work/zlwei/PETSc/petsc-dev/include -I/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/include
-----------------------------------------
Using C linker: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpicc
Using Fortran linker: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpif90
Using libraries: -Wl,-rpath,/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -L/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -lpetsc -lX11 -lpthread -Wl,-rpath,/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -L/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -lflapack -lfblas -lm -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -lmpichf90 -lgfortran -lm -lm -ldl -lmpich -lopa -lmpl -lrt -lgcc_s -ldl
-----------------------------------------
-------------- next part --------------
0 KSP Residual norm 3.783525866986e+02
1 KSP Residual norm 1.355893441623e+02
2 KSP Residual norm 7.589085973838e+01
3 KSP Residual norm 4.823882044088e+01
4 KSP Residual norm 3.576939460641e+01
5 KSP Residual norm 2.568586752716e+01
6 KSP Residual norm 1.911353651617e+01
7 KSP Residual norm 1.476612759706e+01
8 KSP Residual norm 1.120103269246e+01
9 KSP Residual norm 8.447905007266e+00
10 KSP Residual norm 6.370754282832e+00
11 KSP Residual norm 4.663740863807e+00
12 KSP Residual norm 3.270563368805e+00
13 KSP Residual norm 2.221723082951e+00
14 KSP Residual norm 1.499655110516e+00
15 KSP Residual norm 1.025805172424e+00
16 KSP Residual norm 6.958772552651e-01
17 KSP Residual norm 4.398302154107e-01
18 KSP Residual norm 2.533473339850e-01
19 KSP Residual norm 1.446856653276e-01
20 KSP Residual norm 8.823403825208e-02
21 KSP Residual norm 5.562369474397e-02
22 KSP Residual norm 3.414214762893e-02
23 KSP Residual norm 2.080524442410e-02
24 KSP Residual norm 1.195406832279e-02
25 KSP Residual norm 6.116395185712e-03
26 KSP Residual norm 3.571727881359e-03
27 KSP Residual norm 2.211651069789e-03
28 KSP Residual norm 1.307637746982e-03
29 KSP Residual norm 8.576482161323e-04
30 KSP Residual norm 6.057261603377e-04
31 KSP Residual norm 5.157507148603e-04
32 KSP Residual norm 3.933614801888e-04
33 KSP Residual norm 2.865687664919e-04
34 KSP Residual norm 1.847542136621e-04
35 KSP Residual norm 1.141737708009e-04
36 KSP Residual norm 6.706587799191e-05
37 KSP Residual norm 4.120603316253e-05
38 KSP Residual norm 2.698388463745e-05
KSP Object: 8 MPI processes
type: gmres
GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement
GMRES: happy breakdown tolerance 1e-30
maximum iterations=10000
tolerances: relative=1e-07, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using PRECONDITIONED norm type for convergence test
PC Object: 8 MPI processes
type: gamg
MG: type is MULTIPLICATIVE, levels=5 cycles=v
Cycles per PCApply=1
Using Galerkin computed coarse grid matrices
Coarse grid solver -- level -------------------------------
KSP Object: (mg_coarse_) 8 MPI processes
type: gmres
GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement
GMRES: happy breakdown tolerance 1e-30
maximum iterations=1, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: (mg_coarse_) 8 MPI processes
type: bjacobi
block Jacobi: number of blocks = 8
Local solve info for each block is in the following KSP and PC objects:
[0] number of local blocks = 1, first local block number = 0
[0] local block number 0
KSP Object: (mg_coarse_sub_) 1 MPI processes
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
KSP Object: left preconditioning
KSP Object: (mg_coarse_sub_) KSP Object: (mg_coarse_sub_) 1 MPI processes
KSP Object: (mg_coarse_sub_) 1 MPI processes
KSP Object: (mg_coarse_sub_) 1 MPI processes
KSP Object: (mg_coarse_sub_) 1 MPI processes
type: preonly
using NONE norm type for convergence test
PC Object: (mg_coarse_sub_) 1 MPI processes
(mg_coarse_sub_) 1 MPI processes
type: preonly
1 MPI processes
type: preonly
maximum iterations=10000, initial guess is zero
type: preonly
maximum iterations=10000, initial guess is zero
type: preonly
maximum iterations=10000, initial guess is zero
type: preonly
maximum iterations=10000, initial guess is zero
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
type: lu
LU: out-of-place factorization
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
left preconditioning
using NONE norm type for convergence test
PC Object: tolerance for zero pivot 2.22045e-14
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: PC Object: (mg_coarse_sub_) 1 MPI processes
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: (mg_coarse_sub_) 1 MPI processes
type: lu
matrix ordering: nd
factor fill ratio given 5, needed 2.91134
Factored matrix follows:
using NONE norm type for convergence test
PC Object: (mg_coarse_sub_) 1 MPI processes
PC Object: (mg_coarse_sub_) 1 MPI processes
type: lu
(mg_coarse_sub_) 1 MPI processes
type: lu
(mg_coarse_sub_) 1 MPI processes
type: lu
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
Matrix Object: type: lu
LU: out-of-place factorization
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
matrix ordering: nd
factor fill ratio given 5, needed 0
Factored matrix follows:
1 MPI processes
type: seqaij
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
factor fill ratio given 5, needed 0
factor fill ratio given 5, needed 0
Factored matrix follows:
matrix ordering: nd
factor fill ratio given 5, needed 0
factor fill ratio given 5, needed 0
Factored matrix follows:
rows=718, cols=718
Factored matrix follows:
Factored matrix follows:
Matrix Object: 1 MPI processes
package used to perform factorization: petsc
Matrix Object: type: seqaij
total: nonzeros=18324, allocated nonzeros=18324
Matrix Object: 1 MPI processes
1 MPI processes
type: seqaij
Matrix Object: 1 MPI processes
Matrix Object: 1 MPI processes
type: seqaij
total number of mallocs used during MatSetValues calls =0
type: seqaij
rows=0, cols=0
type: seqaij
rows=0, cols=0
rows=0, cols=0
package used to perform factorization: petsc
total: nonzeros=1, allocated nonzeros=1
not using I-node routines
rows=0, cols=0
rows=0, cols=0
total number of mallocs used during MatSetValues calls =0
package used to perform factorization: petsc
package used to perform factorization: petsc
package used to perform factorization: petsc
total: nonzeros=1, allocated nonzeros=1
linear system matrix = precond matrix:
package used to perform factorization: petsc
total: nonzeros=1, allocated nonzeros=1
total: nonzeros=1, allocated nonzeros=1
total number of mallocs used during MatSetValues calls =0
total: nonzeros=1, allocated nonzeros=1
total number of mallocs used during MatSetValues calls =0
total number of mallocs used during MatSetValues calls =0
not using I-node routines
Matrix Object: 1 MPI processes
type: seqaij
total number of mallocs used during MatSetValues calls =0
linear system matrix = precond matrix:
not using I-node routines
not using I-node routines
not using I-node routines
rows=718, cols=718
total: nonzeros=6294, allocated nonzeros=6294
not using I-node routines
Matrix Object: 1 MPI processes
type: seqaij
total number of mallocs used during MatSetValues calls =0
linear system matrix = precond matrix:
linear system matrix = precond matrix:
linear system matrix = precond matrix:
Matrix Object: not using I-node routines
linear system matrix = precond matrix:
Matrix Object: 1 MPI processes
type: seqaij
Matrix Object: 1 MPI processes
1 MPI processes
type: seqaij
rows=0, cols=0
total: nonzeros=0, allocated nonzeros=0
total number of mallocs used during MatSetValues calls =0
not using I-node routines
- - - - - - - - - - - - - - - - - -
Matrix Object: 1 MPI processes
type: seqaij
rows=0, cols=0
total: nonzeros=0, allocated nonzeros=0
type: seqaij
rows=0, cols=0
rows=0, cols=0
total: nonzeros=0, allocated nonzeros=0
rows=0, cols=0
total number of mallocs used during MatSetValues calls =0
total: nonzeros=0, allocated nonzeros=0
total number of mallocs used during MatSetValues calls =0
total: nonzeros=0, allocated nonzeros=0
not using I-node routines
total number of mallocs used during MatSetValues calls =0
not using I-node routines
total number of mallocs used during MatSetValues calls =0
not using I-node routines
not using I-node routines
type: lu
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
factor fill ratio given 5, needed 0
Factored matrix follows:
KSP Object: (mg_coarse_sub_) 1 MPI processes
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
Matrix Object: PC Object: (mg_coarse_sub_) 1 MPI processes
1 MPI processes
type: lu
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
type: seqaij
matrix ordering: nd
factor fill ratio given 5, needed 0
Factored matrix follows:
rows=0, cols=0
Matrix Object: 1 MPI processes
type: seqaij
package used to perform factorization: petsc
rows=0, cols=0
package used to perform factorization: petsc
total: nonzeros=1, allocated nonzeros=1
total: nonzeros=1, allocated nonzeros=1
total number of mallocs used during MatSetValues calls =0
total number of mallocs used during MatSetValues calls =0
not using I-node routines
linear system matrix = precond matrix:
not using I-node routines
Matrix Object: 1 MPI processes
type: seqaij
rows=0, cols=0
linear system matrix = precond matrix:
total: nonzeros=0, allocated nonzeros=0
total number of mallocs used during MatSetValues calls =0
not using I-node routines
Matrix Object: 1 MPI processes
type: seqaij
rows=0, cols=0
total: nonzeros=0, allocated nonzeros=0
total number of mallocs used during MatSetValues calls =0
not using I-node routines
[1] number of local blocks = 1, first local block number = 1
[1] local block number 0
- - - - - - - - - - - - - - - - - -
[2] number of local blocks = 1, first local block number = 2
[2] local block number 0
- - - - - - - - - - - - - - - - - -
[3] number of local blocks = 1, first local block number = 3
[3] local block number 0
- - - - - - - - - - - - - - - - - -
[4] number of local blocks = 1, first local block number = 4
[4] local block number 0
- - - - - - - - - - - - - - - - - -
[5] number of local blocks = 1, first local block number = 5
[5] local block number 0
- - - - - - - - - - - - - - - - - -
[6] number of local blocks = 1, first local block number = 6
[6] local block number 0
- - - - - - - - - - - - - - - - - -
[7] number of local blocks = 1, first local block number = 7
[7] local block number 0
- - - - - - - - - - - - - - - - - -
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=718, cols=718
total: nonzeros=6294, allocated nonzeros=6294
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Down solver (pre-smoother) on level 1 -------------------------------
KSP Object: (mg_levels_1_) 8 MPI processes
type: chebyshev
Chebyshev: eigenvalue estimates: min = 0.0710112, max = 1.49123
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_1_) 8 MPI processes
type: jacobi
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=3821, cols=3821
total: nonzeros=31479, allocated nonzeros=31479
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Up solver (post-smoother) same as down solver (pre-smoother)
Down solver (pre-smoother) on level 2 -------------------------------
KSP Object: (mg_levels_2_) 8 MPI processes
type: chebyshev
Chebyshev: eigenvalue estimates: min = 0.071608, max = 1.50377
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_2_) 8 MPI processes
type: jacobi
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=23143, cols=23143
total: nonzeros=230755, allocated nonzeros=230755
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Up solver (post-smoother) same as down solver (pre-smoother)
Down solver (pre-smoother) on level 3 -------------------------------
KSP Object: (mg_levels_3_) 8 MPI processes
type: chebyshev
Chebyshev: eigenvalue estimates: min = 0.075852, max = 1.59289
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_3_) 8 MPI processes
type: jacobi
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=224819, cols=224819
total: nonzeros=2625247, allocated nonzeros=2625247
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Up solver (post-smoother) same as down solver (pre-smoother)
Down solver (pre-smoother) on level 4 -------------------------------
KSP Object: (mg_levels_4_) 8 MPI processes
type: chebyshev
Chebyshev: eigenvalue estimates: min = 0.0977111, max = 2.05193
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_4_) 8 MPI processes
type: jacobi
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=2000000, cols=2000000
total: nonzeros=13900000, allocated nonzeros=13900000
total number of mallocs used during MatSetValues calls =0
Up solver (post-smoother) same as down solver (pre-smoother)
linear system matrix = precond matrix:
Matrix Object: 8 MPI processes
type: mpiaij
rows=2000000, cols=2000000
total: nonzeros=13900000, allocated nonzeros=13900000
total number of mallocs used during MatSetValues calls =0
Residual norm 4.49376e-07
************************************************************************************************************************
*** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document ***
************************************************************************************************************************
---------------------------------------------- PETSc Performance Summary: ----------------------------------------------
./ex45 on a arch-linux2-c-debug named compute-5-2.local with 8 processors, by zlwei Fri Sep 14 17:59:53 2012
Using Petsc Development HG revision: 98bf11863c3be31b7c2af504314a500bc64d88c9 HG Date: Wed Aug 29 13:51:08 2012 -0500
Max Max/Min Avg Total
Time (sec): 7.150e+01 1.00001 7.150e+01
Objects: 4.570e+02 1.00000 4.570e+02
Flops: 2.338e+09 1.00241 2.335e+09 1.868e+10
Flops/sec: 3.270e+07 1.00241 3.266e+07 2.613e+08
Memory: 2.987e+08 1.00000 2.390e+09
MPI Messages: 7.807e+03 1.08415 7.544e+03 6.035e+04
MPI Message Lengths: 4.598e+07 1.00776 6.071e+03 3.664e+08
MPI Reductions: 6.099e+03 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: 7.1498e+01 100.0% 1.8683e+10 100.0% 6.035e+04 100.0% 6.071e+03 100.0% 6.098e+03 100.0%
------------------------------------------------------------------------------------------------------------------------
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
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)
------------------------------------------------------------------------------------------------------------------------
##########################################################
# #
# WARNING!!! #
# #
# This code was compiled with a debugging option, #
# To get timing results run ./configure #
# using --with-debugging=no, the performance will #
# be generally two or three times faster. #
# #
##########################################################
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
KSPGMRESOrthog 118 1.0 3.8889e+00 1.0 5.63e+08 1.0 0.0e+00 0.0e+00 8.8e+02 5 24 0 0 14 5 24 0 0 14 1158
KSPSetUp 11 1.0 9.3905e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 2.4e+01 0 0 0 0 0 0 0 0 0 0 0
KSPSolve 1 1.0 7.0933e+01 1.0 2.33e+09 1.0 6.0e+04 6.1e+03 6.0e+03 99100100100 99 99100100100 99 263
VecMDot 118 1.0 1.8252e+00 1.0 2.82e+08 1.0 0.0e+00 0.0e+00 1.2e+02 3 12 0 0 2 3 12 0 0 2 1234
VecNorm 165 1.0 1.4453e-01 1.2 2.68e+07 1.0 0.0e+00 0.0e+00 1.6e+02 0 1 0 0 3 0 1 0 0 3 1478
VecScale 804 1.0 1.8971e-01 1.0 5.82e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 2 0 0 0 0 2 0 0 0 2452
VecCopy 206 1.0 2.8914e-01 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
VecSet 744 1.0 1.7086e-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
VecAXPY 1328 1.0 1.5434e+00 1.0 1.83e+08 1.0 0.0e+00 0.0e+00 0.0e+00 2 8 0 0 0 2 8 0 0 0 947
VecAYPX 1280 1.0 1.3966e+00 1.0 1.13e+08 1.0 0.0e+00 0.0e+00 0.0e+00 2 5 0 0 0 2 5 0 0 0 645
VecMAXPY 164 1.0 2.1316e+00 1.0 3.06e+08 1.0 0.0e+00 0.0e+00 0.0e+00 3 13 0 0 0 3 13 0 0 0 1149
VecAssemblyBegin 54 1.0 9.9215e-02 1.9 0.00e+00 0.0 0.0e+00 0.0e+00 1.6e+02 0 0 0 0 3 0 0 0 0 3 0
VecAssemblyEnd 54 1.0 4.9758e-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
VecPointwiseMult 1004 1.0 2.0735e+00 1.1 7.07e+07 1.0 0.0e+00 0.0e+00 0.0e+00 3 3 0 0 0 3 3 0 0 0 273
VecScatterBegin 1458 1.0 3.4748e-01 1.1 0.00e+00 0.0 5.6e+04 6.0e+03 0.0e+00 0 0 94 93 0 0 0 94 93 0 0
VecScatterEnd 1458 1.0 2.9766e-01 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
VecSetRandom 4 1.0 3.8469e-01 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
VecNormalize 164 1.0 1.9133e-01 1.1 3.95e+07 1.0 0.0e+00 0.0e+00 1.6e+02 0 2 0 0 3 0 2 0 0 3 1644
MatMult 1080 1.0 1.5564e+01 1.0 1.11e+09 1.0 4.4e+04 6.9e+03 0.0e+00 22 47 73 83 0 22 47 73 83 0 569
MatMultAdd 160 1.0 7.8439e-01 1.0 2.25e+07 1.0 4.8e+03 9.2e+02 0.0e+00 1 1 8 1 0 1 1 8 1 0 229
MatMultTranspose 160 1.0 7.3742e-01 1.0 2.25e+07 1.0 4.8e+03 9.2e+02 3.2e+02 1 1 8 1 5 1 1 8 1 5 244
MatSolve 80 0.0 1.2254e-02 0.0 2.87e+06 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 235
MatLUFactorSym 1 1.0 1.6282e-0317.0 0.00e+00 0.0 0.0e+00 0.0e+00 5.0e+00 0 0 0 0 0 0 0 0 0 0 0
MatLUFactorNum 1 1.0 2.3890e-03107.7 3.37e+05 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 141
MatConvert 4 1.0 1.1830e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 2.4e+01 0 0 0 0 0 0 0 0 0 0 0
MatScale 4 1.0 8.0437e-02 1.0 4.21e+06 1.0 1.7e+02 6.3e+03 0.0e+00 0 0 0 0 0 0 0 0 0 0 417
MatAssemblyBegin 50 1.0 1.9675e-01 2.4 0.00e+00 0.0 4.3e+02 1.2e+03 5.6e+01 0 0 1 0 1 0 0 1 0 1 0
MatAssemblyEnd 50 1.0 8.5181e-01 1.0 0.00e+00 0.0 1.5e+03 1.5e+03 4.0e+02 1 0 3 1 7 1 0 3 1 7 0
MatGetRow 563366 1.0 2.0994e+00 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
MatGetRowIJ 1 0.0 1.4687e-04 0.0 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
MatGetOrdering 1 0.0 1.5841e-03 0.0 0.00e+00 0.0 0.0e+00 0.0e+00 2.5e-01 0 0 0 0 0 0 0 0 0 0 0
MatCoarsen 4 1.0 1.4392e+00 1.0 0.00e+00 0.0 1.4e+03 9.7e+03 1.2e+02 2 0 2 4 2 2 0 2 4 2 0
MatView 8 1.0 4.0925e-03 2.2 0.00e+00 0.0 0.0e+00 0.0e+00 6.0e+00 0 0 0 0 0 0 0 0 0 0 0
MatPtAP 4 1.0 8.0547e-01 1.1 1.25e+07 1.0 1.5e+03 2.3e+03 2.3e+02 1 1 2 1 4 1 1 2 1 4 123
MatPtAPSymbolic 4 1.0 5.3591e-01 1.1 0.00e+00 0.0 1.3e+03 2.1e+03 2.0e+02 1 0 2 1 3 1 0 2 1 3 0
MatPtAPNumeric 4 1.0 2.6955e-01 1.0 1.25e+07 1.0 1.4e+02 4.7e+03 2.4e+01 0 1 0 0 0 0 1 0 0 0 368
MatTrnMatMult 4 1.0 5.9091e+00 1.0 1.28e+08 1.0 1.1e+03 1.9e+04 2.5e+02 8 5 2 6 4 8 5 2 6 4 172
MatGetLocalMat 12 1.0 2.5454e-01 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 3.2e+01 0 0 0 0 1 0 0 0 0 1 0
MatGetBrAoCol 4 1.0 6.7071e-02 2.8 0.00e+00 0.0 5.2e+02 4.2e+03 1.6e+01 0 0 1 1 0 0 0 1 1 0 0
MatGetSymTrans 8 1.0 1.0458e-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
PCSetUp 2 1.0 2.9746e+01 1.0 2.64e+08 1.0 8.4e+03 7.7e+03 1.7e+03 42 11 14 18 29 42 11 14 18 29 71
PCSetUpOnBlocks 40 1.0 6.5384e-03 5.5 3.37e+05 0.0 0.0e+00 0.0e+00 8.0e+00 0 0 0 0 0 0 0 0 0 0 52
PCApply 40 1.0 2.9190e+01 1.0 1.39e+09 1.0 5.1e+04 5.3e+03 3.6e+03 41 60 84 73 59 41 60 84 73 59 381
PCGAMGgraph_AGG 4 1.0 1.2728e+01 1.0 4.21e+06 1.0 5.2e+02 3.1e+03 1.9e+02 18 0 1 0 3 18 0 1 0 3 3
PCGAMGcoarse_AGG 4 1.0 1.1054e+01 1.0 1.28e+08 1.0 3.5e+03 1.2e+04 4.7e+02 15 5 6 12 8 15 5 6 12 8 92
PCGAMGProl_AGG 4 1.0 2.4394e+00 1.0 0.00e+00 0.0 1.1e+03 4.3e+03 2.0e+02 3 0 2 1 3 3 0 2 1 3 0
PCGAMGPOpt_AGG 4 1.0 3.3855e-05 1.5 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
------------------------------------------------------------------------------------------------------------------------
Memory usage is given in bytes:
Object Type Creations Destructions Memory Descendants' Mem.
Reports information only for process 0.
--- Event Stage 0: Main Stage
Container 1 1 548 0
Krylov Solver 11 11 162856 0
Vector 235 235 142154440 0
Vector Scatter 26 26 26936 0
Matrix 92 92 249866276 0
Matrix Coarsen 4 4 2448 0
Distributed Mesh 2 2 2111040 0
Bipartite Graph 4 4 2736 0
Index Set 64 64 1375492 0
IS L to G Mapping 1 1 1051368 0
Preconditioner 11 11 10092 0
Viewer 2 1 712 0
PetscRandom 4 4 2432 0
========================================================================================================================
Average time to get PetscTime(): 5.96046e-07
Average time for MPI_Barrier(): 0.000152588
Average time for zero size MPI_Send(): 7.42376e-05
#PETSc Option Table entries:
-ksp_monitor
-ksp_rtol 1.0e-7
-ksp_view
-log_summary
-pc_type gamg
#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 run at: Wed Aug 29 14:54:25 2012
Configure options: --prefix=/work/zlwei/PETSc --with-cc=gcc --with-fc=gfortran --download-f-blas-lapack --download-mpich
-----------------------------------------
Libraries compiled on Wed Aug 29 14:54:25 2012 on firefox.bioinfo.ittc.ku.edu
Machine characteristics: Linux-2.6.18-92.1.13.el5-x86_64-with-redhat-5.2-Final
Using PETSc directory: /nfs/work/zlwei/PETSc/petsc-dev
Using PETSc arch: arch-linux2-c-debug
-----------------------------------------
Using C compiler: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -fno-inline -O0 ${COPTFLAGS} ${CFLAGS}
Using Fortran compiler: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpif90 -Wall -Wno-unused-variable -g ${FOPTFLAGS} ${FFLAGS}
-----------------------------------------
Using include paths: -I/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/include -I/nfs/work/zlwei/PETSc/petsc-dev/include -I/nfs/work/zlwei/PETSc/petsc-dev/include -I/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/include
-----------------------------------------
Using C linker: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpicc
Using Fortran linker: /nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/bin/mpif90
Using libraries: -Wl,-rpath,/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -L/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -lpetsc -lX11 -lpthread -Wl,-rpath,/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -L/nfs/work/zlwei/PETSc/petsc-dev/arch-linux2-c-debug/lib -lflapack -lfblas -lm -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -lmpichf90 -lgfortran -lm -lm -ldl -lmpich -lopa -lmpl -lrt -lgcc_s -ldl
-----------------------------------------
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