[petsc-users] HPCToolKit/HPCViewer on OS X
Griffith, Boyce Eugene
boyceg at email.unc.edu
Thu Jan 14 14:30:54 CST 2016
On Jan 14, 2016, at 3:09 PM, Barry Smith <bsmith at mcs.anl.gov<mailto:bsmith at mcs.anl.gov>> wrote:
On Jan 14, 2016, at 2:01 PM, Griffith, Boyce Eugene <boyceg at email.unc.edu<mailto:boyceg at email.unc.edu>> wrote:
On Jan 14, 2016, at 2:24 PM, Barry Smith <bsmith at mcs.anl.gov<mailto:bsmith at mcs.anl.gov>> wrote:
Matt is right, there is a lot of "missing" time from the output. Please send the output from -ksp_view so we can see exactly what solver is being used.
>From the output we have:
Nonlinear solver 78 % of the time (so your "setup code" outside of PETSC is taking about 22% of the time)
Linear solver 77 % of the time (this is reasonable pretty much the entire cost of the nonlinear solve is the linear solve)
Time to set up the preconditioner is 19% (10 + 9)
Time of iteration in KSP 35 % (this is the sum of the vector operations and MatMult() and MatSolve())
So 77 - (19 + 35) = 23 % unexplained time inside the linear solver (custom preconditioner???)
Also getting the results with Instruments or HPCToolkit would be useful (so long as we don't need to install HPCTool ourselves to see the results).
Thanks, Barry (& Matt & Dave) --- This is a solver that is mixing some matrix-based stuff implemented using PETSc along with some matrix-free stuff that is built on top of SAMRAI. Amneet and I should take a look at performance off-list first.
Just put an PetscLogEvent() in (or several) to track that part. Plus put an event or two outside the SNESSolve to track the outside PETSc setup time.
The PETSc time looks reasonable at most I can only image any optimizations we could do bringing it down a small percentage.
Here is a bit more info about what we are trying to do:
This is a Vanka-type MG preconditioner for a Stokes-like system on a structured grid. (Currently just uniform grids, but hopefully soon with AMR.) For the smoother, we are using damped Richardson + ASM with relatively small block subdomains --- e.g., all DOFs associated with 8x8 cells in 2D (~300 DOFs), or 8x8x8 in 3D (~2500 DOFs). Unfortunately, MG iteration counts really tank when using smaller subdomains.
I can't remember whether we have quantified this carefully, but PCASM seems to bog down with smaller subdomains. A question is whether there are different implementation choices that could make the case of "lots of little subdomains" run faster. But before we get to that, Amneet and I should take a more careful look at overall solver performance.
(We are also starting to play around with PCFIELDSPLIT for this problem too, although we don't have many ideas about how to handle the Schur complement.)
Thanks,
-- Boyce
Barry
-- Boyce
Barry
On Jan 14, 2016, at 1:26 AM, Bhalla, Amneet Pal S <amneetb at live.unc.edu<mailto:amneetb at live.unc.edu>> wrote:
On Jan 13, 2016, at 9:17 PM, Griffith, Boyce Eugene <boyceg at email.unc.edu<mailto:boyceg at email.unc.edu>> wrote:
I see one hot spot:
Here is with opt build
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*** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document ***
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---------------------------------------------- PETSc Performance Summary: ----------------------------------------------
./main2d on a linux-opt named aorta with 1 processor, by amneetb Thu Jan 14 02:24:43 2016
Using Petsc Development GIT revision: v3.6.3-3098-ga3ecda2 GIT Date: 2016-01-13 21:30:26 -0600
Max Max/Min Avg Total
Time (sec): 1.018e+00 1.00000 1.018e+00
Objects: 2.935e+03 1.00000 2.935e+03
Flops: 4.957e+08 1.00000 4.957e+08 4.957e+08
Flops/sec: 4.868e+08 1.00000 4.868e+08 4.868e+08
MPI Messages: 0.000e+00 0.00000 0.000e+00 0.000e+00
MPI Message Lengths: 0.000e+00 0.00000 0.000e+00 0.000e+00
MPI Reductions: 0.000e+00 0.00000
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: 1.0183e+00 100.0% 4.9570e+08 100.0% 0.000e+00 0.0% 0.000e+00 0.0% 0.000e+00 0.0%
------------------------------------------------------------------------------------------------------------------------
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 4 1.0 2.9564e-05 1.0 3.31e+04 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 1120
VecDotNorm2 272 1.0 1.4565e-03 1.0 4.25e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 2920
VecMDot 624 1.0 8.4300e-03 1.0 5.29e+06 1.0 0.0e+00 0.0e+00 0.0e+00 1 1 0 0 0 1 1 0 0 0 627
VecNorm 565 1.0 3.8033e-03 1.0 4.38e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 1151
VecScale 86 1.0 5.5480e-04 1.0 1.55e+05 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 279
VecCopy 28 1.0 5.2261e-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 14567 1.0 1.2443e-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
VecAXPY 903 1.0 4.2996e-03 1.0 6.66e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 1550
VecAYPX 225 1.0 1.2550e-03 1.0 8.55e+05 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 681
VecAXPBYCZ 42 1.0 1.7118e-04 1.0 3.45e+05 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 2014
VecWAXPY 70 1.0 1.9503e-04 1.0 2.98e+05 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 1528
VecMAXPY 641 1.0 1.1136e-02 1.0 5.29e+06 1.0 0.0e+00 0.0e+00 0.0e+00 1 1 0 0 0 1 1 0 0 0 475
VecSwap 135 1.0 4.5896e-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
VecAssemblyBegin 745 1.0 4.9477e-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
VecAssemblyEnd 745 1.0 9.2411e-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
VecScatterBegin 40831 1.0 3.4502e-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
BuildTwoSidedF 738 1.0 2.6712e-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
MatMult 513 1.0 9.1235e-02 1.0 7.75e+07 1.0 0.0e+00 0.0e+00 0.0e+00 9 16 0 0 0 9 16 0 0 0 849
MatSolve 13568 1.0 2.3605e-01 1.0 3.45e+08 1.0 0.0e+00 0.0e+00 0.0e+00 23 70 0 0 0 23 70 0 0 0 1460
MatLUFactorSym 84 1.0 3.7430e-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
MatLUFactorNum 85 1.0 3.9623e-02 1.0 4.19e+07 1.0 0.0e+00 0.0e+00 0.0e+00 4 8 0 0 0 4 8 0 0 0 1058
MatILUFactorSym 1 1.0 3.3617e-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
MatScale 4 1.0 2.5511e-04 1.0 2.51e+05 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 984
MatAssemblyBegin 108 1.0 6.3658e-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
MatAssemblyEnd 108 1.0 2.9490e-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
MatGetRow 33120 1.0 2.0157e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0
MatGetRowIJ 85 1.0 1.2145e-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
MatGetSubMatrice 4 1.0 8.4379e-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 85 1.0 7.7887e-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
MatAXPY 4 1.0 4.9596e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 5 0 0 0 0 5 0 0 0 0 0
MatPtAP 4 1.0 4.4426e-02 1.0 4.99e+06 1.0 0.0e+00 0.0e+00 0.0e+00 4 1 0 0 0 4 1 0 0 0 112
MatPtAPSymbolic 4 1.0 2.7664e-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
MatPtAPNumeric 4 1.0 1.6732e-02 1.0 4.99e+06 1.0 0.0e+00 0.0e+00 0.0e+00 2 1 0 0 0 2 1 0 0 0 298
MatGetSymTrans 4 1.0 3.6621e-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
KSPGMRESOrthog 16 1.0 9.7778e-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
KSPSetUp 90 1.0 5.7650e-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 1 1.0 7.8831e-01 1.0 4.90e+08 1.0 0.0e+00 0.0e+00 0.0e+00 77 99 0 0 0 77 99 0 0 0 622
PCSetUp 90 1.0 9.9725e-02 1.0 4.19e+07 1.0 0.0e+00 0.0e+00 0.0e+00 10 8 0 0 0 10 8 0 0 0 420
PCSetUpOnBlocks 112 1.0 8.7547e-02 1.0 4.19e+07 1.0 0.0e+00 0.0e+00 0.0e+00 9 8 0 0 0 9 8 0 0 0 479
PCApply 16 1.0 7.1952e-01 1.0 4.89e+08 1.0 0.0e+00 0.0e+00 0.0e+00 71 99 0 0 0 71 99 0 0 0 680
SNESSolve 1 1.0 7.9225e-01 1.0 4.90e+08 1.0 0.0e+00 0.0e+00 0.0e+00 78 99 0 0 0 78 99 0 0 0 619
SNESFunctionEval 2 1.0 3.2940e-03 1.0 4.68e+04 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 14
SNESJacobianEval 1 1.0 4.7255e-04 1.0 4.26e+03 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 9
------------------------------------------------------------------------------------------------------------------------
Memory usage is given in bytes:
Object Type Creations Destructions Memory Descendants' Mem.
Reports information only for process 0.
--- Event Stage 0: Main Stage
Vector 971 839 15573352 0.
Vector Scatter 290 289 189584 0.
Index Set 1171 823 951928 0.
IS L to G Mapping 110 109 2156656 0.
Application Order 6 6 99952 0.
MatMFFD 1 1 776 0.
Matrix 189 189 24083332 0.
Matrix Null Space 4 4 2432 0.
Krylov Solver 90 90 122720 0.
DMKSP interface 1 1 648 0.
Preconditioner 90 90 89872 0.
SNES 1 1 1328 0.
SNESLineSearch 1 1 984 0.
DMSNES 1 1 664 0.
Distributed Mesh 2 2 9168 0.
Star Forest Bipartite Graph 4 4 3168 0.
Discrete System 2 2 1712 0.
Viewer 1 0 0 0.
========================================================================================================================
Average time to get PetscTime(): 9.53674e-07
#PETSc Option Table entries:
-ib_ksp_converged_reason
-ib_ksp_monitor_true_residual
-ib_snes_type ksponly
-log_summary
-stokes_ib_pc_level_0_sub_pc_factor_nonzeros_along_diagonal
-stokes_ib_pc_level_0_sub_pc_type ilu
-stokes_ib_pc_level_ksp_richardson_self_scale
-stokes_ib_pc_level_ksp_type richardson
-stokes_ib_pc_level_pc_asm_local_type additive
-stokes_ib_pc_level_sub_pc_factor_nonzeros_along_diagonal
-stokes_ib_pc_level_sub_pc_type lu
#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: --CC=mpicc --CXX=mpicxx --FC=mpif90 --with-default-arch=0 --PETSC_ARCH=linux-opt --with-debugging=0 --with-c++-support=1 --with-hypre=1 --download-hypre=1 --with-hdf5=yes --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3
-----------------------------------------
Libraries compiled on Thu Jan 14 01:29:56 2016 on aorta
Machine characteristics: Linux-3.13.0-63-generic-x86_64-with-Ubuntu-14.04-trusty
Using PETSc directory: /not_backed_up/amneetb/softwares/PETSc-BitBucket/PETSc
Using PETSc arch: linux-opt
-----------------------------------------
Using C compiler: mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Qunused-arguments -O3 ${COPTFLAGS} ${CFLAGS}
Using Fortran compiler: mpif90 -fPIC -Wall -Wno-unused-variable -ffree-line-length-0 -Wno-unused-dummy-argument -O3 ${FOPTFLAGS} ${FFLAGS}
-----------------------------------------
Using include paths: -I/not_backed_up/amneetb/softwares/PETSc-BitBucket/PETSc/linux-opt/include -I/not_backed_up/amneetb/softwares/PETSc-BitBucket/PETSc/include -I/not_backed_up/amneetb/softwares/PETSc-BitBucket/PETSc/include -I/not_backed_up/amneetb/softwares/PETSc-BitBucket/PETSc/linux-opt/include -I/not_backed_up/softwares/MPICH/include
-----------------------------------------
Using C linker: mpicc
Using Fortran linker: mpif90
Using libraries: -Wl,-rpath,/not_backed_up/amneetb/softwares/PETSc-BitBucket/PETSc/linux-opt/lib -L/not_backed_up/amneetb/softwares/PETSc-BitBucket/PETSc/linux-opt/lib -lpetsc -Wl,-rpath,/not_backed_up/amneetb/softwares/PETSc-BitBucket/PETSc/linux-opt/lib -L/not_backed_up/amneetb/softwares/PETSc-BitBucket/PETSc/linux-opt/lib -lHYPRE -Wl,-rpath,/not_backed_up/softwares/MPICH/lib -L/not_backed_up/softwares/MPICH/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lmpicxx -lstdc++ -llapack -lblas -lpthread -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lX11 -lm -lmpifort -lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpicxx -lstdc++ -Wl,-rpath,/not_backed_up/softwares/MPICH/lib -L/not_backed_up/softwares/MPICH/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ldl -Wl,-rpath,/not_backed_up/softwares/MPICH/lib -lmpi -lgcc_s -ldl
-----------------------------------------
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