[petsc-users] Help my solver scale
Manuel Valera
mvalera-w at sdsu.edu
Wed May 2 15:19:11 CDT 2018
Hello guys,
We are working in writing a paper about the parallelization of our model
using PETSc, which is very exciting since is the first time we see our
model scaling, but so far i feel my results for the laplacian solver could
be much better,
For example, using CG/Multigrid i get less than 20% of efficiency after 16
cores, up to 64 cores where i get only 8% efficiency,
I am defining efficiency as speedup over number of cores, and speedup as
twall_n/twall_1 where n is the number of cores, i think that's pretty
standard,
The ksp_view for a distributed solve looks like this:
KSP Object: 16 MPI processes
type: cg
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000.
left preconditioning
using PRECONDITIONED norm type for convergence test
PC Object: 16 MPI processes
type: hypre
HYPRE BoomerAMG preconditioning
Cycle type V
Maximum number of levels 25
Maximum number of iterations PER hypre call 1
Convergence tolerance PER hypre call 0.
Threshold for strong coupling 0.25
Interpolation truncation factor 0.
Interpolation: max elements per row 0
Number of levels of aggressive coarsening 0
Number of paths for aggressive coarsening 1
Maximum row sums 0.9
Sweeps down 1
Sweeps up 1
Sweeps on coarse 1
Relax down symmetric-SOR/Jacobi
Relax up symmetric-SOR/Jacobi
Relax on coarse Gaussian-elimination
Relax weight (all) 1.
Outer relax weight (all) 1.
Using CF-relaxation
Not using more complex smoothers.
Measure type local
Coarsen type Falgout
Interpolation type classical
Using nodal coarsening (with HYPRE_BOOMERAMGSetNodal() 1
HYPRE_BoomerAMGSetInterpVecVariant() 1
linear system matrix = precond matrix:
Mat Object: 16 MPI processes
type: mpiaij
rows=213120, cols=213120
total: nonzeros=3934732, allocated nonzeros=8098560
total number of mallocs used during MatSetValues calls =0
has attached near null space
And the log_view for the same case would be:
************************************************************************************************************************
*** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r
-fCourier9' to print this document ***
************************************************************************************************************************
---------------------------------------------- PETSc Performance Summary:
----------------------------------------------
./gcmSeamount on a timings named ocean with 16 processors, by valera Wed
May 2 13:18:21 2018
Using Petsc Development GIT revision: v3.9-163-gbe3efd4 GIT Date:
2018-04-16 10:45:40 -0500
Max Max/Min Avg Total
Time (sec): 1.355e+00 1.00004 1.355e+00
Objects: 4.140e+02 1.00000 4.140e+02
Flop: 7.582e+05 1.09916 7.397e+05 1.183e+07
Flop/sec: 5.594e+05 1.09918 5.458e+05 8.732e+06
MPI Messages: 1.588e+03 1.19167 1.468e+03 2.348e+04
MPI Message Lengths: 7.112e+07 1.37899 4.462e+04 1.048e+09
MPI Reductions: 4.760e+02 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 flop
and VecAXPY() for complex vectors of length N
--> 8N flop
Summary of Stages: ----- Time ------ ----- Flop ----- --- Messages ---
-- Message Lengths -- -- Reductions --
Avg %Total Avg %Total counts
%Total Avg %Total counts %Total
0: Main Stage: 1.3553e+00 100.0% 1.1835e+07 100.0% 2.348e+04
100.0% 4.462e+04 100.0% 4.670e+02 98.1%
------------------------------------------------------------------------------------------------------------------------
See the 'Profiling' chapter of the users' manual for details on
interpreting output.
Phase summary info:
Count: number of times phase was executed
Time and Flop: Max - maximum over all processors
Ratio - ratio of maximum to minimum over all processors
Mess: number of messages sent
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 flop in this
phase
%M - percent messages in this phase %L - percent message lengths
in this phase
%R - percent reductions in this phase
Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over
all processors)
------------------------------------------------------------------------------------------------------------------------
Event Count Time (sec) Flop
--- Global --- --- Stage --- Total
Max Ratio Max Ratio Max Ratio Mess Avg len
Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s
------------------------------------------------------------------------------------------------------------------------
--- Event Stage 0: Main Stage
BuildTwoSidedF 2 1.0 9.1908e-03 2.2 0.00e+00 0.0 3.6e+02 1.6e+05
0.0e+00 1 0 2 6 0 1 0 2 6 0 0
VecTDot 1 1.0 6.4135e-05 1.1 2.66e+04 1.0 0.0e+00 0.0e+00
1.0e+00 0 4 0 0 0 0 4 0 0 0 6646
VecNorm 1 1.0 1.4589e-0347.1 2.66e+04 1.0 0.0e+00 0.0e+00
1.0e+00 0 4 0 0 0 0 4 0 0 0 292
VecScale 14 1.0 3.6144e-04 1.3 4.80e+05 1.1 0.0e+00 0.0e+00
0.0e+00 0 62 0 0 0 0 62 0 0 0 20346
VecCopy 7 1.0 1.0152e-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
VecSet 83 1.0 3.0013e-02 2.3 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
VecPointwiseMult 12 1.0 2.7585e-04 1.4 2.43e+05 1.2 0.0e+00 0.0e+00
0.0e+00 0 31 0 0 0 0 31 0 0 0 13153
VecScatterBegin 111 1.0 2.5293e-02 1.8 0.00e+00 0.0 9.5e+03 3.4e+04
1.9e+01 1 0 40 31 4 1 0 40 31 4 0
VecScatterEnd 92 1.0 4.8771e-02 2.3 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
VecNormalize 1 1.0 2.6941e-05 2.3 1.33e+04 1.0 0.0e+00 0.0e+00
0.0e+00 0 2 0 0 0 0 2 0 0 0 7911
MatConvert 1 1.0 1.1009e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
4.0e+00 1 0 0 0 1 1 0 0 0 1 0
MatAssemblyBegin 3 1.0 2.8401e-02 1.0 0.00e+00 0.0 3.6e+02 1.6e+05
0.0e+00 2 0 2 6 0 2 0 2 6 0 0
MatAssemblyEnd 3 1.0 2.9033e-02 1.0 0.00e+00 0.0 6.0e+01 1.2e+04
2.0e+01 2 0 0 0 4 2 0 0 0 4 0
MatGetRowIJ 2 1.0 1.9073e-06 2.0 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
MatView 1 1.0 3.0398e-04 5.0 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
KSPSetUp 1 1.0 4.7994e-04 2.3 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
KSPSolve 1 1.0 2.4850e-03 2.0 5.33e+04 1.0 0.0e+00 0.0e+00
2.0e+00 0 7 0 0 0 0 7 0 0 0 343
PCSetUp 2 1.0 2.2953e-02 1.0 1.33e+04 1.0 0.0e+00 0.0e+00
6.0e+00 2 2 0 0 1 2 2 0 0 1 9
PCApply 1 1.0 1.3151e-03 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
Vector 172 170 70736264 0.
Matrix 5 5 7125104 0.
Matrix Null Space 1 1 608 0.
Distributed Mesh 18 16 84096 0.
Index Set 73 73 10022204 0.
IS L to G Mapping 18 16 1180828 0.
Star Forest Graph 36 32 27968 0.
Discrete System 18 16 15040 0.
Vec Scatter 67 64 38240520 0.
Krylov Solver 2 2 2504 0.
Preconditioner 2 2 2528 0.
Viewer 2 1 848 0.
========================================================================================================================
Average time to get PetscTime(): 0.
Average time for MPI_Barrier(): 2.38419e-06
Average time for zero size MPI_Send(): 2.11596e-06
#PETSc Option Table entries:
-da_processors_z 1
-ksp_type cg
-ksp_view
-log_view
-pc_hypre_boomeramg_nodal_coarsen 1
-pc_hypre_boomeramg_vec_interp_variant 1
#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: --known-level1-dcache-size=32768
--known-level1-dcache-linesize=64 --known-level1-dcache-assoc=8
--known-sizeof-char=1 --known-sizeof-void-p=8 --known-sizeof-short=2
--known-sizeof-int=4 --known-sizeof-long=8 --known-sizeof-long-long=8
--known-sizeof-float=4 --known-sizeof-double=8 --known-sizeof-size_t=8
--known-bits-per-byte=8 --known-memcmp-ok=1 --known-sizeof-MPI_Comm=8
--known-sizeof-MPI_Fint=4 --known-mpi-long-double=1 --known-mpi-int64_t=1
--known-mpi-c-double-complex=1 --known-has-attribute-aligned=1
PETSC_ARCH=timings --with-mpi-dir=/usr/lib64/openmpi
--with-blaslapack-dir=/usr/lib64 COPTFLAGS=-O3 CXXOPTFLAGS=-O3
FOPTFLAGS=-O3 --with-shared-libraries=1 --download-hypre
--with-debugging=no --with-batch -known-mpi-shared-libraries=0
--known-64-bit-blas-indices=0
-----------------------------------------
Libraries compiled on 2018-04-27 21:13:11 on ocean
Machine characteristics:
Linux-3.10.0-327.36.3.el7.x86_64-x86_64-with-centos-7.2.1511-Core
Using PETSc directory: /home/valera/petsc
Using PETSc arch: timings
-----------------------------------------
Using C compiler: /usr/lib64/openmpi/bin/mpicc -fPIC -Wall
-Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
-fvisibility=hidden -O3
Using Fortran compiler: /usr/lib64/openmpi/bin/mpif90 -fPIC -Wall
-ffree-line-length-0 -Wno-unused-dummy-argument -O3
-----------------------------------------
Using include paths: -I/home/valera/petsc/include
-I/home/valera/petsc/timings/include -I/usr/lib64/openmpi/include
-----------------------------------------
Using C linker: /usr/lib64/openmpi/bin/mpicc
Using Fortran linker: /usr/lib64/openmpi/bin/mpif90
Using libraries: -Wl,-rpath,/home/valera/petsc/timings/lib
-L/home/valera/petsc/timings/lib -lpetsc
-Wl,-rpath,/home/valera/petsc/timings/lib -L/home/valera/petsc/timings/lib
-Wl,-rpath,/usr/lib64 -L/usr/lib64 -Wl,-rpath,/usr/lib64/openmpi/lib
-L/usr/lib64/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5
-L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -lHYPRE -llapack -lblas -lm
-lstdc++ -ldl -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm
-lgcc_s -lquadmath -lpthread -lstdc++ -ldl
What do you see wrong here? what options could i try to improve my solver
scaling?
Thanks so much,
Manuel
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20180502/f42f16a9/attachment.html>
More information about the petsc-users
mailing list