[petsc-users] [EXTERNAL] Re: Performance problem using COO interface
Fackler, Philip
facklerpw at ornl.gov
Mon Jan 23 09:52:08 CST 2023
Thank you for looking into that.
Philip Fackler
Research Software Engineer, Application Engineering Group
Advanced Computing Systems Research Section
Computer Science and Mathematics Division
Oak Ridge National Laboratory
________________________________
From: Junchao Zhang <junchao.zhang at gmail.com>
Sent: Monday, January 23, 2023 10:34
To: Fackler, Philip <facklerpw at ornl.gov>
Cc: Zhang, Junchao <jczhang at mcs.anl.gov>; xolotl-psi-development at lists.sourceforge.net <xolotl-psi-development at lists.sourceforge.net>; petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>; Blondel, Sophie <sblondel at utk.edu>; Roth, Philip <rothpc at ornl.gov>
Subject: [EXTERNAL] Re: [petsc-users] Performance problem using COO interface
Hi, Philip,
It looks the performance of MatPtAP is pretty bad. There are a lot of issues with PtAP, which I am going to address.
MatPtAPNumeric 181 1.0 nan nan 0.00e+00 0.0 3.3e+03 1.8e+04 0.0e+00 56 0 4 21 0 56 0 4 21 0 -nan -nan 0 0.00e+00 0 0.00e+00 0
Thanks.
--Junchao Zhang
On Fri, Jan 20, 2023 at 10:55 AM Fackler, Philip via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
The following is the log_view output for the ported case using 4 MPI tasks.
****************************************************************************************************************************************************************
*** WIDEN YOUR WINDOW TO 160 CHARACTERS. Use 'enscript -r -fCourier9' to print this document ***
****************************************************************************************************************************************************************
------------------------------------------------------------------ PETSc Performance Summary: ------------------------------------------------------------------
Unknown Name on a named iguazu with 4 processors, by 4pf Fri Jan 20 11:53:04 2023
Using Petsc Release Version 3.18.3, unknown
Max Max/Min Avg Total
Time (sec): 1.447e+01 1.000 1.447e+01
Objects: 1.229e+03 1.003 1.226e+03
Flops: 5.053e+09 1.217 4.593e+09 1.837e+10
Flops/sec: 3.492e+08 1.217 3.174e+08 1.269e+09
MPI Msg Count: 1.977e+04 1.067 1.895e+04 7.580e+04
MPI Msg Len (bytes): 7.374e+07 1.088 3.727e+03 2.825e+08
MPI Reductions: 2.065e+03 1.000
Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract)
e.g., VecAXPY() for real vectors of length N --> 2N flops
and VecAXPY() for complex vectors of length N --> 8N flops
Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages --- -- Message Lengths -- -- Reductions --
Avg %Total Avg %Total Count %Total Avg %Total Count %Total
0: Main Stage: 1.4471e+01 100.0% 1.8371e+10 100.0% 7.580e+04 100.0% 3.727e+03 100.0% 2.046e+03 99.1%
------------------------------------------------------------------------------------------------------------------------
See the 'Profiling' chapter of the users' manual for details on interpreting output.
Phase summary info:
Count: number of times phase was executed
Time and Flop: Max - maximum over all processors
Ratio - ratio of maximum to minimum over all processors
Mess: number of messages sent
AvgLen: average message length (bytes)
Reduct: number of global reductions
Global: entire computation
Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop().
%T - percent time in this phase %F - percent flop in this phase
%M - percent messages in this phase %L - percent message lengths in this phase
%R - percent reductions in this phase
Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over all processors)
GPU Mflop/s: 10e-6 * (sum of flop on GPU over all processors)/(max GPU time over all processors)
CpuToGpu Count: total number of CPU to GPU copies per processor
CpuToGpu Size (Mbytes): 10e-6 * (total size of CPU to GPU copies per processor)
GpuToCpu Count: total number of GPU to CPU copies per processor
GpuToCpu Size (Mbytes): 10e-6 * (total size of GPU to CPU copies per processor)
GPU %F: percent flops on GPU in this event
------------------------------------------------------------------------------------------------------------------------
Event Count Time (sec) Flop --- Global --- --- Stage ---- Total
GPU - CpuToGpu - - GpuToCpu - GPU
Max Ratio Max Ratio Max Ratio Mess AvgLen Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s
Mflop/s Count Size Count Size %F
------------------------------------------------------------------------------------------------------------------------
---------------------------------------
--- Event Stage 0: Main Stage
BuildTwoSided 257 1.0 nan nan 0.00e+00 0.0 4.4e+02 8.0e+00 2.6e+02 1 0 1 0 12 1 0 1 0 13 -nan
-nan 0 0.00e+00 0 0.00e+00 0
BuildTwoSidedF 210 1.0 nan nan 0.00e+00 0.0 1.5e+02 4.2e+04 2.1e+02 1 0 0 2 10 1 0 0 2 10 -nan
-nan 0 0.00e+00 0 0.00e+00 0
DMCreateMat 1 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 7.0e+00 10 0 0 0 0 10 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
SFSetGraph 69 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
SFSetUp 47 1.0 nan nan 0.00e+00 0.0 7.3e+02 2.1e+03 4.7e+01 0 0 1 1 2 0 0 1 1 2 -nan
-nan 0 0.00e+00 0 0.00e+00 0
SFBcastBegin 222 1.0 nan nan 0.00e+00 0.0 2.3e+03 1.9e+04 0.0e+00 0 0 3 16 0 0 0 3 16 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
SFBcastEnd 222 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 3 0 0 0 0 3 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
SFReduceBegin 254 1.0 nan nan 0.00e+00 0.0 1.5e+03 1.2e+04 0.0e+00 0 0 2 6 0 0 0 2 6 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
SFReduceEnd 254 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 3 0 0 0 0 3 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
SFFetchOpBegin 1 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
SFFetchOpEnd 1 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
SFPack 8091 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
SFUnpack 8092 1.0 nan nan 4.78e+04 1.5 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
VecDot 60 1.0 nan nan 4.30e+06 1.2 0.0e+00 0.0e+00 6.0e+01 0 0 0 0 3 0 0 0 0 3 -nan
-nan 0 0.00e+00 0 0.00e+00 100
VecMDot 398 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 4.0e+02 0 0 0 0 19 0 0 0 0 19 -nan
-nan 0 0.00e+00 0 0.00e+00 0
VecNorm 641 1.0 nan nan 4.45e+07 1.2 0.0e+00 0.0e+00 6.4e+02 1 1 0 0 31 1 1 0 0 31 -nan
-nan 0 0.00e+00 0 0.00e+00 100
VecScale 601 1.0 nan nan 2.08e+07 1.2 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
VecCopy 3735 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
VecSet 2818 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
VecAXPY 123 1.0 nan nan 8.68e+06 1.2 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
VecAYPX 6764 1.0 nan nan 1.90e+08 1.2 0.0e+00 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
VecAXPBYCZ 2388 1.0 nan nan 1.83e+08 1.2 0.0e+00 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
VecWAXPY 60 1.0 nan nan 4.30e+06 1.2 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
VecMAXPY 681 1.0 nan nan 1.36e+08 1.2 0.0e+00 0.0e+00 0.0e+00 0 3 0 0 0 0 3 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
VecAssemblyBegin 7 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 6.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
VecAssemblyEnd 7 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
VecPointwiseMult 4449 1.0 nan nan 6.06e+07 1.2 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
VecScatterBegin 7614 1.0 nan nan 0.00e+00 0.0 7.1e+04 2.9e+03 1.3e+01 0 0 94 73 1 0 0 94 73 1 -nan
-nan 0 0.00e+00 0 0.00e+00 0
VecScatterEnd 7614 1.0 nan nan 4.78e+04 1.5 0.0e+00 0.0e+00 0.0e+00 3 0 0 0 0 3 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
VecReduceArith 120 1.0 nan nan 8.60e+06 1.2 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
VecReduceComm 60 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 6.0e+01 0 0 0 0 3 0 0 0 0 3 -nan
-nan 0 0.00e+00 0 0.00e+00 0
VecNormalize 401 1.0 nan nan 4.09e+07 1.2 0.0e+00 0.0e+00 4.0e+02 0 1 0 0 19 0 1 0 0 20 -nan
-nan 0 0.00e+00 0 0.00e+00 100
TSStep 20 1.0 1.2908e+01 1.0 5.05e+09 1.2 7.6e+04 3.7e+03 2.0e+03 89 100 100 98 96 89 100 100 98 97 1423
-nan 0 0.00e+00 0 0.00e+00 99
TSFunctionEval 140 1.0 nan nan 1.00e+07 1.2 1.1e+03 3.7e+04 0.0e+00 1 0 1 15 0 1 0 1 15 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
TSJacobianEval 60 1.0 nan nan 1.67e+07 1.2 4.8e+02 3.7e+04 6.0e+01 2 0 1 6 3 2 0 1 6 3 -nan
-nan 0 0.00e+00 0 0.00e+00 87
MatMult 4934 1.0 nan nan 4.16e+09 1.2 5.1e+04 2.7e+03 4.0e+00 15 82 68 49 0 15 82 68 49 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
MatMultAdd 1104 1.0 nan nan 9.00e+07 1.2 8.8e+03 1.4e+02 0.0e+00 1 2 12 0 0 1 2 12 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
MatMultTranspose 1104 1.0 nan nan 9.01e+07 1.2 8.8e+03 1.4e+02 1.0e+00 1 2 12 0 0 1 2 12 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
MatSolve 368 0.0 nan nan 3.57e+04 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatSOR 60 1.0 nan nan 3.12e+07 1.2 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatLUFactorSym 2 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatLUFactorNum 2 1.0 nan nan 4.24e+02 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatConvert 8 1.0 nan nan 0.00e+00 0.0 8.0e+01 1.2e+03 4.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatScale 66 1.0 nan nan 1.48e+07 1.2 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 99
MatResidual 1104 1.0 nan nan 1.01e+09 1.2 1.2e+04 2.9e+03 0.0e+00 4 20 16 12 0 4 20 16 12 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
MatAssemblyBegin 590 1.0 nan nan 0.00e+00 0.0 1.5e+02 4.2e+04 2.0e+02 1 0 0 2 10 1 0 0 2 10 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatAssemblyEnd 590 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 1.4e+02 2 0 0 0 7 2 0 0 0 7 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatGetRowIJ 2 0.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatCreateSubMat 122 1.0 nan nan 0.00e+00 0.0 6.3e+01 1.8e+02 1.7e+02 2 0 0 0 8 2 0 0 0 8 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatGetOrdering 2 0.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatCoarsen 3 1.0 nan nan 0.00e+00 0.0 5.0e+02 1.3e+03 1.2e+02 0 0 1 0 6 0 0 1 0 6 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatZeroEntries 61 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatAXPY 6 1.0 nan nan 1.37e+06 1.2 0.0e+00 0.0e+00 1.8e+01 1 0 0 0 1 1 0 0 0 1 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatTranspose 6 1.0 nan nan 0.00e+00 0.0 2.2e+02 2.9e+04 4.8e+01 1 0 0 2 2 1 0 0 2 2 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatMatMultSym 4 1.0 nan nan 0.00e+00 0.0 2.2e+02 1.7e+03 2.8e+01 0 0 0 0 1 0 0 0 0 1 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatMatMultNum 4 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatPtAPSymbolic 5 1.0 nan nan 0.00e+00 0.0 6.2e+02 5.2e+03 4.4e+01 3 0 1 1 2 3 0 1 1 2 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatPtAPNumeric 181 1.0 nan nan 0.00e+00 0.0 3.3e+03 1.8e+04 0.0e+00 56 0 4 21 0 56 0 4 21 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatGetLocalMat 185 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatSetPreallCOO 1 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 1.0e+01 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
MatSetValuesCOO 60 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
KSPSetUp 483 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 2.2e+01 0 0 0 0 1 0 0 0 0 1 -nan
-nan 0 0.00e+00 0 0.00e+00 0
KSPSolve 60 1.0 1.1843e+01 1.0 4.91e+09 1.2 7.3e+04 2.9e+03 1.2e+03 82 97 97 75 60 82 97 97 75 60 1506
-nan 0 0.00e+00 0 0.00e+00 99
KSPGMRESOrthog 398 1.0 nan nan 7.97e+07 1.2 0.0e+00 0.0e+00 4.0e+02 1 2 0 0 19 1 2 0 0 19 -nan
-nan 0 0.00e+00 0 0.00e+00 100
SNESSolve 60 1.0 1.2842e+01 1.0 5.01e+09 1.2 7.5e+04 3.6e+03 2.0e+03 89 99 100 96 95 89 99 100 96 96 1419
-nan 0 0.00e+00 0 0.00e+00 99
SNESSetUp 1 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 2.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
SNESFunctionEval 120 1.0 nan nan 3.01e+07 1.2 9.6e+02 3.7e+04 0.0e+00 1 1 1 13 0 1 1 1 13 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
SNESJacobianEval 60 1.0 nan nan 1.67e+07 1.2 4.8e+02 3.7e+04 6.0e+01 2 0 1 6 3 2 0 1 6 3 -nan
-nan 0 0.00e+00 0 0.00e+00 87
SNESLineSearch 60 1.0 nan nan 6.99e+07 1.2 9.6e+02 1.9e+04 2.4e+02 1 1 1 6 12 1 1 1 6 12 -nan
-nan 0 0.00e+00 0 0.00e+00 100
PCSetUp_GAMG+ 60 1.0 nan nan 3.53e+07 1.2 5.2e+03 1.4e+04 4.3e+02 62 1 7 25 21 62 1 7 25 21 -nan
-nan 0 0.00e+00 0 0.00e+00 96
PCGAMGCreateG 3 1.0 nan nan 1.32e+06 1.2 2.2e+02 2.9e+04 4.2e+01 1 0 0 2 2 1 0 0 2 2 -nan
-nan 0 0.00e+00 0 0.00e+00 0
GAMG Coarsen 3 1.0 nan nan 0.00e+00 0.0 5.0e+02 1.3e+03 1.2e+02 1 0 1 0 6 1 0 1 0 6 -nan
-nan 0 0.00e+00 0 0.00e+00 0
GAMG MIS/Agg 3 1.0 nan nan 0.00e+00 0.0 5.0e+02 1.3e+03 1.2e+02 0 0 1 0 6 0 0 1 0 6 -nan
-nan 0 0.00e+00 0 0.00e+00 0
PCGAMGProl 3 1.0 nan nan 0.00e+00 0.0 7.8e+01 7.8e+02 4.8e+01 0 0 0 0 2 0 0 0 0 2 -nan
-nan 0 0.00e+00 0 0.00e+00 0
GAMG Prol-col 3 1.0 nan nan 0.00e+00 0.0 5.2e+01 5.8e+02 2.1e+01 0 0 0 0 1 0 0 0 0 1 -nan
-nan 0 0.00e+00 0 0.00e+00 0
GAMG Prol-lift 3 1.0 nan nan 0.00e+00 0.0 2.6e+01 1.2e+03 1.5e+01 0 0 0 0 1 0 0 0 0 1 -nan
-nan 0 0.00e+00 0 0.00e+00 0
PCGAMGOptProl 3 1.0 nan nan 3.40e+07 1.2 5.8e+02 2.4e+03 1.1e+02 1 1 1 0 6 1 1 1 0 6 -nan
-nan 0 0.00e+00 0 0.00e+00 100
GAMG smooth 3 1.0 nan nan 2.85e+05 1.2 1.9e+02 1.9e+03 3.0e+01 0 0 0 0 1 0 0 0 0 1 -nan
-nan 0 0.00e+00 0 0.00e+00 43
PCGAMGCreateL 3 1.0 nan nan 0.00e+00 0.0 4.8e+02 6.5e+03 8.0e+01 3 0 1 1 4 3 0 1 1 4 -nan
-nan 0 0.00e+00 0 0.00e+00 0
GAMG PtAP 3 1.0 nan nan 0.00e+00 0.0 4.5e+02 7.1e+03 2.7e+01 3 0 1 1 1 3 0 1 1 1 -nan
-nan 0 0.00e+00 0 0.00e+00 0
GAMG Reduce 1 1.0 nan nan 0.00e+00 0.0 3.6e+01 3.7e+01 5.3e+01 0 0 0 0 3 0 0 0 0 3 -nan
-nan 0 0.00e+00 0 0.00e+00 0
PCGAMG Gal l00 60 1.0 nan nan 0.00e+00 0.0 1.1e+03 1.4e+04 9.0e+00 46 0 1 6 0 46 0 1 6 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
PCGAMG Opt l00 1 1.0 nan nan 0.00e+00 0.0 4.8e+01 1.7e+02 7.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
PCGAMG Gal l01 60 1.0 nan nan 0.00e+00 0.0 1.6e+03 2.9e+04 9.0e+00 13 0 2 16 0 13 0 2 16 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
PCGAMG Opt l01 1 1.0 nan nan 0.00e+00 0.0 7.2e+01 4.8e+03 7.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
PCGAMG Gal l02 60 1.0 nan nan 0.00e+00 0.0 1.1e+03 1.2e+03 1.7e+01 0 0 1 0 1 0 0 1 0 1 -nan
-nan 0 0.00e+00 0 0.00e+00 0
PCGAMG Opt l02 1 1.0 nan nan 0.00e+00 0.0 7.2e+01 2.2e+02 7.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
PCSetUp 182 1.0 nan nan 3.53e+07 1.2 5.3e+03 1.4e+04 7.7e+02 64 1 7 27 37 64 1 7 27 38 -nan
-nan 0 0.00e+00 0 0.00e+00 96
PCSetUpOnBlocks 368 1.0 nan nan 4.24e+02 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
PCApply 60 1.0 nan nan 4.85e+09 1.2 7.3e+04 2.9e+03 1.1e+03 81 96 96 75 54 81 96 96 75 54 -nan
-nan 0 0.00e+00 0 0.00e+00 99
KSPSolve_FS_0 60 1.0 nan nan 3.12e+07 1.2 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
KSPSolve_FS_1 60 1.0 nan nan 4.79e+09 1.2 7.2e+04 2.9e+03 1.1e+03 81 95 96 75 54 81 95 96 75 54 -nan
-nan 0 0.00e+00 0 0.00e+00 100
--- Event Stage 1: Unknown
------------------------------------------------------------------------------------------------------------------------
---------------------------------------
Object Type Creations Destructions. Reports information only for process 0.
--- Event Stage 0: Main Stage
Container 14 14
Distributed Mesh 9 9
Index Set 120 120
IS L to G Mapping 10 10
Star Forest Graph 87 87
Discrete System 9 9
Weak Form 9 9
Vector 761 761
TSAdapt 1 1
TS 1 1
DMTS 1 1
SNES 1 1
DMSNES 3 3
SNESLineSearch 1 1
Krylov Solver 11 11
DMKSP interface 1 1
Matrix 171 171
Matrix Coarsen 3 3
Preconditioner 11 11
Viewer 2 1
PetscRandom 3 3
--- Event Stage 1: Unknown
========================================================================================================================
Average time to get PetscTime(): 3.82e-08
Average time for MPI_Barrier(): 2.2968e-06
Average time for zero size MPI_Send(): 3.371e-06
#PETSc Option Table entries:
-log_view
#End of PETSc Option Table entries
Compiled without FORTRAN kernels
Compiled with 64 bit PetscInt
Compiled with full precision matrices (default)
sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 sizeof(PetscScalar) 8 sizeof(PetscInt) 8
Configure options: PETSC_DIR=/home2/4pf/petsc PETSC_ARCH=arch-kokkos-serial --prefix=/home2/4pf/.local/serial --with-cc=mpicc --with-cxx=mpicxx --with-fc=0 --with-cudac=0 --with-cuda=0 --with-shared-libraries --with-64-bit-indices --with-debugging=0 --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --with-kokkos-dir=/home2/4pf/.local/serial --with-kokkos-kernels-dir=/home2/4pf/.local/serial --download-f2cblaslapack
-----------------------------------------
Libraries compiled on 2023-01-06 18:21:31 on iguazu
Machine characteristics: Linux-4.18.0-383.el8.x86_64-x86_64-with-glibc2.28
Using PETSc directory: /home2/4pf/.local/serial
Using PETSc arch:
-----------------------------------------
Using C compiler: mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3
-----------------------------------------
Using include paths: -I/home2/4pf/.local/serial/include
-----------------------------------------
Using C linker: mpicc
Using libraries: -Wl,-rpath,/home2/4pf/.local/serial/lib -L/home2/4pf/.local/serial/lib -lpetsc -Wl,-rpath,/home2/4pf/.local/serial/lib64 -L/home2/4pf/.local/serial/lib64 -Wl,-rpath,/home2/4pf/.local/serial/lib -L/home2/4pf/.local/serial/lib -lkokkoskernels -lkokkoscontainers -lkokkoscore -lf2clapack -lf2cblas -lm -lX11 -lquadmath -lstdc++ -ldl
-----------------------------------------
---
Philip Fackler
Research Software Engineer, Application Engineering Group
Advanced Computing Systems Research Section
Computer Science and Mathematics Division
Oak Ridge National Laboratory
________________________________
From: Zhang, Junchao <jczhang at mcs.anl.gov<mailto:jczhang at mcs.anl.gov>>
Sent: Tuesday, January 17, 2023 17:25
To: Fackler, Philip <facklerpw at ornl.gov<mailto:facklerpw at ornl.gov>>; xolotl-psi-development at lists.sourceforge.net<mailto:xolotl-psi-development at lists.sourceforge.net> <xolotl-psi-development at lists.sourceforge.net<mailto:xolotl-psi-development at lists.sourceforge.net>>; petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>
Cc: Mills, Richard Tran <rtmills at anl.gov<mailto:rtmills at anl.gov>>; Blondel, Sophie <sblondel at utk.edu<mailto:sblondel at utk.edu>>; Roth, Philip <rothpc at ornl.gov<mailto:rothpc at ornl.gov>>
Subject: [EXTERNAL] Re: Performance problem using COO interface
Hi, Philip,
Could you add -log_view and see what functions are used in the solve? Since it is CPU-only, perhaps with -log_view of different runs, we can easily see which functions slowed down.
--Junchao Zhang
________________________________
From: Fackler, Philip <facklerpw at ornl.gov<mailto:facklerpw at ornl.gov>>
Sent: Tuesday, January 17, 2023 4:13 PM
To: xolotl-psi-development at lists.sourceforge.net<mailto:xolotl-psi-development at lists.sourceforge.net> <xolotl-psi-development at lists.sourceforge.net<mailto:xolotl-psi-development at lists.sourceforge.net>>; petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>
Cc: Mills, Richard Tran <rtmills at anl.gov<mailto:rtmills at anl.gov>>; Zhang, Junchao <jczhang at mcs.anl.gov<mailto:jczhang at mcs.anl.gov>>; Blondel, Sophie <sblondel at utk.edu<mailto:sblondel at utk.edu>>; Roth, Philip <rothpc at ornl.gov<mailto:rothpc at ornl.gov>>
Subject: Performance problem using COO interface
In Xolotl's feature-petsc-kokkos branch I have ported the code to use petsc's COO interface for creating the Jacobian matrix (and the Kokkos interface for interacting with Vec entries). As the attached plots show for one case, while the code for computing the RHSFunction and RHSJacobian perform similarly (or slightly better) after the port, the performance for the solve as a whole is significantly worse.
Note:
This is all CPU-only (so kokkos and kokkos-kernels are built with only the serial backend).
The dev version is using MatSetValuesStencil with the default implementations for Mat and Vec.
The port version is using MatSetValuesCOO and is run with -dm_mat_type aijkokkos -dm_vec_type kokkos.
The port/def version is using MatSetValuesCOO and is run with -dm_vec_type kokkos (using the default Mat implementation).
So, this seems to be due be a performance difference in the petsc implementations. Please advise. Is this a known issue? Or am I missing something?
Thank you for the help,
Philip Fackler
Research Software Engineer, Application Engineering Group
Advanced Computing Systems Research Section
Computer Science and Mathematics Division
Oak Ridge National Laboratory
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