[petsc-users] [EXTERNAL] Re: Kokkos backend for Mat and Vec diverging when running on CUDA device.
Fackler, Philip
facklerpw at ornl.gov
Mon Dec 5 11:08:03 CST 2022
Junchao,
Thank you for working on this. If you open the parameter file for, say, the PSI_2 system test case (benchmarks/params_system_PSI_2.txt), simply add -dm_mat_type aijkokkos -dm_vec_type kokkos?` to the "petscArgs=" field (or the corresponding cusparse/cuda option).
Thanks,
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: Thursday, December 1, 2022 17:05
To: Fackler, Philip <facklerpw at ornl.gov>
Cc: 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: Re: [EXTERNAL] Re: [petsc-users] Kokkos backend for Mat and Vec diverging when running on CUDA device.
Hi, Philip,
Sorry for the long delay. I could not get something useful from the -log_view output. Since I have already built xolotl, could you give me instructions on how to do a xolotl test to reproduce the divergence with petsc GPU backends (but fine on CPU)?
Thank you.
--Junchao Zhang
On Wed, Nov 16, 2022 at 1:38 PM Fackler, Philip <facklerpw at ornl.gov<mailto:facklerpw at ornl.gov>> wrote:
------------------------------------------------------------------ PETSc Performance Summary: ------------------------------------------------------------------
Unknown Name on a named PC0115427 with 1 processor, by 4pf Wed Nov 16 14:36:46 2022
Using Petsc Development GIT revision: v3.18.1-115-gdca010e0e9a GIT Date: 2022-10-28 14:39:41 +0000
Max Max/Min Avg Total
Time (sec): 6.023e+00 1.000 6.023e+00
Objects: 1.020e+02 1.000 1.020e+02
Flops: 1.080e+09 1.000 1.080e+09 1.080e+09
Flops/sec: 1.793e+08 1.000 1.793e+08 1.793e+08
MPI Msg Count: 0.000e+00 0.000 0.000e+00 0.000e+00
MPI Msg Len (bytes): 0.000e+00 0.000 0.000e+00 0.000e+00
MPI Reductions: 0.000e+00 0.000
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: 6.0226e+00 100.0% 1.0799e+09 100.0% 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 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
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DMCreateMat 1 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
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SFSetGraph 3 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
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SFSetUp 3 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
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SFPack 4647 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 4647 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
VecDot 190 1.0 nan nan 2.11e+06 1.0 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+00 100
VecMDot 775 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
VecNorm 1728 1.0 nan nan 1.92e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 2 0 0 0 0 2 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
VecScale 1983 1.0 nan nan 6.24e+06 1.0 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
VecCopy 780 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 4955 1.0 nan nan 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 0
VecAXPY 190 1.0 nan nan 2.11e+06 1.0 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+00 100
VecAYPX 597 1.0 nan nan 6.64e+06 1.0 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
VecAXPBYCZ 643 1.0 nan nan 1.79e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 2 0 0 0 0 2 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 100
VecWAXPY 502 1.0 nan nan 5.58e+06 1.0 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
VecMAXPY 1159 1.0 nan nan 3.68e+07 1.0 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
VecScatterBegin 4647 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 2 5.14e-03 0 0.00e+00 0
VecScatterEnd 4647 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
VecReduceArith 380 1.0 nan nan 4.23e+06 1.0 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+00 100
VecReduceComm 190 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
VecNormalize 965 1.0 nan nan 1.61e+07 1.0 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
TSStep 20 1.0 5.8699e+00 1.0 1.08e+09 1.0 0.0e+00 0.0e+00 0.0e+00 97100 0 0 0 97100 0 0 0 184
-nan 2 5.14e-03 0 0.00e+00 54
TSFunctionEval 597 1.0 nan nan 6.64e+06 1.0 0.0e+00 0.0e+00 0.0e+00 63 1 0 0 0 63 1 0 0 0 -nan
-nan 1 3.36e-04 0 0.00e+00 100
TSJacobianEval 190 1.0 nan nan 3.37e+07 1.0 0.0e+00 0.0e+00 0.0e+00 24 3 0 0 0 24 3 0 0 0 -nan
-nan 0 0.00e+00 0 0.00e+00 97
MatMult 1930 1.0 nan nan 4.46e+08 1.0 0.0e+00 0.0e+00 0.0e+00 1 41 0 0 0 1 41 0 0 0 -nan
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MatMultTranspose 1 1.0 nan nan 3.44e+05 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 -nan
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MatSolve 965 1.0 nan nan 5.04e+07 1.0 0.0e+00 0.0e+00 0.0e+00 1 5 0 0 0 1 5 0 0 0 -nan
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MatSOR 965 1.0 nan nan 3.33e+08 1.0 0.0e+00 0.0e+00 0.0e+00 4 31 0 0 0 4 31 0 0 0 -nan
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MatLUFactorNum 190 1.0 nan nan 1.16e+08 1.0 0.0e+00 0.0e+00 0.0e+00 1 11 0 0 0 1 11 0 0 0 -nan
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MatScale 190 1.0 nan nan 3.26e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 3 0 0 0 0 3 0 0 0 -nan
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MatAssemblyBegin 761 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
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MatAssemblyEnd 761 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
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MatCreateSubMats 380 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
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SNESLineSearch 190 1.0 nan nan 1.05e+08 1.0 0.0e+00 0.0e+00 0.0e+00 53 10 0 0 0 53 10 0 0 0 -nan
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PCSetUp 570 1.0 nan nan 1.16e+08 1.0 0.0e+00 0.0e+00 0.0e+00 2 11 0 0 0 2 11 0 0 0 -nan
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KSPSolve_FS_0 965 1.0 nan nan 3.33e+08 1.0 0.0e+00 0.0e+00 0.0e+00 4 31 0 0 0 4 31 0 0 0 -nan
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KSPSolve_FS_1 965 1.0 nan nan 1.66e+08 1.0 0.0e+00 0.0e+00 0.0e+00 2 15 0 0 0 2 15 0 0 0 -nan
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--- Event Stage 1: Unknown
------------------------------------------------------------------------------------------------------------------------
---------------------------------------
Object Type Creations Destructions. Reports information only for process 0.
--- Event Stage 0: Main Stage
Container 5 5
Distributed Mesh 2 2
Index Set 11 11
IS L to G Mapping 1 1
Star Forest Graph 7 7
Discrete System 2 2
Weak Form 2 2
Vector 49 49
TSAdapt 1 1
TS 1 1
DMTS 1 1
SNES 1 1
DMSNES 3 3
SNESLineSearch 1 1
Krylov Solver 4 4
DMKSP interface 1 1
Matrix 4 4
Preconditioner 4 4
Viewer 2 1
--- Event Stage 1: Unknown
========================================================================================================================
Average time to get PetscTime(): 3.14e-08
#PETSc Option Table entries:
-log_view
-log_view_gpu_times
#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=/home/4pf/repos/petsc PETSC_ARCH=arch-kokkos-cuda-no-tpls --with-cc=mpicc --with-cxx=mpicxx --with-fc=0 --with-cuda --with-debugging=0 --with-shared-libraries --prefix=/home/4pf/build/petsc/cuda-no-tpls/install --with-64-bit-indices --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --CUDAOPTFLAGS=-O3 --with-kokkos-dir=/home/4pf/build/kokkos/cuda/install --with-kokkos-kernels-dir=/home/4pf/build/kokkos-kernels/cuda-no-tpls/install
-----------------------------------------
Libraries compiled on 2022-11-01 21:01:08 on PC0115427
Machine characteristics: Linux-5.15.0-52-generic-x86_64-with-glibc2.35
Using PETSc directory: /home/4pf/build/petsc/cuda-no-tpls/install
Using PETSc arch:
-----------------------------------------
Using C compiler: mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow -fstack-protector -fvisibility=hidden -O3
-----------------------------------------
Using include paths: -I/home/4pf/build/petsc/cuda-no-tpls/install/include -I/home/4pf/build/kokkos-kernels/cuda-no-tpls/install/include -I/home/4pf/build/kokkos/cuda/install/include -I/usr/local/cuda-11.8/include
-----------------------------------------
Using C linker: mpicc
Using libraries: -Wl,-rpath,/home/4pf/build/petsc/cuda-no-tpls/install/lib -L/home/4pf/build/petsc/cuda-no-tpls/install/lib -lpetsc -Wl,-rpath,/home/4pf/build/kokkos-kernels/cuda-no-tpls/install/lib -L/home/4pf/build/kokkos-kernels/cuda-no-tpls/install/lib -Wl,-rpath,/home/4pf/build/kokkos/cuda/install/lib -L/home/4pf/build/kokkos/cuda/install/lib -Wl,-rpath,/usr/local/cuda-11.8/lib64 -L/usr/local/cuda-11.8/lib64 -L/usr/local/cuda-11.8/lib64/stubs -lkokkoskernels -lkokkoscontainers -lkokkoscore -llapack -lblas -lm -lcudart -lnvToolsExt -lcufft -lcublas -lcusparse -lcusolver -lcurand -lcuda -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: Junchao Zhang <junchao.zhang at gmail.com<mailto:junchao.zhang at gmail.com>>
Sent: Tuesday, November 15, 2022 13:03
To: Fackler, Philip <facklerpw at ornl.gov<mailto:facklerpw at ornl.gov>>
Cc: 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>>; Blondel, Sophie <sblondel at utk.edu<mailto:sblondel at utk.edu>>; Roth, Philip <rothpc at ornl.gov<mailto:rothpc at ornl.gov>>
Subject: Re: [EXTERNAL] Re: [petsc-users] Kokkos backend for Mat and Vec diverging when running on CUDA device.
Can you paste -log_view result so I can see what functions are used?
--Junchao Zhang
On Tue, Nov 15, 2022 at 10:24 AM Fackler, Philip <facklerpw at ornl.gov<mailto:facklerpw at ornl.gov>> wrote:
Yes, most (but not all) of our system test cases fail with the kokkos/cuda or cuda backends. All of them pass with the CPU-only kokkos backend.
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<mailto:junchao.zhang at gmail.com>>
Sent: Monday, November 14, 2022 19:34
To: Fackler, Philip <facklerpw at ornl.gov<mailto:facklerpw at ornl.gov>>
Cc: 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>>; Blondel, Sophie <sblondel at utk.edu<mailto:sblondel at utk.edu>>; Zhang, Junchao <jczhang at mcs.anl.gov<mailto:jczhang at mcs.anl.gov>>; Roth, Philip <rothpc at ornl.gov<mailto:rothpc at ornl.gov>>
Subject: [EXTERNAL] Re: [petsc-users] Kokkos backend for Mat and Vec diverging when running on CUDA device.
Hi, Philip,
Sorry to hear that. It seems you could run the same code on CPUs but not no GPUs (with either petsc/Kokkos backend or petsc/cuda backend, is it right?
--Junchao Zhang
On Mon, Nov 14, 2022 at 12:13 PM Fackler, Philip via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
This is an issue I've brought up before (and discussed in-person with Richard). I wanted to bring it up again because I'm hitting the limits of what I know to do, and I need help figuring this out.
The problem can be reproduced using Xolotl's "develop" branch built against a petsc build with kokkos and kokkos-kernels enabled. Then, either add the relevant kokkos options to the "petscArgs=" line in the system test parameter file(s), or just replace the system test parameter files with the ones from the "feature-petsc-kokkos" branch. See here the files that begin with "params_system_".
Note that those files use the "kokkos" options, but the problem is similar using the corresponding cuda/cusparse options. I've already tried building kokkos-kernels with no TPLs and got slightly different results, but the same problem.
Any help would be appreciated.
Thanks,
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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