Thanks Karl, Matt,
I thought I created all vectors of CUSP type. I'll double check.
I was trying to find vectors that I may have accidentally setup not with
CUSP type through somehow interface with the SNES solver?
I'll also double check w/ the cuda examples as Karl suggested.
There are 6 Tesla M2070 on this box, but i'm only running on one of them.
On Sat, Nov 17, 2012 at 2:42 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Sat, Nov 17, 2012 at 3:05 PM, David Fuentes <fuentesdt at gmail.com>
> wrote:
> > Thanks Jed.
> > I was trying to run it in dbg mode to verify if all significant parts of
> the
> > solver were running on the GPU and not on the CPU by mistake.
> > I cant pinpoint what part of the solver is running on the CPU. When I run
> > top while running the solver there seems to be ~800% CPU utilization
> > that I wasn't expecting. I cant tell if i'm slowing things down by
> > transferring between CPU/GPU on accident?
>
> 1) I am not sure what you mean by 800%, but it is definitely
> legitimate to want to know where you are computing.
>
> 2) At least some computation is happening on the GPU. I can tell this from
> the
> Vec/MatCopyToGPU events.
>
> 3) Your flop rates are not great. The MatMult is about half what we
> get on the Tesla, but you
> could have another card without good support for double precision.
> The vector ops however
> are pretty bad.
>
> 4) It looks like half the flops are in MatMult, which is definitely on
> the card, and the others are in
> vector operations. Do you create any other vectors without the CUSP
> type?
>
> Matt
>
> > thanks again,
> > df
> >
> > On Sat, Nov 17, 2012 at 1:49 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:
> >>
> >> Please read the large boxed message about debugging mode.
> >>
> >> (Replying from phone so can't make it 72 point blinking red, sorry.)
> >>
> >> On Nov 17, 2012 1:41 PM, "David Fuentes" <fuentesdt at gmail.com> wrote:
> >>>
> >>> thanks Matt,
> >>>
> >>> My log summary is below.
> >>>
> >>>
> >>>
> ************************************************************************************************************************
> >>> *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r
> >>> -fCourier9' to print this document ***
> >>>
> >>>
> ************************************************************************************************************************
> >>>
> >>> ---------------------------------------------- PETSc Performance
> Summary:
> >>> ----------------------------------------------
> >>>
> >>> ./FocusUltraSoundModel on a gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg named
> >>> SCRGP2 with 1 processor, by fuentes Sat Nov 17 13:35:06 2012
> >>> Using Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT
> 2012
> >>>
> >>> Max Max/Min Avg Total
> >>> Time (sec): 3.164e+01 1.00000 3.164e+01
> >>> Objects: 4.100e+01 1.00000 4.100e+01
> >>> Flops: 2.561e+09 1.00000 2.561e+09 2.561e+09
> >>> Flops/sec: 8.097e+07 1.00000 8.097e+07 8.097e+07
> >>> Memory: 2.129e+08 1.00000 2.129e+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: 4.230e+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 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: 3.1636e+01 100.0% 2.5615e+09 100.0% 0.000e+00
> >>> 0.0% 0.000e+00 0.0% 4.220e+02 99.8%
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------------------------------------------------
> >>> 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
> >>>
> >>> ComputeFunction 52 1.0 3.9104e-01 1.0 0.00e+00 0.0 0.0e+00
> 0.0e+00
> >>> 3.0e+00 1 0 0 0 1 1 0 0 0 1 0
> >>> VecDot 50 1.0 3.2072e-02 1.0 9.70e+07 1.0 0.0e+00
> 0.0e+00
> >>> 0.0e+00 0 4 0 0 0 0 4 0 0 0 3025
> >>> VecMDot 50 1.0 1.3100e-01 1.0 9.70e+07 1.0 0.0e+00
> 0.0e+00
> >>> 0.0e+00 0 4 0 0 0 0 4 0 0 0 741
> >>> VecNorm 200 1.0 9.7943e-02 1.0 3.88e+08 1.0 0.0e+00
> 0.0e+00
> >>> 0.0e+00 0 15 0 0 0 0 15 0 0 0 3963
> >>> VecScale 100 1.0 1.3496e-01 1.0 9.70e+07 1.0 0.0e+00
> 0.0e+00
> >>> 0.0e+00 0 4 0 0 0 0 4 0 0 0 719
> >>> VecCopy 150 1.0 4.8405e-01 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
> >>> VecSet 164 1.0 2.9707e-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
> >>> VecAXPY 50 1.0 3.2194e-02 1.0 9.70e+07 1.0 0.0e+00
> 0.0e+00
> >>> 0.0e+00 0 4 0 0 0 0 4 0 0 0 3014
> >>> VecWAXPY 50 1.0 2.9040e-01 1.0 4.85e+07 1.0 0.0e+00
> 0.0e+00
> >>> 0.0e+00 1 2 0 0 0 1 2 0 0 0 167
> >>> VecMAXPY 100 1.0 5.4555e-01 1.0 1.94e+08 1.0 0.0e+00
> 0.0e+00
> >>> 0.0e+00 2 8 0 0 0 2 8 0 0 0 356
> >>> VecPointwiseMult 100 1.0 5.3003e-01 1.0 9.70e+07 1.0 0.0e+00
> 0.0e+00
> >>> 0.0e+00 2 4 0 0 0 2 4 0 0 0 183
> >>> VecScatterBegin 53 1.0 1.8660e-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
> >>> VecReduceArith 101 1.0 6.9973e-02 1.0 1.96e+08 1.0 0.0e+00
> 0.0e+00
> >>> 0.0e+00 0 8 0 0 0 0 8 0 0 0 2801
> >>> VecReduceComm 51 1.0 1.0252e-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
> >>> VecNormalize 100 1.0 1.8565e-01 1.0 2.91e+08 1.0 0.0e+00
> 0.0e+00
> >>> 0.0e+00 1 11 0 0 0 1 11 0 0 0 1568
> >>> VecCUSPCopyTo 152 1.0 5.8016e-01 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
> >>> VecCUSPCopyFrom 201 1.0 6.0029e-01 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
> >>> MatMult 100 1.0 6.8465e-01 1.0 1.25e+09 1.0 0.0e+00
> 0.0e+00
> >>> 0.0e+00 2 49 0 0 0 2 49 0 0 0 1825
> >>> MatAssemblyBegin 3 1.0 3.3379e-06 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 3 1.0 2.7767e-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
> >>> MatZeroEntries 1 1.0 2.0346e-02 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
> >>> MatCUSPCopyTo 3 1.0 1.4056e-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
> >>> SNESSolve 1 1.0 2.2094e+01 1.0 2.56e+09 1.0 0.0e+00
> 0.0e+00
> >>> 3.7e+02 70100 0 0 88 70100 0 0 89 116
> >>> SNESFunctionEval 51 1.0 3.9031e-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
> >>> SNESJacobianEval 50 1.0 1.3191e+00 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
> >>> SNESLineSearch 50 1.0 6.2922e+00 1.0 1.16e+09 1.0 0.0e+00
> 0.0e+00
> >>> 5.0e+01 20 45 0 0 12 20 45 0 0 12 184
> >>> KSPGMRESOrthog 50 1.0 4.0436e-01 1.0 1.94e+08 1.0 0.0e+00
> 0.0e+00
> >>> 5.0e+01 1 8 0 0 12 1 8 0 0 12 480
> >>> KSPSetUp 50 1.0 2.1935e-02 1.0 0.00e+00 0.0 0.0e+00
> 0.0e+00
> >>> 1.5e+01 0 0 0 0 4 0 0 0 0 4 0
> >>> KSPSolve 50 1.0 1.3230e+01 1.0 1.40e+09 1.0 0.0e+00
> 0.0e+00
> >>> 3.2e+02 42 55 0 0 75 42 55 0 0 75 106
> >>> PCSetUp 50 1.0 1.9897e+00 1.0 0.00e+00 0.0 0.0e+00
> 0.0e+00
> >>> 4.9e+01 6 0 0 0 12 6 0 0 0 12 0
> >>> PCApply 100 1.0 5.7457e-01 1.0 9.70e+07 1.0 0.0e+00
> 0.0e+00
> >>> 4.0e+00 2 4 0 0 1 2 4 0 0 1 169
> >>>
> >>>
> ------------------------------------------------------------------------------------------------------------------------
> >>>
> >>> 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 2 2 1096 0
> >>> Vector 16 16 108696592 0
> >>> Vector Scatter 2 2 1240 0
> >>> Matrix 1 1 96326824 0
> >>> Distributed Mesh 3 3 7775936 0
> >>> Bipartite Graph 6 6 4104 0
> >>> Index Set 5 5 3884908 0
> >>> IS L to G Mapping 1 1 3881760 0
> >>> SNES 1 1 1268 0
> >>> SNESLineSearch 1 1 840 0
> >>> Viewer 1 0 0 0
> >>> Krylov Solver 1 1 18288 0
> >>> Preconditioner 1 1 792 0
> >>>
> >>>
> ========================================================================================================================
> >>> Average time to get PetscTime(): 9.53674e-08
> >>> #PETSc Option Table entries:
> >>> -da_vec_type cusp
> >>> -dm_mat_type seqaijcusp
> >>> -ksp_monitor
> >>> -log_summary
> >>> -pc_type jacobi
> >>> -snes_converged_reason
> >>> -snes_monitor
> >>> #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: Fri Nov 16 08:40:52 2012
> >>> Configure options: --with-clanguage=C++ --with-mpi-dir=/usr
> >>> --with-shared-libraries --with-cuda-arch=sm_20 --CFLAGS=-O0
> --CXXFLAGS=-O0
> >>> --CUDAFLAGS=-O0 --with-etags=1 --with-mpi4py=0
> >>>
> --with-blas-lapack-lib="[/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_rt.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_intel_thread.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_core.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libiomp5.so]"
> >>> --download-blacs --download-superlu_dist --download-triangle
> >>> --download-parmetis --download-metis --download-mumps
> --download-scalapack
> >>> --with-cuda=1 --with-cusp=1 --with-thrust=1
> >>> --with-cuda-dir=/opt/apps/cuda/4.2//cuda --with-sieve=1
> >>> --download-exodusii=yes --download-netcdf --with-boost=1
> >>> --with-boost-dir=/usr --download-fiat=yes --download-generator
> >>> --download-scientificpython --with-matlab=1 --with-matlab-engine=1
> >>> --with-matlab-dir=/opt/MATLAB/R2011a
> >>> -----------------------------------------
> >>> Libraries compiled on Fri Nov 16 08:40:52 2012 on SCRGP2
> >>> Machine characteristics:
> >>> Linux-2.6.32-41-server-x86_64-with-debian-squeeze-sid
> >>> Using PETSc directory: /opt/apps/PETSC/petsc-3.3-p4
> >>> Using PETSc arch: gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg
> >>> -----------------------------------------
> >>>
> >>> Using C compiler: /usr/bin/mpicxx -O0 -g -fPIC ${COPTFLAGS}
> ${CFLAGS}
> >>> Using Fortran compiler: /usr/bin/mpif90 -fPIC -Wall
> -Wno-unused-variable
> >>> -g ${FOPTFLAGS} ${FFLAGS}
> >>> -----------------------------------------
> >>>
> >>> Using include paths:
> >>>
> -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include
> >>> -I/opt/apps/PETSC/petsc-3.3-p4/include
> >>> -I/opt/apps/PETSC/petsc-3.3-p4/include
> >>>
> -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include
> >>> -I/opt/apps/cuda/4.2//cuda/include
> >>> -I/opt/apps/PETSC/petsc-3.3-p4/include/sieve
> >>> -I/opt/MATLAB/R2011a/extern/include -I/usr/include
> >>>
> -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/cbind/include
> >>>
> -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/forbind/include
> >>> -I/usr/include/mpich2
> >>> -----------------------------------------
> >>>
> >>> Using C linker: /usr/bin/mpicxx
> >>> Using Fortran linker: /usr/bin/mpif90
> >>> Using libraries:
> >>>
> -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib
> >>> -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib
> >>> -lpetsc
> >>>
> -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib
> >>> -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib
> >>> -ltriangle -lX11 -lpthread -lsuperlu_dist_3.1 -lcmumps -ldmumps
> -lsmumps
> >>> -lzmumps -lmumps_common -lpord -lparmetis -lmetis -lscalapack -lblacs
> >>> -Wl,-rpath,/opt/apps/cuda/4.2//cuda/lib64
> -L/opt/apps/cuda/4.2//cuda/lib64
> >>> -lcufft -lcublas -lcudart -lcusparse
> >>>
> -Wl,-rpath,/opt/MATLAB/R2011a/sys/os/glnxa64:/opt/MATLAB/R2011a/bin/glnxa64:/opt/MATLAB/R2011a/extern/lib/glnxa64
> >>> -L/opt/MATLAB/R2011a/bin/glnxa64
> -L/opt/MATLAB/R2011a/extern/lib/glnxa64
> >>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc
> >>> -Wl,-rpath,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib
> >>> -L/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib -lmkl_rt -lmkl_intel_thread
> >>> -lmkl_core -liomp5 -lexoIIv2for -lexodus -lnetcdf_c++ -lnetcdf
> >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.4.3
> >>> -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -lmpichf90 -lgfortran -lm -lm
> >>> -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lpthread
> -lrt
> >>> -lgcc_s -ldl
> >>> -----------------------------------------
> >>>
> >>>
> >>>
> >>> On Sat, Nov 17, 2012 at 11:02 AM, Matthew Knepley <knepley at gmail.com>
> >>> wrote:
> >>>>
> >>>> On Sat, Nov 17, 2012 at 10:50 AM, David Fuentes <fuentesdt at gmail.com>
> >>>> wrote:
> >>>> > Hi,
> >>>> >
> >>>> > I'm using petsc 3.3p4
> >>>> > I'm trying to run a nonlinear SNES solver on GPU with gmres and
> jacobi
> >>>> > PC
> >>>> > using VECSEQCUSP and MATSEQAIJCUSP datatypes for the rhs and
> jacobian
> >>>> > matrix
> >>>> > respectively.
> >>>> > When running top I still see significant CPU utilization (800-900
> >>>> > %CPU)
> >>>> > during the solve ? possibly from some multithreaded operations ?
> >>>> >
> >>>> > Is this expected ?
> >>>> > I was thinking that since I input everything into the solver as a
> CUSP
> >>>> > datatype, all linear algebra operations would be on the GPU device
> >>>> > from
> >>>> > there and wasn't expecting to see such CPU utilization during the
> >>>> > solve ?
> >>>> > Do I probably have an error in my code somewhere ?
> >>>>
> >>>> We cannot answer performance questions without -log_summary
> >>>>
> >>>> Matt
> >>>>
> >>>> > Thanks,
> >>>> > David
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> What most experimenters take for granted before they begin their
> >>>> experiments is infinitely more interesting than any results to which
> >>>> their experiments lead.
> >>>> -- Norbert Wiener
> >>>
> >>>
> >
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which
> their experiments lead.
> -- Norbert Wiener
>
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