[petsc-users] CPU utilization during GPU solver
David Fuentes
fuentesdt at gmail.com
Sat Nov 17 14:05:03 CST 2012
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?
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
>>>
>>
>>
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