understanding the output from -info
Ben Tay
zonexo at gmail.com
Sat Feb 10 03:17:52 CST 2007
Hi,
I've repeated the test with n,m = 800. Now serial takes around 11mins while
parallel with 4 processors took 6mins. Does it mean that the problem must be
pretty large before it is more superior to use parallel? Moreover 800x800
means there's 640000 unknowns. My problem is a 2D CFD code which typically
has 200x80=16000 unknowns. Does it mean that I won't be able to benefit from
running in parallel?
Btw, this is the parallel's log_summary:
Event Count Time (sec)
Flops/sec --- 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
MatMult 1265 1.0 7.0615e+01 1.2 3.22e+07 1.2 7.6e+03 6.4e+03
0.0e+00 16 11100100 0 16 11100100 0 103
MatSolve 1265 1.0 4.7820e+01 1.2 4.60e+07 1.2 0.0e+00 0.0e+00
0.0e+00 11 11 0 0 0 11 11 0 0 0 152
MatLUFactorNum 1 1.0 2.5703e-01 2.3 1.27e+07 2.3 0.0e+00 0.0e+00
0.0e+00 0 0 0 0 0 0 0 0 0 0 22
MatILUFactorSym 1 1.0 1.8933e-01 4.1 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
MatAssemblyBegin 1 1.0 4.2153e-01 3.5 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
MatAssemblyEnd 1 1.0 3.6475e-01 1.5 0.00e+00 0.0 6.0e+00 3.2e+03
1.3e+01 0 0 0 0 0 0 0 0 0 0 0
MatGetOrdering 1 1.0 1.2088e-02 1.0 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
VecMDot 1224 1.0 1.5314e+02 1.2 4.63e+07 1.2 0.0e+00 0.0e+00
1.2e+03 36 36 0 0 31 36 36 0 0 31 158
VecNorm 1266 1.0 1.0215e+02 1.1 4.31e+06 1.1 0.0e+00 0.0e+00
1.3e+03 24 2 0 0 33 24 2 0 0 33 16
VecScale 1265 1.0 3.7467e+00 1.5 8.34e+07 1.5 0.0e+00 0.0e+00
0.0e+00 1 1 0 0 0 1 1 0 0 0 216
VecCopy 41 1.0 2.5530e-01 2.8 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 1308 1.0 3.2717e+00 1.4 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 82 1.0 5.3338e-01 2.8 1.40e+08 2.8 0.0e+00 0.0e+00
0.0e+00 0 0 0 0 0 0 0 0 0 0 197
VecMAXPY 1265 1.0 4.6234e+01 1.2 1.74e+08 1.2 0.0e+00 0.0e+00
0.0e+00 10 38 0 0 0 10 38 0 0 0 557
VecScatterBegin 1265 1.0 1.5684e-01 1.6 0.00e+00 0.0 7.6e+03 6.4e+03
0.0e+00 0 0100100 0 0 0100100 0 0
VecScatterEnd 1265 1.0 4.3167e+01 1.3 0.00e+00 0.0 0.0e+00 0.0e+00
0.0e+00 9 0 0 0 0 9 0 0 0 0 0
VecNormalize 1265 1.0 1.0459e+02 1.1 6.21e+06 1.1 0.0e+00 0.0e+00
1.3e+03 25 4 0 0 32 25 4 0 0 32 23
KSPGMRESOrthog 1224 1.0 1.9035e+02 1.1 7.00e+07 1.1 0.0e+00 0.0e+00
1.2e+03 45 72 0 0 31 45 72 0 0 31 254
KSPSetup 2 1.0 5.1674e-01 1.2 0.00e+00 0.0 0.0e+00 0.0e+00
1.0e+01 0 0 0 0 0 0 0 0 0 0 0
KSPSolve 1 1.0 4.0269e+02 1.0 4.16e+07 1.0 7.6e+03 6.4e+03
3.9e+03 99100100100 99 99100100100 99 166
PCSetUp 2 1.0 4.5924e-01 2.6 8.23e+06 2.6 0.0e+00 0.0e+00
6.0e+00 0 0 0 0 0 0 0 0 0 0 12
PCSetUpOnBlocks 1 1.0 4.5847e-01 2.6 8.26e+06 2.6 0.0e+00 0.0e+00
4.0e+00 0 0 0 0 0 0 0 0 0 0 13
PCApply 1265 1.0 5.0990e+01 1.2 4.33e+07 1.2 0.0e+00 0.0e+00
1.3e+03 12 11 0 0 32 12 11 0 0 32 143
------------------------------------------------------------------------------------------------------------------------
Memory usage is given in bytes:
Object Type Creations Destructions Memory Descendants' Mem.
--- Event Stage 0: Main Stage
Matrix 4 4 643208 0
Index Set 5 5 1924296 0
Vec 41 41 47379984 0
Vec Scatter 1 1 0 0
Krylov Solver 2 2 16880 0
Preconditioner 2 2 196 0
========================================================================================================================
Average time to get PetscTime(): 1.00136e-06
Average time for MPI_Barrier(): 4.00066e-05
Average time for zero size MPI_Send(): 1.70469e-05
OptionTable: -log_summary
Compiled without FORTRAN kernels
Compiled with full precision matrices (default)
sizeof(short) 2 sizeof(int) 4 sizeof(long) 4 sizeof(void*) 4
sizeof(PetscScalar) 8
Configure run at: Thu Jan 18 12:23:31 2007
Configure options: --with-vendor-compilers=intel --with-x=0 --with-shared
--with-blas-lapack-dir=/lsftmp/g0306332/inter/mkl/lib/32
--with-mpi-dir=/opt/mpich/myrinet/intel/
-----------------------------------------
On 2/10/07, Ben Tay <zonexo at gmail.com> wrote:
>
> Hi,
>
> I tried to use ex2f.F as a test code. I've changed the number n,m from 3
> to 500 each. I ran the code using 1 processor and then with 4 processor. I
> then repeat the same with the following modification:
>
>
> do i=1,10
>
> call KSPSolve(ksp,b,x,ierr)
>
> end do
> I've added to do loop to make the solving repeat 10 times.
>
> In both cases, the serial code is faster, e.g. 1 taking 2.4 min while the
> other 3.3 min.
>
> Here's the log_summary:
>
>
> ---------------------------------------------- PETSc Performance Summary:
> ----------------------------------------------
>
> ./ex2f on a linux-mpi named atlas12.nus.edu.sg with 4 processors, by
> g0306332 Sat Feb 10 16:21:36 2007
> Using Petsc Release Version 2.3.2, Patch 8, Tue Jan 2 14:33:59 PST 2007
> HG revision: ebeddcedcc065e32fc252af32cf1d01ed4fc7a80
>
> Max Max/Min Avg Total
> Time (sec): 2.213e+02 1.00051 2.212e+02
> Objects: 5.500e+01 1.00000 5.500e+01
> Flops: 4.718e+09 1.00019 4.718e+09 1.887e+10
> Flops/sec: 2.134e+07 1.00070 2.133e+07 8.531e+07
>
> Memory: 3.186e+07 1.00069 1.274e+08
> MPI Messages: 1.832e+03 2.00000 1.374e+03 5.496e+03
> MPI Message Lengths: 7.324e+06 2.00000 3.998e+03 2.197e+07
> MPI Reductions: 7.112e+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: 2.2120e+02 100.0% 1.8871e+10 100.0% 5.496e+03
> 100.0% 3.998e+03 100.0% 2.845e+03 100.0%
>
>
> ------------------------------------------------------------------------------------------------------------------------
> 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 Flops/sec: 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 config/configure.py #
> # using --with-debugging=no, the performance will #
> # be generally two or three times faster. #
> # #
> ##########################################################
>
>
>
>
> ##########################################################
> # #
> # WARNING!!! #
> # #
> # This code was run without the PreLoadBegin() #
> # macros. To get timing results we always recommend #
> # preloading. otherwise timing numbers may be #
> # meaningless. #
> ##########################################################
>
>
> Event Count Time (sec)
> Flops/sec --- 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
>
> MatMult 915 1.0 4.4291e+01 1.3 1.50e+07 1.3 5.5e+03 4.0e+03
> 0.0e+00 18 11100100 0 18 11100100 0 46
> MatSolve 915 1.0 1.5684e+01 1.1 3.56e+07 1.1 0.0e+00 0.0e+00
> 0.0e+00 7 11 0 0 0 7 11 0 0 0 131
> MatLUFactorNum 1 1.0 5.1654e-02 1.4 1.48e+07 1.4 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 43
> MatILUFactorSym 1 1.0 1.6838e-02 1.1 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
> MatAssemblyBegin 1 1.0 3.2428e-01 1.6 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
> MatAssemblyEnd 1 1.0 1.3120e+00 1.1 0.00e+00 0.0 6.0e+00 2.0e+03
> 1.3e+01 1 0 0 0 0 1 0 0 0 0 0
> MatGetOrdering 1 1.0 4.1590e-03 1.2 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
> VecMDot 885 1.0 8.5091e+01 1.1 2.27e+07 1.1 0.0e+00 0.0e+00
> 8.8e+02 36 36 0 0 31 36 36 0 0 31 80
> VecNorm 916 1.0 6.6747e+01 1.1 1.81e+06 1.1 0.0e+00 0.0e+00
> 9.2e+02 29 2 0 0 32 29 2 0 0 32 7
> VecScale 915 1.0 1.1430e+00 2.2 1.12e+08 2.2 0.0e+00 0.0e+00
> 0.0e+00 0 1 0 0 0 0 1 0 0 0 200
> VecCopy 30 1.0 1.2816e-01 5.7 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 947 1.0 7.8979e-01 1.3 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
> VecAXPY 60 1.0 5.5332e-02 1.1 1.51e+08 1.1 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 542
> VecMAXPY 915 1.0 1.5004e+01 1.3 1.54e+08 1.3 0.0e+00 0.0e+00
> 0.0e+00 6 38 0 0 0 6 38 0 0 0 483
> VecScatterBegin 915 1.0 9.0358e-02 1.4 0.00e+00 0.0 5.5e+03 4.0e+03
> 0.0e+00 0 0100100 0 0 0100100 0 0
> VecScatterEnd 915 1.0 3.5136e+01 1.4 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 14 0 0 0 0 14 0 0 0 0 0
> VecNormalize 915 1.0 6.7272e+01 1.0 2.68e+06 1.0 0.0e+00 0.0e+00
> 9.2e+02 30 4 0 0 32 30 4 0 0 32 10
> KSPGMRESOrthog 885 1.0 9.8478e+01 1.1 3.87e+07 1.1 0.0e+00 0.0e+00
> 8.8e+02 42 72 0 0 31 42 72 0 0 31 138
> KSPSetup 2 1.0 6.1918e-01 1.2 0.00e+00 0.0 0.0e+00 0.0e+00
> 1.0e+01 0 0 0 0 0 0 0 0 0 0 0
> KSPSolve 1 1.0 2.1892e+02 1.0 2.15e+07 1.0 5.5e+03 4.0e+03
> 2.8e+03 99100100100 99 99100100100 99 86
> PCSetUp 2 1.0 7.3292e-02 1.3 9.84e+06 1.3 0.0e+00 0.0e+00
> 6.0e+00 0 0 0 0 0 0 0 0 0 0 30
> PCSetUpOnBlocks 1 1.0 7.2706e-02 1.3 9.97e+06 1.3 0.0e+00 0.0e+00
> 4.0e+00 0 0 0 0 0 0 0 0 0 0 31
> PCApply 915 1.0 1.6508e+01 1.1 3.27e+07 1.1 0.0e+00 0.0e+00
> 9.2e+02 7 11 0 0 32 7 11 0 0 32 124
> ------------------------------------------------------------------------------------------------------------------------
>
>
> Memory usage is given in bytes:
>
> Object Type Creations Destructions Memory Descendants' Mem.
>
> --- Event Stage 0: Main Stage
>
> Matrix 4 4 252008 0
> Index Set 5 5 753096 0
> Vec 41 41 18519984 0
> Vec Scatter 1 1 0 0
> Krylov Solver 2 2 16880 0
> Preconditioner 2 2 196 0
> ========================================================================================================================
>
> Average time to get PetscTime(): 1.09673e-06
> Average time for MPI_Barrier(): 4.18186e-05
> Average time for zero size MPI_Send(): 2.62856e-05
> OptionTable: -log_summary
> Compiled without FORTRAN kernels
> Compiled with full precision matrices (default)
> sizeof(short) 2 sizeof(int) 4 sizeof(long) 4 sizeof(void*) 4
> sizeof(PetscScalar) 8
> Configure run at: Thu Jan 18 12:23:31 2007
> Configure options: --with-vendor-compilers=intel --with-x=0 --with-shared
> --with-blas-lapack-dir=/lsftmp/g0306332/inter/mkl/lib/32
> --with-mpi-dir=/opt/mpich/myrinet/intel/
> -----------------------------------------
> Libraries compiled on Thu Jan 18 12:24:41 SGT 2007 on atlas1.nus.edu.sg
> Machine characteristics: Linux atlas1.nus.edu.sg 2.4.21-20.ELsmp #1 SMP
> Wed Sep 8 17:29:34 GMT 2004 i686 i686 i386 GNU/Linux
> Using PETSc directory: /nas/lsftmp/g0306332/petsc-2.3.2-p8
> Using PETSc arch: linux-mpif90
> -----------------------------------------
> Using C compiler: /opt/mpich/myrinet/intel/bin/mpicc -fPIC -g
> Using Fortran compiler: /opt/mpich/myrinet/intel/bin/mpif90 -I. -fPIC -g
> -w90 -w
> -----------------------------------------
> Using include paths: -I/nas/lsftmp/g0306332/petsc- 2.3.2-p8-I/nas/lsftmp/g0306332/petsc-
> 2.3.2-p8/bmake/linux-mpif90 -I/nas/lsftmp/g0306332/petsc-2.3.2-p8/include
> -I/opt/mpich/myrinet/intel/include
> ------------------------------------------
> Using C linker: /opt/mpich/myrinet/intel/bin/mpicc -fPIC -g
> Using Fortran linker: /opt/mpich/myrinet/intel/bin/mpif90 -I. -fPIC -g
> -w90 -w
> Using libraries: -Wl,-rpath,/nas/lsftmp/g0306332/petsc-2.3.2-p8/lib/linux-mpif90
> -L/nas/lsftmp/g0306332/petsc-2.3.2-p8/lib/linux-mpif90 -lpetscts
> -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc
> -Wl,-rpath,/lsftmp/g0306332/inter/mkl/lib/32
> -L/lsftmp/g0306332/inter/mkl/lib/32 -lmkl_lapack -lmkl_ia32 -lguide
> -lPEPCF90 -Wl,-rpath,/opt/intel/compiler70/ia32/lib
> -Wl,-rpath,/opt/mpich/myrinet/intel/lib -L/opt/mpich/myrinet/intel/lib
> -Wl,-rpath,-rpath -Wl,-rpath,-ldl -L-ldl -lmpich -Wl,-rpath,-L -lgm
> -lpthread -Wl,-rpath,/opt/intel/compiler70/ia32/lib
> -Wl,-rpath,/opt/intel/compiler70/ia32/lib -L/opt/intel/compiler70/ia32/lib
> -Wl,-rpath,/usr/lib -Wl,-rpath,/usr/lib -L/usr/lib -limf -lirc -lcprts -lcxa
> -lunwind -ldl -lmpichf90 -Wl,-rpath,/opt/gm/lib -L/opt/gm/lib -lPEPCF90
> -Wl,-rpath,/opt/intel/compiler70/ia32/lib -L/opt/intel/compiler70/ia32/lib
> -Wl,-rpath,/usr/lib -L/usr/lib -lintrins -lIEPCF90 -lF90 -lm -Wl,-rpath,\
> -Wl,-rpath,\ -L\ -ldl -lmpich -Wl,-rpath,\ -L\ -lgm -lpthread
> -Wl,-rpath,/opt/intel/compiler70/ia32/lib -L/opt/intel/compiler70/ia32/lib
> -Wl,-rpath,/usr/lib -L/usr/lib -limf -lirc -lcprts -lcxa -lunwind -ldl
> ------------------------------------------
>
> So is there something wrong with the server's mpi implementation?
>
> Thank you.
>
>
>
> On 2/10/07, Satish Balay <balay at mcs.anl.gov> wrote:
> >
> > Looks like MatMult = 24sec Out of this the scatter time is: 22sec.
> > Either something is wrong with your run - or MPI is really broken..
> >
> > Satish
> >
> > > > > MatMult 3927 1.0 2.4071e+01 1.3 6.14e+06 1.4 2.4e+04
> > 1.3e+03
> > > > > VecScatterBegin 3927 1.0 2.8672e-01 3.9 0.00e+00 0.0 2.4e+04
> > 1.3e+03
> > > > > VecScatterEnd 3927 1.0 2.2135e+01 1.5 0.00e+00 0.0 0.0e+00
> > 0.0e+00
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20070210/dad7ae05/attachment.htm>
More information about the petsc-users
mailing list