[petsc-users] Weird behavior for log_summary
Michele Rosso
mrosso at uci.edu
Mon Jun 8 12:16:59 CDT 2015
Hi Barry,
I run a small test case like you suggested: this results in no error,
but the problem with log_summary still persists.
Please find attached the output of log_summary.
Thanks,
Michele
On Fri, 2015-06-05 at 21:34 -0500, Barry Smith wrote:
> [NID 04001] 2015-06-04 19:07:24 Apid 25022256: initiated application termination
> Application 25022256 exit signals: Killed
> Application 25022256 resources: utime ~271s, stime ~15107s, Rss ~188536, inblocks ~5078831, outblocks ~12517984
>
> Usually this kind of message indicates that either the OS or the batch system killed the process for some reason: often because it ran out of time or maybe memory.
>
> Can you run in batch with a request for more time? Do smaller jobs run through ok?
>
> If utime means user time and stime means system time then this is very bad, the system time is HUGE relative to the user time.
>
> Barry
>
>
>
>
> > On Jun 5, 2015, at 9:22 PM, Michele Rosso <mrosso at uci.edu> wrote:
> >
> > Hi,
> >
> > I am checking the performances of my code via -log_summary, but the output is incomplete (please see attached) file.
> > I configured petsc with the following options:
> >
> > if __name__ == '__main__':
> > import sys
> > import os
> > sys.path.insert(0, os.path.abspath('config'))
> > import configure
> > configure_options = [
> > '--with-batch=1 ',
> > '--known-mpi-shared=0 ',
> > '--known-mpi-shared-libraries=0',
> > '--known-memcmp-ok ',
> > '--with-blas-lapack-lib=-L/opt/acml/5.3.1/gfortran64/lib -lacml',
> > '--COPTFLAGS=-march=bdver1 -fopenmp -O3 -ffast-math -fPIC ',
> > '--FOPTFLAGS=-march=bdver1 -fopenmp -O3 -ffast-math -fPIC ',
> > '--CXXOPTFLAGS=-march=bdver1 -fopenmp -O3 -ffast-math -fPIC ',
> > '--with-x=0 ',
> > '--with-debugging=0',
> > '--with-clib-autodetect=0 ',
> > '--with-cxxlib-autodetect=0 ',
> > '--with-fortranlib-autodetect=0 ',
> > '--with-shared-libraries=0 ',
> > '--with-mpi-compilers=1 ',
> > '--with-cc=cc ',
> > '--with-cxx=CC ',
> > '--with-fc=ftn ',
> > # '--with-64-bit-indices',
> > '--download-hypre=1',
> > '--download-blacs=1 ',
> > '--download-scalapack=1 ',
> > '--download-superlu_dist=1 ',
> > '--download-metis=1 ',
> > '--download-parmetis=1 ',
> > ]
> > configure.petsc_configure(configure_options)
> >
> > Any idea about this issue?
> > Thanks,
> >
> > Michele
> >
> >
> >
> >
> > <log_summary>
>
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************************************************************************************************************************
*** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document ***
************************************************************************************************************************
---------------------------------------------- PETSc Performance Summary: ----------------------------------------------
./test3.exe on a gnu-opt-32idx named . with 16 processors, by mrosso Mon Jun 8 11:54:16 2015
Using Petsc Release Version 3.5.4, May, 23, 2015
Max Max/Min Avg Total
Time (sec): 4.387e-01 1.00635 4.373e-01
Objects: 5.410e+02 1.00000 5.410e+02
Flops: 2.648e+07 1.00131 2.647e+07 4.234e+08
Flops/sec: 6.072e+07 1.00727 6.052e+07 9.683e+08
MPI Messages: 1.668e+03 1.06992 1.614e+03 2.582e+04
MPI Message Lengths: 2.914e+06 1.05005 1.763e+03 4.552e+07
MPI Reductions: 1.106e+03 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: 4.3732e-01 100.0% 4.2344e+08 100.0% 2.582e+04 100.0% 1.763e+03 100.0% 1.105e+03 99.9%
------------------------------------------------------------------------------------------------------------------------
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 (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 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)
------------------------------------------------------------------------------------------------------------------------
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
------------------------------------------------------------------------------------------------------------------------
Memory usage is given in bytes:
Object Type Creations Destructions Memory Descendants' Mem.
Reports information only for process 0.
--- Event Stage 0: Main Stage
Vector 240 134 1196608 0
Vector Scatter 30 0 0 0
Matrix 88 0 0 0
Matrix Null Space 4 0 0 0
Distributed Mesh 10 0 0 0
Star Forest Bipartite Graph 20 0 0 0
Discrete System 10 0 0 0
Index Set 76 68 140480 0
IS L to G Mapping 10 0 0 0
Krylov Solver 20 4 4640 0
DMKSP interface 8 0 0 0
Preconditioner 20 4 4000 0
Viewer 5 4 2976 0
========================================================================================================================
Average time to get PetscTime(): 9.53674e-08
Average time for MPI_Barrier(): 6.62804e-06
Average time for zero size MPI_Send(): 2.25008e-06
#PETSc Option Table entries:
-ksp_initial_guess_nonzero yes
-ksp_norm_type unpreconditioned
-ksp_rtol 1e-9
-ksp_type cg
-log_summary
-mg_coarse_ksp_type preonly
-mg_coarse_pc_factor_mat_solver_package superlu_dist
-mg_coarse_pc_type lu
-mg_levels_ksp_max_it 1
-mg_levels_ksp_type richardson
-options_left
-pc_mg_galerkin
-pc_mg_levels 3
-pc_type mg
#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 options: --known-level1-dcache-size=16384 --known-level1-dcache-linesize=64 --known-level1-dcache-assoc=4 --known-memcmp-ok=1 --known-sizeof-char=1 --known-sizeof-void-p=8 --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8 --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8 --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-sizeof-MPI_Comm=4 --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1 --known-mpi-int64_t=1 --known-mpi-c-double-complex=1 --known-sdot-returns-double=0 --known-snrm2-returns-double=0 --with-batch="1 " --known-mpi-shared="0 " --known-mpi-shared-libraries=0 --known-memcmp-ok --with-blas-lapack-lib="-L/opt/acml/5.3.1/gfortran64/lib -lacml" --COPTFLAGS="-march=bdver1 -fopenmp -O3 -ffast-math -fPIC " --FOPTFLAGS="-march=bdver1 -fopenmp -O3 -ffast-math -fPIC " --CXXOPTFLAGS="-march=bdver1 -fopenmp -O3 -ffast-math -fPIC " --with-x="0 " --with-debugging=0 --with-clib-autodetect="0 " --with-cxxlib-autodetect="0 " --with-fortranlib-autodetect="0 " --with-shared-libraries="0 " --with-mpi-compilers="1 " --with-cc="cc " --with-cxx="CC " --with-fc="ftn " --download-hypre=1 --download-blacs="1 " --download-scalapack="1 " --download-superlu_dist="1 " --download-metis="1 " --download-parmetis="1 " PETSC_ARCH=gnu-opt-32idx
-----------------------------------------
Libraries compiled on Wed Jun 3 14:35:20 2015 on h2ologin3
Machine characteristics: Linux-3.0.101-0.46-default-x86_64-with-SuSE-11-x86_64
Using PETSc directory: /mnt/a/u/sciteam/mrosso/LIBS/petsc-3.5.4
Using PETSc arch: gnu-opt-32idx
-----------------------------------------
Using C compiler: cc -march=bdver1 -fopenmp -O3 -ffast-math -fPIC ${COPTFLAGS} ${CFLAGS}
Using Fortran compiler: ftn -march=bdver1 -fopenmp -O3 -ffast-math -fPIC ${FOPTFLAGS} ${FFLAGS}
-----------------------------------------
Using include paths: -I/mnt/a/u/sciteam/mrosso/LIBS/petsc-3.5.4/gnu-opt-32idx/include -I/mnt/a/u/sciteam/mrosso/LIBS/petsc-3.5.4/include -I/mnt/a/u/sciteam/mrosso/LIBS/petsc-3.5.4/include -I/mnt/a/u/sciteam/mrosso/LIBS/petsc-3.5.4/gnu-opt-32idx/include
-----------------------------------------
Using C linker: cc
Using Fortran linker: ftn
Using libraries: -Wl,-rpath,/mnt/a/u/sciteam/mrosso/LIBS/petsc-3.5.4/gnu-opt-32idx/lib -L/mnt/a/u/sciteam/mrosso/LIBS/petsc-3.5.4/gnu-opt-32idx/lib -lpetsc -Wl,-rpath,/mnt/a/u/sciteam/mrosso/LIBS/petsc-3.5.4/gnu-opt-32idx/lib -L/mnt/a/u/sciteam/mrosso/LIBS/petsc-3.5.4/gnu-opt-32idx/lib -lsuperlu_dist_3.3 -lHYPRE -L/opt/acml/5.3.1/gfortran64/lib -lacml -lparmetis -lmetis -lpthread -lssl -lcrypto -ldl
-----------------------------------------
#PETSc Option Table entries:
-ksp_initial_guess_nonzero yes
-ksp_norm_type unpreconditioned
-ksp_rtol 1e-9
-ksp_type cg
-log_summary
-mg_coarse_ksp_type preonly
-mg_coarse_pc_factor_mat_solver_package superlu_dist
-mg_coarse_pc_type lu
-mg_levels_ksp_max_it 1
-mg_levels_ksp_type richardson
-options_left
-pc_mg_galerkin
-pc_mg_levels 3
-pc_type mg
#End of PETSc Option Table entries
There are no unused options.
[NID 15170] 2015-06-08 11:54:16 Apid 25082027: initiated application termination
Application 25082027 resources: utime ~1s, stime ~9s, Rss ~27320, inblocks ~19758, outblocks ~49423
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