[CIG-SHORT] Pylith Running on cluster
Matthew Knepley
knepley at mcs.anl.gov
Mon Dec 15 14:46:37 PST 2014
On Mon, Dec 15, 2014 at 4:32 PM, Xiao Ma <xiaoma5 at illinois.edu> wrote:
> Hi Matt,
> I have successfuly run the example problem /barshearwave/quad4 with 3
> nodes 12 cores per each nodes. I am wondering about the "fork" wanning , is
> it has something to do with this hanging for my large simulation?
>
Again, I do not think it was hanging, just calculating. You could run a
smaller example
and extrapolate the time (residual evaluation is nearly linear).
Thanks,
Matt
> Here's the stderr file :
> *****************************************
>
> ----------------------------------------
>
> Begin Torque Prologue (Mon Dec 15 16:24:20 2014)
>
> Job ID: 1820108.cc-mgmt1.campuscluster.illinois.edu
>
> Username: xiaoma5
>
> Group: cee_elbanna
>
> Job Name: YOURJOBNAME
>
> Limits:
> ncpus=1,neednodes=3:ppn=12,nodes=3:ppn=12,walltime=04:00:00
>
> Job Queue: secondary
>
> Account: cee_elbanna
>
> Nodes: taub335 taub339 taub349
>
> End Torque Prologue
>
> ----------------------------------------
>
> --------------------------------------------------------------------------
>
> An MPI process has executed an operation involving a call to the
>
> "fork()" system call to create a child process. Open MPI is currently
>
> operating in a condition that could result in memory corruption or
>
> other system errors; your MPI job may hang, crash, or produce silent
>
> data corruption. The use of fork() (or system() or other calls that
>
> create child processes) is strongly discouraged.
>
>
>
> The process that invoked fork was:
>
>
>
> Local host: taub339 (PID 8722)
>
> MPI_COMM_WORLD rank: 12
>
>
>
> If you are *absolutely sure* that your application will successfully
>
> and correctly survive a call to fork(), you may disable this warning
>
> by setting the mpi_warn_on_fork MCA parameter to 0.
>
> --------------------------------------------------------------------------
>
> [12]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [12]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
>
> [12]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [12]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[12]PETSC
> ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find
> memory corruption errors
>
> [12]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> and run
>
> [12]PETSC ERROR: to get more information on the crash.
>
> [12]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [12]PETSC ERROR: Signal received
>
> [12]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
>
> [12]PETSC ERROR: Petsc Development GIT revision:
> c754102742ddd04620cbeb83ad83e0546d180516 GIT Date: 2014-07-16 16:18:38
> -0500
>
> [12]PETSC ERROR: /home/xiaoma5/project-cse/pylith/bin/mpinemesis on a
> arch-pylith named taub339 by xiaoma5 Mon Dec 15 16:24:24 2014
>
> [12]PETSC ERROR: Configure options
> --prefix=/home/xiaoma5/project-cse/pylith --with-c2html=0 --with-x=0
> --with-clanguage=C --with-mpicompilers=1 --with-debugging=0
> --with-shared-libraries=1 --download-chaco=1 --download-ml=1
> --download-fblaslapack=1 --with-hdf5=1
> --with-hdf5-include=/home/xiaoma5/project-cse/pylith/include
> --with-hdf5-lib=/home/xiaoma5/project-cse/pylith/lib/libhdf5.dylib
> --LIBS=-lz CPPFLAGS="-I/home/xiaoma5/project-cse/pylith/include "
> LDFLAGS="-L/home/xiaoma5/project-cse/pylith/lib " CFLAGS="-g -O2"
> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS="-g -O2"
> PETSC_DIR=/home/xiaoma5/project-cse/src/pylith/pylith-installer-2.0.3-0/petsc-pylith
> PETSC_ARCH=arch-pylith
>
> [12]PETSC ERROR: #1 User provided function() line 0 in unknown file
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'WARNING: No initial
> state given for friction model 'Slip weakening'. Using default value of
> zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> Slip weakeningWARNING: No initial state given for friction model 'Slip
> weakening'. Using default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.'. Using default value of zero.WARNING: No initial
> state given for friction model 'Slip weakening
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> '. Using default value of zero.
>
>
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> WARNING: No initial state given for friction model 'WARNING: No initial
> state given for friction model 'Slip weakening'. Using default value of
> zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> Slip weakening'. Using default value of zero.
>
> WARNING: No initial state given for friction model 'Slip weakening'. Using
> default value of zero.
>
> [taub349:25960] 35 more processes have sent help message
> help-mpi-runtime.txt / mpi_init:warn-fork
>
> [taub349:25960] Set MCA parameter "orte_base_help_aggregate" to 0 to see
> all help / error messages
>
> ----------------------------------------
>
> Begin Torque Epilogue (Mon Dec 15 16:25:12 2014)
>
> Job ID: 1820108.cc-mgmt1.campuscluster.illinois.edu
>
> Username: xiaoma5
>
> Group: cee_elbanna
>
> Job Name: YOURJOBNAME
>
> Session: 25928
>
> Limits:
> ncpus=1,neednodes=3:ppn=12,nodes=3:ppn=12,walltime=04:00:00
>
> Resources:
> cput=00:15:43,energy_used=0,mem=3103924kb,vmem=15945788kb,walltime=00:00:52
>
> Job Queue: secondary
>
> Account: cee_elbanna
>
> Nodes: taub335 taub339 taub349
>
> End Torque Epilogue
>
> ----------------------------------------
>
> *******************************************
>
> Log file:
>
> ********************************************
> e: 66.70 MB
>
> -- [8] CPU time: 00:00:32, Memory usage: 83.98 MB
> >>
> /home/xiaoma5/project-cse/pylith/lib/python2.7/site-packages/pylith/problems/Formulation.py:282:finalize
> -- explicit(debug)
> -- [0] CPU time: 00:00:28, Memory usage: 94.72 MB
> >>
> /home/xiaoma5/project-cse/pylith/lib/python2.7/site-packages/pylith/utils/PetscManager.py:75:finalize
> -- petsc(info
> -- Finalizing PETSc.
>
> ************************************************************************************************************************
> *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r
> -fCourier9' to print this document ***
>
> ************************************************************************************************************************
>
> ---------------------------------------------- PETSc Performance Summary:
> ----------------------------------------------
>
> /home/xiaoma5/project-cse/pylith/bin/mpinemesis on a arch-pylith named
> taub349 with 36 processors, by xiaoma5 Mon Dec 15 16:25:11 2014
> Using Petsc Development GIT revision:
> c754102742ddd04620cbeb83ad83e0546d180516 GIT Date: 2014-07-16 16:18:38
> -0500
>
> Max Max/Min Avg Total
> Time (sec): 4.720e+01 1.00131 4.718e+01
> Objects: 1.915e+03 1.01970 1.881e+03
> Flops: 5.677e+05 1.71888 4.357e+05 1.569e+07
> Flops/sec: 1.204e+04 1.72009 9.236e+03 3.325e+05
> MPI Messages: 2.819e+04 10.26753 5.824e+03 2.097e+05
> MPI Message Lengths: 6.475e+05 12.45007 2.070e+01 4.340e+06
> MPI Reductions: 3.624e+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: 1.0368e-01 0.2% 0.0000e+00 0.0% 0.000e+00
> 0.0% 0.000e+00 0.0% 0.000e+00 0.0%
> 1: Meshing: 3.3931e-01 0.7% 4.7200e+02 0.0% 1.116e+03
> 0.5% 2.961e-01 1.4% 3.400e+01 0.9%
> 2: Setup: 3.5577e+00 7.5% 2.5808e+04 0.2% 3.112e+03
> 1.5% 1.982e-01 1.0% 2.890e+02 8.0%
> 3: Reform Jacobian: 1.0409e-02 0.0% 2.2680e+04 0.1% 3.640e+02
> 0.2% 4.752e-02 0.2% 3.000e+00 0.1%
> 4: Reform Residual: 5.9408e-01 1.3% 1.2995e+07 82.8% 6.588e+04
> 31.4% 7.018e+00 33.9% 6.000e+00 0.2%
> 6: Prestep: 1.9647e-01 0.4% 1.9200e+03 0.0% 0.000e+00
> 0.0% 0.000e+00 0.0% 1.000e+00 0.0%
> 7: Step: 1.1146e+01 23.6% 1.8517e+06 11.8% 4.398e+04
> 21.0% 4.684e+00 22.6% 8.000e+00 0.2%
> 8: Poststep: 3.0956e+01 65.6% 7.8912e+05 5.0% 9.522e+04
> 45.4% 8.453e+00 40.8% 3.282e+03 90.6%
> 9: Finalize: 2.7305e-01 0.6% 0.0000e+00 0.0% 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 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
>
>
> --- Event Stage 1: Meshing
>
> MeIm create 1 1.0 3.2108e-01 1.2 1.60e+01 1.3 1.1e+03 5.6e+01
> 3.4e+01 1 0 1 1 1 87100100100100 0
> MeIm adjTopo 1 1.0 2.1299e-02 2.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 5.0e+00 0 0 0 0 0 5 0 0 0 15 0
> VecScale 1 1.0 1.9569e-0316.4 1.60e+01 1.3 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0100 0 0 0 0
> DMPlexInterp 1 1.0 4.7829e-0338.5 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
> DMPlexPartition 1 1.0 7.3867e-02 1.1 0.00e+00 0.0 3.6e+02 3.6e+01
> 7.0e+00 0 0 0 0 0 21 0 32 21 21 0
> DMPlexDistribute 1 1.0 1.4583e-01 1.1 0.00e+00 0.0 1.1e+03 5.6e+01
> 2.7e+01 0 0 1 1 1 42 0100100 79 0
> DMPlexDistCones 1 1.0 3.1788e-03 2.8 0.00e+00 0.0 3.2e+02 6.4e+01
> 2.0e+00 0 0 0 0 0 1 0 29 33 6 0
> DMPlexDistLabels 1 1.0 1.2003e-02 9.3 0.00e+00 0.0 0.0e+00 0.0e+00
> 1.4e+01 0 0 0 0 0 1 0 0 3 41 0
> DMPlexDistribSF 1 1.0 9.6750e-03172.7 0.00e+00 0.0 1.1e+02 1.3e+02
> 0.0e+00 0 0 0 0 0 3 0 10 23 0 0
> DMPlexDistField 1 1.0 5.4257e-02 1.0 0.00e+00 0.0 3.2e+02 3.7e+01
> 4.0e+00 0 0 0 0 0 16 0 29 20 12 0
> DMPlexStratify 5 1.2 8.7202e-03 8.8 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 1 0 0 0 0 0
> SFSetGraph 8 1.0 2.2359e-0317.2 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
> SFBcastBegin 13 1.0 2.4010e-0232.6 0.00e+00 0.0 8.3e+02 5.7e+01
> 5.0e+00 0 0 0 1 0 4 0 74 76 15 0
> SFBcastEnd 13 1.0 3.2347e-021085.4 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 5 0 0 0 0 0
> SFReduceBegin 2 1.0 1.2650e-0310.5 0.00e+00 0.0 1.4e+02 8.4e+01
> 1.0e+00 0 0 0 0 0 0 0 13 20 3 0
> SFReduceEnd 2 1.0 9.5749e-03331.9 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
> SFFetchOpBegin 1 1.0 6.3119e-02 1.1 0.00e+00 0.0 1.1e+02 4.0e+00
> 1.0e+00 0 0 0 0 0 18 0 10 1 3 0
> SFFetchOpEnd 1 1.0 2.9888e-03272.5 0.00e+00 0.0 3.6e+01 4.0e+00
> 0.0e+00 0 0 0 0 0 0 0 3 0 0 0
> Dist distribute 1 1.0 1.4688e-01 1.1 0.00e+00 0.0 1.1e+03 5.6e+01
> 2.7e+01 0 0 1 1 1 42 0100100 79 0
> Refin refine 1 1.0 7.1526e-06 1.9 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
>
> --- Event Stage 2: Setup
>
> VecView 3 1.0 9.3205e-02 1.6 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 2 0 0 0 0 0
> VecScale 2 1.0 3.8147e-06 0.0 8.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 3
> VecCopy 9 1.0 1.1010e-021003.9 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 57 1.0 3.8862e-05 1.6 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
> VecAssemblyBegin 1 1.0 3.6640e-03 3.1 0.00e+00 0.0 0.0e+00 0.0e+00
> 3.0e+00 0 0 0 0 0 0 0 0 0 1 0
> VecAssemblyEnd 1 1.0 2.1458e-06 2.2 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
> MatAssemblyBegin 1 1.0 1.1921e-06 0.0 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 1 1.0 1.3553e-0221.5 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
> MatGetRow 36 0.0 3.0994e-06 0.0 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
> DMPlexStratify 3 1.0 4.7922e-0522.3 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
> SFSetGraph 9 1.0 2.4319e-05 2.0 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
> SFBcastBegin 94 1.0 8.8076e-0210.4 0.00e+00 0.0 2.6e+03 1.3e+01
> 2.0e+00 0 0 1 1 0 1 0 82 78 1 0
> SFBcastEnd 94 1.0 1.2429e-012896.2 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 1 0 0 0 0 0
> SFReduceBegin 12 1.0 1.3537e-03 5.0 0.00e+00 0.0 1.4e+02 1.7e+01
> 8.0e+00 0 0 0 0 0 0 0 4 6 3 0
> SFReduceEnd 12 1.0 1.0816e-022668.6 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
> TSEx preinit 1 1.0 3.2516e-01 1.2 0.00e+00 0.0 0.0e+00 0.0e+00
> 6.0e+00 1 0 0 0 0 9 0 0 0 2 0
> TSEx verify 1 1.0 6.1519e-03 2.6 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
> TSEx init 1 1.0 3.2335e+00 1.0 9.48e+02 2.0 3.1e+03 1.3e+01
> 2.8e+02 7 0 1 1 8 89100100100 98 0
> DtUn preinit 1 1.0 1.0014e-05 1.7 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
> DtUn verify 1 1.0 1.0014e-05 1.7 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
> DtUn init 1 1.0 5.5075e-05 1.4 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
> ElEx verify 1 1.0 3.9580e-03 3.4 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
> ElEx init 1 1.0 6.2873e-01 1.1 9.48e+02 3.0 1.8e+03 1.3e+01
> 5.1e+01 1 0 1 1 1 17 98 58 57 18 0
> MaPlSn verify 1 1.0 3.5861e-03 6.7 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
> OutM init 3 1.0 3.0861e-03 2.6 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
> OutM open 5 1.0 1.1633e+00 1.0 8.00e+00 0.0 2.6e+01 9.5e+00
> 3.4e+01 2 0 0 0 1 32 0 1 1 12 0
> OutM writeInfo 3 1.0 2.0797e+00 1.0 2.16e+02 2.3 1.7e+03 1.3e+01
> 1.2e+02 4 0 1 1 3 58 22 53 53 42 0
> AbBC verify 2 1.0 1.8461e-0332.4 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
> AbBC init 2 1.0 2.5861e-03 1.6 1.12e+02 0.0 0.0e+00 0.0e+00
> 1.0e+01 0 0 0 0 0 0 1 0 0 3 0
> DiBC verify 1 1.0 1.0610e-04 3.4 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
> DiBC init 1 1.0 6.8124e-0257.2 0.00e+00 0.0 2.3e+02 1.3e+01
> 1.0e+01 0 0 0 0 0 1 0 7 7 3 0
> CoDy verify 1 1.0 5.9795e-04 1.4 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
> CoDy init 1 1.0 1.9730e+00 1.0 1.54e+02 0.0 2.6e+02 1.7e+01
> 1.7e+02 4 0 0 0 5 55 1 8 11 60 0
>
> --- Event Stage 3: Reform Jacobian
>
> VecSet 2 1.0 8.1062e-06 4.2 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
> SFSetGraph 1 1.0 7.1526e-06 2.3 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
> SFBcastBegin 1 1.0 4.0770e-0521.4 0.00e+00 0.0 9.1e+01 4.2e+01
> 0.0e+00 0 0 0 0 0 0 0 25 39 0 0
> SFBcastEnd 1 1.0 3.3319e-03 0.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 6 0 0 0 0 0
> SFReduceBegin 1 1.0 3.4111e-0355.0 0.00e+00 0.0 2.7e+02 2.2e+01
> 1.0e+00 0 0 0 0 0 26 0 75 61 33 0
> SFReduceEnd 1 1.0 2.0981e-0522.0 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
> ElIJ setup 1 1.0 2.0981e-05 4.2 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
> ElIJ compute 1 1.0 7.4148e-05 2.9 8.40e+02 3.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 99 0 0 0 302
> AdIJ setup 2 1.0 1.3018e-04 2.4 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 1 0 0 0 0 0
> AdIJ compute 2 1.0 3.2187e-05 0.0 1.40e+02 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 1 0 0 0 9
> FaIJ setup 1 1.0 2.1458e-06 0.0 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
> FaIJ compute 1 1.0 9.5367e-07 0.0 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
>
> --- Event Stage 4: Reform Residual
>
> VecSet 480 1.0 1.0936e-03 3.5 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
> SFSetGraph 2 1.0 1.3113e-05 2.6 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
> SFBcastBegin 240 1.0 1.4002e-03 3.8 0.00e+00 0.0 2.2e+04 2.2e+01
> 0.0e+00 0 0 10 11 0 0 0 33 33 0 0
> SFBcastEnd 240 1.0 6.1437e-014552.8 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 30 0 0 0 0 0
> SFReduceBegin 480 1.0 4.9629e-03 1.8 0.00e+00 0.0 4.4e+04 2.2e+01
> 2.0e+00 0 0 21 23 0 1 0 67 67 33 0
> SFReduceEnd 480 1.0 6.6732e-011913.2 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 1 0 0 0 0 60 0 0 0 0 0
> ElIR setup 240 1.0 3.2091e-03 1.4 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
> ElIR compute 240 1.0 5.5752e-03 1.5 4.58e+05 3.0 0.0e+00 0.0e+00
> 0.0e+00 0 78 0 0 0 1 94 0 0 0 2190
> AdIR setup 480 1.0 2.5492e-03 1.5 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
> AdIR compute 480 1.0 4.8966e-03103.2 4.42e+04 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 1 0 0 0 0 1 0 0 0 18
> FaIR setup 240 1.0 4.1564e-03 1.3 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 1 0 0 0 0 0
> FaIR compute 240 1.0 2.7990e-04 6.5 7.68e+03 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 55
>
> --- Event Stage 5: Unknown
>
>
> --- Event Stage 6: Prestep
>
> TSEx timestep 240 1.0 1.0135e-0155.1 7.20e+01 3.0 0.0e+00 0.0e+00
> 1.0e+00 0 0 0 0 0 34100 0 0100 0
> TSEx prestep 240 1.0 1.4796e-01 1.7 8.40e+02 3.0 3.6e+02 2.7e+01
> 3.0e+00 0 0 0 0 0 601181 0 0300 0
>
> --- Event Stage 7: Step
>
> VecSet 481 1.0 1.4012e-03 2.0 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
> VecAXPY 240 1.0 5.3819e-02148.5 9.60e+03 1.7 0.0e+00 0.0e+00
> 0.0e+00 0 1 0 0 0 0 12 0 0 0 4
> SFSetGraph 1 1.0 5.0068e-06 2.6 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
> SFBcastBegin 242 1.0 5.0166e-03 7.6 0.00e+00 0.0 2.2e+04 2.2e+01
> 0.0e+00 0 0 10 11 0 0 0 50 50 0 0
> SFBcastEnd 242 1.0 2.3892e+0014565.2 0.00e+00 0.0 0.0e+00
> 0.0e+00 0.0e+00 2 0 0 0 0 7 0 0 0 0 0
> SFReduceBegin 240 1.0 2.5533e-0152.1 0.00e+00 0.0 2.2e+04 2.2e+01
> 1.0e+00 0 0 11 11 0 0 0 50 50 12 0
> SFReduceEnd 240 1.0 1.7751e+004097.6 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 1 0 0 0 0 6 0 0 0 0 0
> FaAS setup 240 1.0 3.3627e-03 1.2 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
> FaAS compute 240 1.0 6.9878e-03325.7 7.43e+04 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 1 0 0 0 0 8 0 0 0 21
> SoLu setup 240 1.0 2.1734e-03 1.2 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
> SoLu solve 240 1.0 9.5439e-04 1.4 3.84e+03 1.3 0.0e+00 0.0e+00
> 0.0e+00 0 1 0 0 0 0 6 0 0 0 119
> SoLu adjust 240 1.0 2.6357e+00 4.9 1.30e+05 3.2 4.4e+04 2.2e+01
> 8.0e+00 3 11 21 23 0 13 94100100100 1
>
> --- Event Stage 8: Poststep
>
> VecView 240 1.0 3.6254e+00 1.4 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 7 0 0 0 0 10 0 0 0 0 0
> VecCopy 1704 1.0 2.8782e-03 1.5 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 488 1.0 3.1400e-04 1.5 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 240 1.0 5.7673e-04 3.2 9.60e+03 1.7 0.0e+00 0.0e+00
> 0.0e+00 0 1 0 0 0 0 29 0 0 0 399
> VecAssemblyBegin 240 1.0 7.7466e-02 1.6 0.00e+00 0.0 0.0e+00 0.0e+00
> 7.2e+02 0 0 0 0 20 0 0 0 0 22 0
> VecAssemblyEnd 240 1.0 4.9138e-04 1.6 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
> SFBcastBegin 808 1.0 3.2768e-03 2.2 0.00e+00 0.0 4.7e+04 1.3e+01
> 0.0e+00 0 0 22 14 0 0 0 49 34 0 0
> SFBcastEnd 808 1.0 5.1820e-011300.7 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
> SFReduceBegin 720 1.0 3.9566e-03 3.7 0.00e+00 0.0 2.2e+03 2.1e+01
> 0.0e+00 0 0 1 1 0 0 0 2 3 0 0
> SFReduceEnd 720 1.0 3.7780e-01886.3 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
> TSEx poststep 240 1.0 3.2119e+01 1.1 4.09e+04 2.2 9.5e+04 1.9e+01
> 3.3e+03 66 5 45 41 91 100100100100100 0
> TSEx write 240 1.0 2.8331e+01 1.0 2.22e+04 1.7 1.1e+04 1.9e+01
> 2.3e+03 59 3 5 5 63 89 68 12 12 70 0
> ElEx poststep 240 1.0 4.8757e-03 1.2 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
> ElEx write 240 1.0 1.8991e-01 1.1 1.96e+04 3.0 8.8e+03 1.8e+01
> 1.4e+02 0 3 4 4 4 1 66 9 9 4 3
> OutM writeData 720 1.0 3.2015e+01 1.1 2.22e+04 1.7 9.5e+04 1.9e+01
> 3.3e+03 65 3 45 41 91 100 68100100100 0
> AbBC poststep 480 1.0 8.2965e-03 1.4 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
> AbBC write 480 1.0 2.9407e-03 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
> CoDy poststep 240 1.0 1.1666e-02 2.2 9.12e+03 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 2 0 0 0 2
> CoDy write 240 1.0 2.8130e+01 1.0 9.12e+03 0.0 2.2e+03 2.1e+01
> 2.2e+03 58 0 1 1 60 89 2 2 3 66 0
>
> --- Event Stage 9: Finalize
>
> TSEx finalize 1 1.0 2.8769e-01 1.1 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 1 0 0 0 0 100 0 0 0 0 0
> OutM close 3 1.0 8.8396e-02 3.2 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 14 0 0 0 0 0
>
> ------------------------------------------------------------------------------------------------------------------------
>
> 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 0 52 30160 0
> Vector 0 76 118528 0
> Distributed Mesh 0 81 357552 0
> Star Forest Bipartite Graph 0 85 70032 0
> Discrete System 0 81 64800 0
> Index Set 0 14 11112 0
> Section 0 230 155480 0
> Viewer 1 0 0 0
>
> --- Event Stage 1: Meshing
>
> Container 2 2 1160 0
> Vector 4 3 8712 0
> Distributed Mesh 11 9 41376 0
> Star Forest Bipartite Graph 29 26 21608 0
> Discrete System 11 9 7200 0
> Index Set 45 45 40828 0
> IS L to G Mapping 1 1 1972 0
> Section 25 21 14196 0
>
> --- Event Stage 2: Setup
>
> Container 106 58 33640 0
> Vector 85 15 23184 0
> Matrix 1 1 5436 0
> Distributed Mesh 82 8 35200 0
> Star Forest Bipartite Graph 164 87 71104 0
> Discrete System 82 8 6400 0
> Index Set 23 13 10404 0
> Section 259 73 49348 0
> Viewer 3 2 1432 0
>
> --- Event Stage 3: Reform Jacobian
>
> Section 6 0 0 0
>
> --- Event Stage 4: Reform Residual
>
> Index Set 4 0 0 0
> Section 16 0 0 0
>
> --- Event Stage 5: Unknown
>
>
> --- Event Stage 6: Prestep
>
>
> --- Event Stage 7: Step
>
> Container 6 3 1740 0
> Vector 2 0 0 0
> Distributed Mesh 2 0 0 0
> Star Forest Bipartite Graph 4 2 1632 0
> Discrete System 2 0 0 0
> Section 11 2 1352 0
>
> --- Event Stage 8: Poststep
>
> Container 18 11 6380 0
> Vector 16 4 6248 0
> Distributed Mesh 13 2 8800 0
> Star Forest Bipartite Graph 26 15 12240 0
> Discrete System 13 2 1600 0
> Index Set 25 25 19992 0
> Section 685 654 442104 0
> Viewer 132 132 95040 0
>
> --- Event Stage 9: Finalize
>
> Container 0 6 3480 0
> Vector 0 9 14192 0
> Distributed Mesh 0 8 35200 0
> Star Forest Bipartite Graph 0 8 6528 0
> Discrete System 0 8 6400 0
> Section 0 22 14872 0
> Viewer 0 1 712 0
>
> ========================================================================================================================
> Average time to get PetscTime(): 0
> Average time for MPI_Barrier(): 2.81811e-05
> Average time for zero size MPI_Send(): 1.47687e-06
> #PETSc Option Table entries:
> -log_summary
> #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: --prefix=/home/xiaoma5/project-cse/pylith
> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
> --with-debugging=0 --with-shared-libraries=1 --download-chaco=1
> --download-ml=1 --download-fblaslapack=1 --with-hdf5=1
> --with-hdf5-include=/home/xiaoma5/project-cse/pylith/include
> --with-hdf5-lib=/home/xiaoma5/project-cse/pylith/lib/libhdf5.dylib
> --LIBS=-lz CPPFLAGS="-I/home/xiaoma5/project-cse/pylith/include "
> LDFLAGS="-L/home/xiaoma5/project-cse/pylith/lib " CFLAGS="-g -O2"
> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS="-g -O2"
> PETSC_DIR=/home/xiaoma5/project-cse/src/pylith/pylith-installer-2.0.3-0/petsc-pylith
> PETSC_ARCH=arch-pylith
> -----------------------------------------
> Libraries compiled on Sun Dec 14 15:39:18 2014 on taubh2
> Machine characteristics:
> Linux-2.6.32-431.29.2.el6.x86_64-x86_64-with-centos-6.5-Final
> Using PETSc directory:
> /home/xiaoma5/project-cse/src/pylith/pylith-installer-2.0.3-0/petsc-pylith
> Using PETSc arch: arch-pylith
> -----------------------------------------
>
> Using C compiler: mpicc -g -O2 -fPIC
> -I/home/xiaoma5/project-cse/pylith/include ${COPTFLAGS} ${CFLAGS}
> Using Fortran compiler: mpif90 -fPIC -Wall -Wno-unused-variable
> -ffree-line-length-0 -O -I/home/xiaoma5/project-cse/pylith/include
> ${FOPTFLAGS} ${FFLAGS} -I/home/xiaoma5/project-cse/pylith/include
> -----------------------------------------
>
> Using include paths:
> -I/home/xiaoma5/project-cse/src/pylith/pylith-installer-2.0.3-0/petsc-pylith/arch-pylith/include
> -I/home/xiaoma5/project-cse/src/pylith/pylith-installer-2.0.3-0/petsc-pylith/include
> -I/home/xiaoma5/project-cse/src/pylith/pylith-installer-2.0.3-0/petsc-pylith/include
> -I/home/xiaoma5/project-cse/src/pylith/pylith-installer-2.0.3-0/petsc-pylith/arch-pylith/include
> -I/projects/cse/shared/xiaoma5/src/pylith/pylith-installer-2.0.3-0/petsc-pylith/arch-pylith/include
> -I/home/xiaoma5/project-cse/pylith/include
> -I/usr/local/mpi/openmpi-1.6.5-gcc-4.7.1/include
> -----------------------------------------
>
> Using C linker: mpicc
> Using Fortran linker: mpif90
> Using libraries:
> -Wl,-rpath,/home/xiaoma5/project-cse/src/pylith/pylith-installer-2.0.3-0/petsc-pylith/arch-pylith/lib
> -L/home/xiaoma5/project-cse/src/pylith/pylith-installer-2.0.3-0/petsc-pylith/arch-pylith/lib
> -lpetsc
> -Wl,-rpath,/projects/cse/shared/xiaoma5/src/pylith/pylith-installer-2.0.3-0/petsc-pylith/arch-pylith/lib
> -L/projects/cse/shared/xiaoma5/src/pylith/pylith-installer-2.0.3-0/petsc-pylith/arch-pylith/lib
> -lml -Wl,-rpath,/home/xiaoma5/project-cse/pylith/lib
> -L/home/xiaoma5/project-cse/pylith/lib
> -Wl,-rpath,/usr/local/torque-releases/torque-4.2.6/lib
> -L/usr/local/torque-releases/torque-4.2.6/lib
> -Wl,-rpath,/usr/local/mpi/openmpi-1.6.5-gcc-4.7.1/lib
> -L/usr/local/mpi/openmpi-1.6.5-gcc-4.7.1/lib
> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.4.7
> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -lmpi_cxx -lstdc++ -lflapack
> -lfblas -lpthread -lssl -lcrypto -lchaco -lhdf5 -lmpi_f90 -lmpi_f77
> -lgfortran -lm -lmpi_cxx -lstdc++ -ldl -lz -lmpi -libverbs -lrt -lnsl
> -lutil -ltorque -lgcc_s -lpthread -ldl -lz
> -----------------------------------------
> *************************************
>
> --
>
> -------------------------------------------------------------------------------------
> *Xiao Ma*
> Graduate Research Assistant
> MS program in Structural Engineering
> University of Illinois at Urbana-Champaign
> E-mail: *xiaoma5 at illinois.edu <xiaoma5 at illinois.edu>*
>
> --------------------------------------------------------------------------------------
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
--
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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