Ahh yes, I see. I have added the following text to PetscOptionsInsertFile() to clarify
Usually, instead of using this command, one should list the file name in the call to PetscInitialize(), this insures that certain options such as -log_summary or -malloc_debug are processed properly. This routine only sets options into the options database that will be processed by later calls to XXXSetFromOptions() it should not be used for options listed under PetscInitialize(). > On Jul 1, 2015, at 4:52 PM, Michele Rosso <[email protected]> wrote: > > Hi Barry, > > I accidentally found out what triggers the problem with log_summary. > If I specify log_summary from command line, it works as expected. If instead > I open and load an options file with -log_summary in it, > the output is incomplete. > I am actually concerned about using options files now because this weird > behavior could affect the correct loading of other options as well. > > 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 <[email protected]> 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> >> >> >> >
