Barry, thank you for the clarification!
Best, Michele On Wed, 2015-07-01 at 20:02 -0500, Barry Smith wrote: > 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> > >> > >> > >> > > >
