You are creating or duplicating vectors and not destroying them so they will swallow up more and more memory. Make sure every create/duplicate has a corresponding destroy.
Barry On May 3, 2012, at 10:38 PM, Bo Sun wrote: > Hi Barry, > Thank you for your reply. Sorry to confuse you. The strange data means that > when I run the case using only one cpu, after some steps, the case blows up > or give wrong data. I think that is because the local memory is not enough. > And some case gives the following error message " > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Out of memory. This could be due to allocating > [0]PETSC ERROR: too large an object or bleeding by not properly > [0]PETSC ERROR: destroying unneeded objects. > [0]PETSC ERROR: Memory allocated 0 Memory used by process 1882513408 > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. > [0]PETSC ERROR: Memory requested 2628072! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11 09:28:45 CST > 2012 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: ./main on a arch-linu named lightningsmp.its.iastate.edu by > sciam Thu May 3 15:58:24 2012 > [0]PETSC ERROR: Libraries linked from > /work/doe_ar1/sciam/petsc-3.2-p6/arch-linux2-c-opt/lib > [0]PETSC ERROR: Configure run at Wed Apr 4 12:45:08 2012 > [0]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 > --with-debugging=0 FOPTFLAGS="-O3 -qarch=p4 -qtune=p4" > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: PetscMallocAlign() line 49 in src/sys/memory/mal.c > [0]PETSC ERROR: VecCreate_Seq() line 40 in src/vec/vec/impls/seq/bvec3.c > [0]PETSC ERROR: VecSetType() line 53 in src/vec/vec/interface/vecreg.c > [0]PETSC ERROR: VecDuplicate_Seq() line 800 in src/vec/vec/impls/seq/bvec2.c > [0]PETSC ERROR: VecDuplicate() line 541 in src/vec/vec/interface/vector.c > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[0]PETSC > ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find > memory corruption errors > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and > run > [0]PETSC ERROR: to get more information on the crash. > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Signal received! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11 09:28:45 CST > 2012 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: ./main on a arch-linu named lightningsmp.its.iastate.edu by > sciam Thu May 3 15:58:24 2012 > [0]PETSC ERROR: Libraries linked from > /work/doe_ar1/sciam/petsc-3.2-p6/arch-linux2-c-opt/lib > [0]PETSC ERROR: Configure run at Wed Apr 4 12:45:08 2012 > [0]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 > --with-debugging=0 FOPTFLAGS="-O3 -qarch=p4 -qtune=p4" > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown > file > ------------------------------------------------------------------------------------------------------------------------------ > > The input from fortran array to petsc vector and output from petsc vector to > fortran array happens in each loop. I guess that I didn't do appropriate > destroy to the vector in petsc. > > Regards, > Bo > > On Wed, May 2, 2012 at 11:01 PM, Barry Smith <bsmith at mcs.anl.gov> wrote: > > On May 2, 2012, at 11:32 PM, Bo Sun wrote: > > > Hi there, > > I am coding using Fortran 90 with petsc. I extract the results from vector > > in petsc as follows, > > > > PetscScalar, pointer :: xx_v(:) > > Vec pet_u > > > > .............. > > call VecGetArrayF90(pet_u,xx_v,ierr) > > data_for_fortran = xx_v > > call VecRestoreArrayF90(pet_u,xx_v,ierr) > > ................... > > > > > > For small size of vector, there is no problem. But when the size of vector > > is above million, some strange data appear. > > What do you mean strange data? Is this reproducable? Do two different > Fortran compilers give the same problem? I you can send us a simple Fortran > code that demonstrates the problem we can try to reproduce it. Please send > such a bug report to petsc-maint at mcs.anl.gov > > VecGetArrayF90() is generally the way to go, other things are more > cumbersome. > > > > > > Could you recommend another way to output the data of vector in petsc into > > fortran array ? > > > > > > Thanks, > > Bo > > > > > -- > -------------------------------------------------------------------- > CFD > Mechanical Engineering > Iowa State University > 50011
