On 10 March 2011 19:37, Ethan Coon <ecoon at lanl.gov> wrote: > >> > >> > Will get patches for these (and the doc fix). >> > >> >> Could you also consider the patch below? I think the CHKMEMQ macros >> should not be there, we are not calling "untrusted" user code, right? > > Oh crap, thanks, there's a bit more cruft that I thought I had removed. > >> And the missing free is causing the following output in petsc4py >> testsuite: >> >> $ python test/runtests.py -i da >> [0 at nikola] Python 2.6 (/usr/bin/python) >> [0 at nikola] PETSc 3.1.0-p7 development (conf: 'arch-linux2-c-opt') >> [0 at nikola] petsc4py 1.1.2 (build/lib.linux-x86_64-2.6/petsc4py) >> [0]Total space allocated 123685312 bytes >> [ 0]10137008 bytes DMSetUp_DA_3D() line 1272 in >> /usr/local/petsc/dev/src/dm/impls/da/da3.c >> [ 0]1302848 bytes DMSetUp_DA_3D() line 1272 in >> /usr/local/petsc/dev/src/dm/impls/da/da3.c >> >> >> diff -r 3923fa35e382 src/dm/impls/da/da2.c >> --- a/src/dm/impls/da/da2.c ? Thu Mar 10 15:03:35 2011 -0600 >> +++ b/src/dm/impls/da/da2.c ? Thu Mar 10 19:03:28 2011 -0300 >> @@ -1734,7 +1734,6 @@ >> ? ?/* ?ierr = >> PetscLogObjectMemory(da,nn*dof*sizeof(PetscInt));CHKERRQ(ierr);*/ >> ? ?ierr = ISGetIndices(ltogis, &idx_full); >> ? ?ierr = >> PetscMemcpy(idx_cpy,idx_full,nn*dof*sizeof(PetscInt));CHKERRQ(ierr); >> - ?CHKMEMQ; >> ? ?ierr = ISRestoreIndices(ltogis, &idx_full); >> ? ?ierr = ISLocalToGlobalMappingCreateIS(ltogis,&da->ltogmap);CHKERRQ(ierr); >> ? ?ierr = PetscLogObjectParent(da,da->ltogmap);CHKERRQ(ierr); >> diff -r 3923fa35e382 src/dm/impls/da/da3.c >> --- a/src/dm/impls/da/da3.c ? Thu Mar 10 15:03:35 2011 -0600 >> +++ b/src/dm/impls/da/da3.c ? Thu Mar 10 19:03:28 2011 -0300 >> @@ -1273,7 +1273,6 @@ >> ? ?/* ierr = PetscLogObjectMemory(da,nn*dof*sizeof(PetscInt));CHKERRQ(ierr); >> */ >> ? ?ierr = ISGetIndices(ltogis, &idx_full); >> ? ?ierr = >> PetscMemcpy(idx_cpy,idx_full,nn*dof*sizeof(PetscInt));CHKERRQ(ierr); >> - ?CHKMEMQ; >> ? ?ierr = ISRestoreIndices(ltogis, &idx_full); >> ? ?ierr = ISLocalToGlobalMappingCreateIS(ltogis,&da->ltogmap);CHKERRQ(ierr); >> ? ?ierr = PetscLogObjectParent(da,da->ltogmap);CHKERRQ(ierr); >> diff -r 3923fa35e382 src/dm/impls/da/dadestroy.c >> --- a/src/dm/impls/da/dadestroy.c ? ? Thu Mar 10 15:03:35 2011 -0600 >> +++ b/src/dm/impls/da/dadestroy.c ? ? Thu Mar 10 19:03:28 2011 -0300 >> @@ -106,6 +106,7 @@ >> ? ? ?ierr = AODestroy(dd->ao);CHKERRQ(ierr); >> ? ?} >> >> + ?ierr = PetscFree(dd->idx);CHKERRQ(ierr); >> ? ?ierr = PetscFree(dd->lx);CHKERRQ(ierr); >> ? ?ierr = PetscFree(dd->ly);CHKERRQ(ierr); >> ? ?ierr = PetscFree(dd->lz);CHKERRQ(ierr); >> >> > > Hmm, I didn't add the dd->idx, so I'm suprised it wasn't free'd already. > I also wasn't sure when/if to log the memory, since it seemed to be in > there for some stuff and not for others in the previous code. >
You should just log it in the DM object, just uncomment the line in the 2D and 3D setup code > With the copy (your next email) to the IS, shouldn't that changeset leak > memory? ?I think it also needs a PetscFree(idx) then as well... > My two patches are cumulative... Take into account that DMDestroy_DA applies to 1/2/3D, while the setup code is different. The free(idx) at the common destoy() should be enough (provided you use COPY_VALUES for the 1D code) > > Will get these fixes in, > With both patches applied, petsc4py testsuite pass cleanly (and mem leaks seems to go away). So I'm more or less confident on your (huge) changes + my (tiny) fixes -- Lisandro Dalcin --------------- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169