March 2011 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] DMDA_*PERIODIC and DMDA_XYZGHOSTED
by Lisandro Dalcin 10 Mar '11

10 Mar '11

On 10 March 2011 21:45, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > On Mar 10, 2011, at 6:22 PM, Lisandro Dalcin wrote: > >> On 10 March 2011 20:57, Ethan Coon <ecoon(a)lanl.gov> wrote: >>> Attached patch makes this change, and updates the website with the API >>> change. >>> >>> Also it fixes a few stray 'DAPeriodicType's in conf/adic*.init, which >>> I'm guessing was just missed in the previous change to DMDAPeriodicType? >> >> Do we really need backward compatibility DMDA_XYZPERIODIC and friends? > > Is the | business all fine and dandy for Fortran? If so then I agree we should remove the "noise". > Well, you can use '+' (with a bit care) in any Fortran, right?. This is the way the MPI standard does things for some enumerations (file modes, RMA assertions). However, if DMDA_XYZPERIODIC and friends do no go away because of Fortran issues, then we should definitely define DMDA_{XY|XZ|YZ}GHOSTED. -- 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

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Re: [petsc-dev] DMDA_*PERIODIC and DMDA_XYZGHOSTED
by Barry Smith 10 Mar '11

10 Mar '11

On Mar 10, 2011, at 6:22 PM, Lisandro Dalcin wrote: > On 10 March 2011 20:57, Ethan Coon <ecoon(a)lanl.gov> wrote: >> Attached patch makes this change, and updates the website with the API >> change. >> >> Also it fixes a few stray 'DAPeriodicType's in conf/adic*.init, which >> I'm guessing was just missed in the previous change to DMDAPeriodicType? > > Do we really need backward compatibility DMDA_XYZPERIODIC and friends? Is the | business all fine and dandy for Fortran? If so then I agree we should remove the "noise". Barry > IMHO, I think it introduces API noise for very little benefit (taking > into account the huge changes to DA API for next release)... > > > -- > 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

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Re: [petsc-dev] DMDA_*PERIODIC and DMDA_XYZGHOSTED
by Lisandro Dalcin 10 Mar '11

10 Mar '11

On 10 March 2011 20:57, Ethan Coon <ecoon(a)lanl.gov> wrote: > Attached patch makes this change, and updates the website with the API > change. > > Also it fixes a few stray 'DAPeriodicType's in conf/adic*.init, which > I'm guessing was just missed in the previous change to DMDAPeriodicType? Do we really need backward compatibility DMDA_XYZPERIODIC and friends? IMHO, I think it introduces API noise for very little benefit (taking into account the huge changes to DA API for next release)... -- 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

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Re: [petsc-dev] Compiling petsc with superlu_dist, hypre and mumps on hopper II
by Satish Balay 10 Mar '11

10 Mar '11

attaching the configure file that worked with petsc-dev. I haven't tried petsc-31 Satish On Thu, 10 Mar 2011, fabien delalondre wrote: > Hi, > > Which argument should I pass to pass to compile petsc on hopper II with > superlu_dist, hypre and mumps (download) ? Without external package > --with-mpi=0 works fine but then the external packages complain about it (no > mpi specified). I tried to use and also modify the arch-cray-xt5-opt.py > configure file but I did not go through it yet (Invalid mpiexec specified: > /usr/common/acts/PETSc/3.0.0/bin/mpiexec.aprun). Instead of wasting time, I > guess you guys will provide an answer pretty quickly. > > Thanks for your help. > > Fabien > >

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Re: [petsc-dev] DMDA_*PERIODIC and DMDA_XYZGHOSTED
by Satish Balay 10 Mar '11

10 Mar '11

pushed.. satish On Thu, 10 Mar 2011, Ethan Coon wrote: > Attached patch makes this change, and updates the website with the API > change. > > Also it fixes a few stray 'DAPeriodicType's in conf/adic*.init, which > I'm guessing was just missed in the previous change to DMDAPeriodicType? > > mq is my friend, > > > Ethan > > > On Thu, 2011-03-10 at 17:38 -0600, Barry Smith wrote: > > On Mar 10, 2011, at 5:36 PM, Ethan Coon wrote: > > > > > > > > > > > The one thing I didn't change is the name of the DMDASetPeriodicity() > > > method, which I wasn't sure what to go to. > > > > DMDASetBoundaryType()? > > > > Barry > > > > > > > > > > Ethan > > > > > > > > > > > >>> > > >>> 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 > > >> > > >> > > > > > > -- > > > ------------------------------------ > > > Ethan Coon > > > Post-Doctoral Researcher > > > Applied Mathematics - T-5 > > > Los Alamos National Laboratory > > > 505-665-8289 > > > > > > http://www.ldeo.columbia.edu/~ecoon/ > > > ------------------------------------ > > > <dmda-periodicity-update.txt> > > > >

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Re: [petsc-dev] DMDA_*PERIODIC and DMDA_XYZGHOSTED
by Ethan Coon 10 Mar '11

10 Mar '11

Attached patch makes this change, and updates the website with the API change. Also it fixes a few stray 'DAPeriodicType's in conf/adic*.init, which I'm guessing was just missed in the previous change to DMDAPeriodicType? mq is my friend, Ethan On Thu, 2011-03-10 at 17:38 -0600, Barry Smith wrote: > On Mar 10, 2011, at 5:36 PM, Ethan Coon wrote: > > > > > > > The one thing I didn't change is the name of the DMDASetPeriodicity() > > method, which I wasn't sure what to go to. > > DMDASetBoundaryType()? > > Barry > > > > > > Ethan > > > > > > > >>> > >>> 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 > >> > >> > > > > -- > > ------------------------------------ > > Ethan Coon > > Post-Doctoral Researcher > > Applied Mathematics - T-5 > > Los Alamos National Laboratory > > 505-665-8289 > > > > http://www.ldeo.columbia.edu/~ecoon/ > > ------------------------------------ > > <dmda-periodicity-update.txt> > -- ------------------------------------ Ethan Coon Post-Doctoral Researcher Applied Mathematics - T-5 Los Alamos National Laboratory 505-665-8289 http://www.ldeo.columbia.edu/~ecoon/ ------------------------------------

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Re: [petsc-dev] DMDA_*PERIODIC and DMDA_XYZGHOSTED
by Satish Balay 10 Mar '11

10 Mar '11

patch now added to petsc-dev satish On Thu, 10 Mar 2011, Ethan Coon wrote: > > > > > > > > > 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 > > > > Ok, done. > > > > 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) > > > > Ah, I see my confusion... previously the memory had been shared with the > da->l2gmap, and so it was destroyed by that. I missed the fact that > your second change was in da1. This passes valgrind's memcheck. Thanks > for clearing that up, Lisandro. > > This patch does the change from DMDAPeriodicType -> DMDABoundaryType and > deals with Lisandro's memory fixes. > > The one thing I didn't change is the name of the DMDASetPeriodicity() > method, which I wasn't sure what to go to. > > Ethan > > > > > > > > > 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 > > > > > >

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Re: [petsc-dev] DMDA_*PERIODIC and DMDA_XYZGHOSTED
by Barry Smith 10 Mar '11

10 Mar '11

On Mar 10, 2011, at 5:36 PM, Ethan Coon wrote: > > > The one thing I didn't change is the name of the DMDASetPeriodicity() > method, which I wasn't sure what to go to. DMDASetBoundaryType()? Barry > > Ethan > > > >>> >>> 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 >> >> > > -- > ------------------------------------ > Ethan Coon > Post-Doctoral Researcher > Applied Mathematics - T-5 > Los Alamos National Laboratory > 505-665-8289 > > http://www.ldeo.columbia.edu/~ecoon/ > ------------------------------------ > <dmda-periodicity-update.txt>

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Re: [petsc-dev] DMDA_*PERIODIC and DMDA_XYZGHOSTED
by Ethan Coon 10 Mar '11

10 Mar '11

> > > > 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 > Ok, done. > > 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) > Ah, I see my confusion... previously the memory had been shared with the da->l2gmap, and so it was destroyed by that. I missed the fact that your second change was in da1. This passes valgrind's memcheck. Thanks for clearing that up, Lisandro. This patch does the change from DMDAPeriodicType -> DMDABoundaryType and deals with Lisandro's memory fixes. The one thing I didn't change is the name of the DMDASetPeriodicity() method, which I wasn't sure what to go to. Ethan > > > > 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 > > -- ------------------------------------ Ethan Coon Post-Doctoral Researcher Applied Mathematics - T-5 Los Alamos National Laboratory 505-665-8289 http://www.ldeo.columbia.edu/~ecoon/ ------------------------------------

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Re: [petsc-dev] Compiling petsc with superlu_dist, hypre and mumps on hopper II
by Barry Smith 10 Mar '11

10 Mar '11

On Mar 10, 2011, at 4:46 PM, fabien delalondre wrote: > Hi, > > Which argument should I pass to pass to compile petsc on hopper II with superlu_dist, hypre and mumps (download) ? Without external package --with-mpi=0 works fine but then the external packages complain about it (no mpi specified). I tried to use and also modify the arch-cray-xt5-opt.py configure file but I did not go through it yet (Invalid mpiexec specified: /usr/common/acts/PETSc/3.0.0/bin/mpiexec.aprun). Instead of wasting time, I guess you guys will provide an answer pretty quickly. Satish, Why does --with-mpiexec have to be set on hopper? And why to this crazy location that may not always exist? Requiring the user to set this beast to some strange thing at configure time is not reasonable. We need a model that doesn't require strange knowledge like this. Barry > > Thanks for your help. > > Fabien > > -- > Fabien Delalondre, PhD. > Senior Research Associate, Scientific Computation Research Center (SCOREC). > Rensselaer Polytechnic Institute (RPI), Troy, NY. > Email: delalf(a)scorec.rpi.edu, Phone: (518)-276-8045 >

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