February 2021 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] TSSetConvergedReason(ts,TS_CONVERGED_USER);
by Stefano Zampini 18 Feb '21

18 Feb '21

Mark monitors are not supposed to change the TS. You can think at monitors being 'const' methods of the TS. Also, TSMonitor is called at the beginning of each step , see here https://gitlab.com/petsc/petsc/-/blob/master/src/ts/interface/ts.c#L4169 Il giorno gio 18 feb 2021 alle ore 15:16 Mark Adams <mfadams(a)lbl.gov> ha scritto: > TSSetConvergedReason(ts,TS_CONVERGED_USER); > > does not seem to stop the iteration in a user monitor function. I have > verified that it works from a post step method. Is this intentional? > > Mark > -- Stefano

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TSSetConvergedReason(ts,TS_CONVERGED_USER);
by Mark Adams 18 Feb '21

18 Feb '21

TSSetConvergedReason(ts,TS_CONVERGED_USER); does not seem to stop the iteration in a user monitor function. I have verified that it works from a post step method. Is this intentional? Mark

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Re: [petsc-dev] Rebuilding pets-library only
by Barry Smith 17 Feb '21

17 Feb '21

Blaise, I think I fixed this a few months ago for petsc4py. It is suppose to have the right dependencies so petsc4py does not get rebuilt if it does not need to be. (For example it depends on the PETSc include files but not on the PETSc source files). If it still insists on rebuilding petsc4py when it should not in master please let us know the details so we can fix this. Barry > On Feb 17, 2021, at 10:17 AM, Blaise A Bourdin <bourdin(a)lsu.edu> wrote: > > Thanks > > Blaise > > >> On Feb 17, 2021, at 10:03 AM, Jed Brown <jed(a)jedbrown.org <mailto:[email protected]>> wrote: >> >> make libs should do that. >> >> Blaise A Bourdin <bourdin(a)lsu.edu <mailto:[email protected]>> writes: >> >>> Hi, >>> >>> Is there a way to rebuild the petsc library only, skipping rebuilding mpi4py and petsc4py if petsc is configured with them? I know I can ctrl-C this step if all I want is to rebuild the lib, but I would not mind a more elegant way.. >>> >>> Regards, >>> Blaise >>> >>> -- >>> A.K. & Shirley Barton Professor of Mathematics >>> Adjunct Professor of Mechanical Engineering >>> Adjunct of the Center for Computation & Technology >>> Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, USA >>> Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web http://www.math.lsu.edu/~bourdin <http://www.math.lsu.edu/~bourdin> > > -- > A.K. & Shirley Barton Professor of Mathematics > Adjunct Professor of Mechanical Engineering > Adjunct of the Center for Computation & Technology > Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, USA > Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web http://www.math.lsu.edu/~bourdin <http://www.math.lsu.edu/~bourdin>

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Re: [petsc-dev] Fortran interface for DMCreateSuperDM
by Satish Balay 17 Feb '21

17 Feb '21

For example check PCBJacobiGetSubKSP in src/ksp/pc/impls/bjacobi/ftn-custom/zbjacobif.c [and the fortran note in man page] PCASMGetLocalSubdomains() looks similar [in src/ksp/pc/impls/asm/ftn-custom/zasmf.c] Satish On Wed, 17 Feb 2021, Blaise A Bourdin wrote: > Hi, > > I am porting src/dm/impls/plex/tests/ex26.c to fortran90 but am having a hard time figuring out how to write the fortran binding for DMCreateSuperDM. > Can anybody help? > > Regards, > Blaise >

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Fortran interface for DMCreateSuperDM
by Blaise A Bourdin 17 Feb '21

17 Feb '21

Hi, I am porting src/dm/impls/plex/tests/ex26.c to fortran90 but am having a hard time figuring out how to write the fortran binding for DMCreateSuperDM. Can anybody help? Regards, Blaise -- A.K. & Shirley Barton Professor of Mathematics Adjunct Professor of Mechanical Engineering Adjunct of the Center for Computation & Technology Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, USA Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web http://www.math.lsu.edu/~bourdin

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Re: [petsc-dev] Rebuilding pets-library only
by Blaise A Bourdin 17 Feb '21

17 Feb '21

Thanks Blaise On Feb 17, 2021, at 10:03 AM, Jed Brown <jed(a)jedbrown.org<mailto:[email protected]>> wrote: make libs should do that. Blaise A Bourdin <bourdin(a)lsu.edu<mailto:[email protected]>> writes: Hi, Is there a way to rebuild the petsc library only, skipping rebuilding mpi4py and petsc4py if petsc is configured with them? I know I can ctrl-C this step if all I want is to rebuild the lib, but I would not mind a more elegant way.. Regards, Blaise -- A.K. & Shirley Barton Professor of Mathematics Adjunct Professor of Mechanical Engineering Adjunct of the Center for Computation & Technology Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, USA Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web http://www.math.lsu.edu/~bourdin -- A.K. & Shirley Barton Professor of Mathematics Adjunct Professor of Mechanical Engineering Adjunct of the Center for Computation & Technology Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, USA Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web http://www.math.lsu.edu/~bourdin

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Re: [petsc-dev] Rebuilding pets-library only
by Jed Brown 17 Feb '21

17 Feb '21

make libs should do that. Blaise A Bourdin <bourdin(a)lsu.edu> writes: > Hi, > > Is there a way to rebuild the petsc library only, skipping rebuilding mpi4py and petsc4py if petsc is configured with them? I know I can ctrl-C this step if all I want is to rebuild the lib, but I would not mind a more elegant way.. > > Regards, > Blaise > > -- > A.K. & Shirley Barton Professor of Mathematics > Adjunct Professor of Mechanical Engineering > Adjunct of the Center for Computation & Technology > Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, USA > Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web http://www.math.lsu.edu/~bourdin

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Rebuilding pets-library only
by Blaise A Bourdin 17 Feb '21

17 Feb '21

Hi, Is there a way to rebuild the petsc library only, skipping rebuilding mpi4py and petsc4py if petsc is configured with them? I know I can ctrl-C this step if all I want is to rebuild the lib, but I would not mind a more elegant way.. Regards, Blaise -- A.K. & Shirley Barton Professor of Mathematics Adjunct Professor of Mechanical Engineering Adjunct of the Center for Computation & Technology Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, USA Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web http://www.math.lsu.edu/~bourdin

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Re: [petsc-dev] Fortran macOS Linkage Warning
by Jacob Faibussowitsch 15 Feb '21

15 Feb '21

Yes, this also seems to work on my end. Best regards, Jacob Faibussowitsch (Jacob Fai - booss - oh - vitch) Cell: (312) 694-3391 > On Feb 15, 2021, at 12:05, Satish Balay <balay(a)mcs.anl.gov> wrote: > > Does setting MACOSX_DEPLOYMENT_TARGET also work? > > Satish > > On Mon, 15 Feb 2021, Jacob Faibussowitsch wrote: > >> I think this problem ultimately stems from the fact that gcc/g++ and gfortran are not from the same people on macOS. It seems like clang is configured to build for 11.0 target, whilst gcc defaults to newest available target. And indeed if I change my compile command there is no warning: >> >> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc-10 -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined dynamic_lookup && rm -rf ./build >> >> Note I now call gcc-10 as the linker which is the __actual__ gcc (not clang in a trench coat). >> >> Best regards, >> >> Jacob Faibussowitsch >> (Jacob Fai - booss - oh - vitch) >> Cell: (312) 694-3391 >> >>> On Feb 15, 2021, at 11:46, Jacob Faibussowitsch <jacob.fai(a)gmail.com> wrote: >>> >>> Ok so if I pass -mmacosx-version-min=11.2 to the linker the warning disappears... >>> >>> Best regards, >>> >>> Jacob Faibussowitsch >>> (Jacob Fai - booss - oh - vitch) >>> Cell: (312) 694-3391 >>> >>>> On Feb 15, 2021, at 11:41, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: >>>> >>>> I can reproduce the warning compiling just that simple code you listed. This is the compile command: >>>> >>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined dynamic_lookup && rm -rf ./build >>>> >>>> And error: >>>> ld: warning: object file (./build/conftest.o) was built for newer macOS version (11.2) than being linked (11.0) >>>> >>>> Note I recently uninstalled and reinstalled command line tools too, which does not seem to have fixed it. >>>> >>>> Best regards, >>>> >>>> Jacob Faibussowitsch >>>> (Jacob Fai - booss - oh - vitch) >>>> Cell: (312) 694-3391 >>>> >>>>> On Feb 15, 2021, at 11:30, Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: >>>>> >>>>> Here is the compile command and the warning: >>>>> >>>>>>>>>>> >>>>> ===== Checking linker >>>>> Executing: gfortran -c -o /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o -I/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.F90 >>>>> Successful compile: >>>>> Source: >>>>> function foo(a) >>>>> real:: a,x,bar >>>>> common /xx/ x >>>>> x=a >>>>> foo = bar(x) >>>>> end >>>>> Executing: gcc -o /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/libconftest.dylib -dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o >>>>> Possible ERROR while running linker: >>>>> stderr: >>>>> ld: warning: object file (/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>> Accepted FC PIC code without compiler flag >>>>> ============================================================================================= >>>>> <<<<<< >>>>> >>>>> Its likely due to the way brew built gfortran. You can try compiling a simple test code and see if you can reproduce this warning. >>>>> >>>>> There is a related issue at: >>>>> >>>>> https://github.com/spack/spack/issues/21644 <https://github.com/spack/spack/issues/21644> <https://github.com/spack/spack/issues/21644 <https://github.com/spack/spack/issues/21644>> >>>>> >>>>> Satish >>>>> >>>>> >>>>> On Sat, 13 Feb 2021, Jacob Faibussowitsch wrote: >>>>> >>>>>> Hello All, >>>>>> >>>>>> I’ve been getting these warnings for weeks, at first I figured it was due to gfortran brew package not being updated for Big Sur, but since it has persisted through a few gfortran brew updates I’m thinking it may be petsc related. This is on clean build on master. >>>>>> >>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/classes/bag/f2003-src/fsrc/bagenum.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/f90-src/fsrc/f90_fwrap.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/objects/f2003-src/fsrc/optionenum.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/fsrc/somefort.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/f90-mod/petscsysmod.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Jacob Faibussowitsch >>>>>> (Jacob Fai - booss - oh - vitch) >>>>>> Cell: (312) 694-3391

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Re: [petsc-dev] Fortran macOS Linkage Warning
by Satish Balay 15 Feb '21

15 Feb '21

Does setting MACOSX_DEPLOYMENT_TARGET also work? Satish On Mon, 15 Feb 2021, Jacob Faibussowitsch wrote: > I think this problem ultimately stems from the fact that gcc/g++ and gfortran are not from the same people on macOS. It seems like clang is configured to build for 11.0 target, whilst gcc defaults to newest available target. And indeed if I change my compile command there is no warning: > > mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc-10 -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined dynamic_lookup && rm -rf ./build > > Note I now call gcc-10 as the linker which is the __actual__ gcc (not clang in a trench coat). > > Best regards, > > Jacob Faibussowitsch > (Jacob Fai - booss - oh - vitch) > Cell: (312) 694-3391 > > > On Feb 15, 2021, at 11:46, Jacob Faibussowitsch <jacob.fai(a)gmail.com> wrote: > > > > Ok so if I pass -mmacosx-version-min=11.2 to the linker the warning disappears... > > > > Best regards, > > > > Jacob Faibussowitsch > > (Jacob Fai - booss - oh - vitch) > > Cell: (312) 694-3391 > > > >> On Feb 15, 2021, at 11:41, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: > >> > >> I can reproduce the warning compiling just that simple code you listed. This is the compile command: > >> > >> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined dynamic_lookup && rm -rf ./build > >> > >> And error: > >> ld: warning: object file (./build/conftest.o) was built for newer macOS version (11.2) than being linked (11.0) > >> > >> Note I recently uninstalled and reinstalled command line tools too, which does not seem to have fixed it. > >> > >> Best regards, > >> > >> Jacob Faibussowitsch > >> (Jacob Fai - booss - oh - vitch) > >> Cell: (312) 694-3391 > >> > >>> On Feb 15, 2021, at 11:30, Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]>> wrote: > >>> > >>> Here is the compile command and the warning: > >>> > >>>>>>>>> > >>> ===== Checking linker > >>> Executing: gfortran -c -o /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o -I/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.F90 > >>> Successful compile: > >>> Source: > >>> function foo(a) > >>> real:: a,x,bar > >>> common /xx/ x > >>> x=a > >>> foo = bar(x) > >>> end > >>> Executing: gcc -o /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/libconftest.dylib -dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o > >>> Possible ERROR while running linker: > >>> stderr: > >>> ld: warning: object file (/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o) was built for newer macOS version (11.2) than being linked (11.0) > >>> Accepted FC PIC code without compiler flag > >>> ============================================================================================= > >>> <<<<<< > >>> > >>> Its likely due to the way brew built gfortran. You can try compiling a simple test code and see if you can reproduce this warning. > >>> > >>> There is a related issue at: > >>> > >>> https://github.com/spack/spack/issues/21644 <https://github.com/spack/spack/issues/21644> > >>> > >>> Satish > >>> > >>> > >>> On Sat, 13 Feb 2021, Jacob Faibussowitsch wrote: > >>> > >>>> Hello All, > >>>> > >>>> I’ve been getting these warnings for weeks, at first I figured it was due to gfortran brew package not being updated for Big Sur, but since it has persisted through a few gfortran brew updates I’m thinking it may be petsc related. This is on clean build on master. > >>>> > >>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/classes/bag/f2003-src/fsrc/bagenum.o) was built for newer macOS version (11.2) than being linked (11.0) > >>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/f90-src/fsrc/f90_fwrap.o) was built for newer macOS version (11.2) than being linked (11.0) > >>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/objects/f2003-src/fsrc/optionenum.o) was built for newer macOS version (11.2) than being linked (11.0) > >>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/fsrc/somefort.o) was built for newer macOS version (11.2) than being linked (11.0) > >>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/f90-mod/petscsysmod.o) was built for newer macOS version (11.2) than being linked (11.0) > >>>> > >>>> Best regards, > >>>> > >>>> Jacob Faibussowitsch > >>>> (Jacob Fai - booss - oh - vitch) > >>>> Cell: (312) 694-3391 > >>>> > >> > > > >

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