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

Re: [petsc-dev] Are pipelines down?
by Satish Balay 12 Mar '21

12 Mar '21

And I see you started one pipeline: https://gitlab.com/danfinn/petsc/-/jobs/1091965415 its started on 'danfinn/petsc' repo - that doesn't have petsc CI permissions. You should 'run pipeline' from https://gitlab.com/petsc/petsc/-/merge_requests/3707//pipelines And the pipeline started by Pierre shows (formatting) errors that need fixing. https://gitlab.com/petsc/petsc/-/jobs/1093419052 Satish On Fri, 12 Mar 2021, Satish Balay via petsc-dev wrote: > Only folk in developer group have permissions to use the CI resources > [to avoid drive by hacks and consumption of resources etc] > > And as a developer you have to create a 'new pipeline' - not use the > auto-started pipeline [this auto-stated pipeline from a fork is from a > user account that does not have access to CI resources - so these > pipelines will stay stuck] > > I think its best for one of the developers to start the pipeline after > verifying the code is ok to run. If any of the reviewers approve - > then I can do this. > > Satish > > On Fri, 12 Mar 2021, Matthew Knepley wrote: > > > On Fri, Mar 12, 2021 at 9:26 AM Pierre Jolivet <pierre(a)joliv.et> wrote: > > > > > You are linking to the forks, i.e., not …/petsc/petsc/…, you’ll never see > > > anything going on there, I think. > > > I’ve started the pipelines by clicking “Run Pipeline” here > > > https://gitlab.com/petsc/petsc/-/merge_requests/3616/pipelines and there > > > https://gitlab.com/petsc/petsc/-/merge_requests/3707/pipelines > > > > > > > Thanks Pierre. There are things I obviously do not understand about Gitlab > > :) > > > > Matt > > > > > > > Thanks, > > > Pierre > > > > > > On 12 Mar 2021, at 3:02 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > > > > > On Fri, Mar 12, 2021 at 7:29 AM Matthew Knepley <knepley(a)gmail.com> wrote: > > > > > >> On Thu, Mar 11, 2021 at 11:24 PM Satish Balay <balay(a)mcs.anl.gov> wrote: > > >> > > >>> For forks - a member of the developer group needs to start a new > > >>> pipeline. (after basic checks on the changes) > > >>> > > >> > > >> The original pipeline just sat pending in the source check, so I > > >> cancelled it. > > >> > > >> I created a new pipeline, but it is just sitting pending in the source > > >> check > > >> > > >> https://gitlab.com/danfinn/petsc/-/pipelines/269297070 > > >> > > >> Why will this not run? > > >> > > > > > > Same problem for Connor's branch: > > > https://gitlab.com/connorjward/petsc/-/pipelines/269584870 > > > > > > Matt > > > > > > > > >> Thanks, > > >> > > >> Matt > > >> > > >> > > >>> Satish > > >>> > > >>> On Thu, 11 Mar 2021, Jed Brown wrote: > > >>> > > >>> > Says the pipeline was canceled. The branch comes from a fork so it > > >>> should need approval to run. > > >>> > > > >>> > https://gitlab.com/petsc/petsc/-/merge_requests/3707 > > >>> > > > >>> > Matthew Knepley <knepley(a)gmail.com> writes: > > >>> > > > >>> > > https://gitlab.com/danfinn/petsc/-/pipelines/269297070 > > >>> > > > > >>> > > Thanks, > > >>> > > > > >>> > > Matt > > >>> > > > > >>> > > -- > > >>> > > What most experimenters take for granted before they begin their > > >>> > > experiments is infinitely more interesting than any results to which > > >>> their > > >>> > > experiments lead. > > >>> > > -- Norbert Wiener > > >>> > > > > >>> > > https://www.cse.buffalo.edu/~knepley/ < > > >>> http://www.cse.buffalo.edu/~knepley/> > > >>> > > > >>> > > >>> > > >> > > >> -- > > >> What most experimenters take for granted before they begin their > > >> experiments is infinitely more interesting than any results to which their > > >> experiments lead. > > >> -- Norbert Wiener > > >> > > >> https://www.cse.buffalo.edu/~knepley/ > > >> <http://www.cse.buffalo.edu/~knepley/> > > >> > > > > > > > > > -- > > > What most experimenters take for granted before they begin their > > > experiments is infinitely more interesting than any results to which their > > > experiments lead. > > > -- Norbert Wiener > > > > > > https://www.cse.buffalo.edu/~knepley/ > > > <http://www.cse.buffalo.edu/~knepley/> > > > > > > > > > > > > > >

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Re: [petsc-dev] Are pipelines down?
by Satish Balay 12 Mar '21

12 Mar '21

Only folk in developer group have permissions to use the CI resources [to avoid drive by hacks and consumption of resources etc] And as a developer you have to create a 'new pipeline' - not use the auto-started pipeline [this auto-stated pipeline from a fork is from a user account that does not have access to CI resources - so these pipelines will stay stuck] I think its best for one of the developers to start the pipeline after verifying the code is ok to run. If any of the reviewers approve - then I can do this. Satish On Fri, 12 Mar 2021, Matthew Knepley wrote: > On Fri, Mar 12, 2021 at 9:26 AM Pierre Jolivet <pierre(a)joliv.et> wrote: > > > You are linking to the forks, i.e., not …/petsc/petsc/…, you’ll never see > > anything going on there, I think. > > I’ve started the pipelines by clicking “Run Pipeline” here > > https://gitlab.com/petsc/petsc/-/merge_requests/3616/pipelines and there > > https://gitlab.com/petsc/petsc/-/merge_requests/3707/pipelines > > > > Thanks Pierre. There are things I obviously do not understand about Gitlab > :) > > Matt > > > > Thanks, > > Pierre > > > > On 12 Mar 2021, at 3:02 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > > > On Fri, Mar 12, 2021 at 7:29 AM Matthew Knepley <knepley(a)gmail.com> wrote: > > > >> On Thu, Mar 11, 2021 at 11:24 PM Satish Balay <balay(a)mcs.anl.gov> wrote: > >> > >>> For forks - a member of the developer group needs to start a new > >>> pipeline. (after basic checks on the changes) > >>> > >> > >> The original pipeline just sat pending in the source check, so I > >> cancelled it. > >> > >> I created a new pipeline, but it is just sitting pending in the source > >> check > >> > >> https://gitlab.com/danfinn/petsc/-/pipelines/269297070 > >> > >> Why will this not run? > >> > > > > Same problem for Connor's branch: > > https://gitlab.com/connorjward/petsc/-/pipelines/269584870 > > > > Matt > > > > > >> Thanks, > >> > >> Matt > >> > >> > >>> Satish > >>> > >>> On Thu, 11 Mar 2021, Jed Brown wrote: > >>> > >>> > Says the pipeline was canceled. The branch comes from a fork so it > >>> should need approval to run. > >>> > > >>> > https://gitlab.com/petsc/petsc/-/merge_requests/3707 > >>> > > >>> > Matthew Knepley <knepley(a)gmail.com> writes: > >>> > > >>> > > https://gitlab.com/danfinn/petsc/-/pipelines/269297070 > >>> > > > >>> > > Thanks, > >>> > > > >>> > > Matt > >>> > > > >>> > > -- > >>> > > What most experimenters take for granted before they begin their > >>> > > experiments is infinitely more interesting than any results to which > >>> their > >>> > > experiments lead. > >>> > > -- Norbert Wiener > >>> > > > >>> > > https://www.cse.buffalo.edu/~knepley/ < > >>> http://www.cse.buffalo.edu/~knepley/> > >>> > > >>> > >>> > >> > >> -- > >> What most experimenters take for granted before they begin their > >> experiments is infinitely more interesting than any results to which their > >> experiments lead. > >> -- Norbert Wiener > >> > >> https://www.cse.buffalo.edu/~knepley/ > >> <http://www.cse.buffalo.edu/~knepley/> > >> > > > > > > -- > > What most experimenters take for granted before they begin their > > experiments is infinitely more interesting than any results to which their > > experiments lead. > > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > <http://www.cse.buffalo.edu/~knepley/> > > > > > > > >

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Re: [petsc-dev] Are pipelines down?
by Matthew Knepley 12 Mar '21

12 Mar '21

On Fri, Mar 12, 2021 at 9:26 AM Pierre Jolivet <pierre(a)joliv.et> wrote: > You are linking to the forks, i.e., not …/petsc/petsc/…, you’ll never see > anything going on there, I think. > I’ve started the pipelines by clicking “Run Pipeline” here > https://gitlab.com/petsc/petsc/-/merge_requests/3616/pipelines and there > https://gitlab.com/petsc/petsc/-/merge_requests/3707/pipelines > Thanks Pierre. There are things I obviously do not understand about Gitlab :) Matt > Thanks, > Pierre > > On 12 Mar 2021, at 3:02 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > On Fri, Mar 12, 2021 at 7:29 AM Matthew Knepley <knepley(a)gmail.com> wrote: > >> On Thu, Mar 11, 2021 at 11:24 PM Satish Balay <balay(a)mcs.anl.gov> wrote: >> >>> For forks - a member of the developer group needs to start a new >>> pipeline. (after basic checks on the changes) >>> >> >> The original pipeline just sat pending in the source check, so I >> cancelled it. >> >> I created a new pipeline, but it is just sitting pending in the source >> check >> >> https://gitlab.com/danfinn/petsc/-/pipelines/269297070 >> >> Why will this not run? >> > > Same problem for Connor's branch: > https://gitlab.com/connorjward/petsc/-/pipelines/269584870 > > Matt > > >> Thanks, >> >> Matt >> >> >>> Satish >>> >>> On Thu, 11 Mar 2021, Jed Brown wrote: >>> >>> > Says the pipeline was canceled. The branch comes from a fork so it >>> should need approval to run. >>> > >>> > https://gitlab.com/petsc/petsc/-/merge_requests/3707 >>> > >>> > Matthew Knepley <knepley(a)gmail.com> writes: >>> > >>> > > https://gitlab.com/danfinn/petsc/-/pipelines/269297070 >>> > > >>> > > Thanks, >>> > > >>> > > Matt >>> > > >>> > > -- >>> > > What most experimenters take for granted before they begin their >>> > > experiments is infinitely more interesting than any results to which >>> their >>> > > experiments lead. >>> > > -- Norbert Wiener >>> > > >>> > > https://www.cse.buffalo.edu/~knepley/ < >>> http://www.cse.buffalo.edu/~knepley/> >>> > >>> >>> >> >> -- >> What most experimenters take for granted before they begin their >> experiments is infinitely more interesting than any results to which their >> experiments lead. >> -- Norbert Wiener >> >> https://www.cse.buffalo.edu/~knepley/ >> <http://www.cse.buffalo.edu/~knepley/> >> > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > <http://www.cse.buffalo.edu/~knepley/> > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] Are pipelines down?
by Pierre Jolivet 12 Mar '21

12 Mar '21

You are linking to the forks, i.e., not …/petsc/petsc/…, you’ll never see anything going on there, I think. I’ve started the pipelines by clicking “Run Pipeline” here https://gitlab.com/petsc/petsc/-/merge_requests/3616/pipelines <https://gitlab.com/petsc/petsc/-/merge_requests/3616/pipelines> and there https://gitlab.com/petsc/petsc/-/merge_requests/3707/pipelines <https://gitlab.com/petsc/petsc/-/merge_requests/3707/pipelines> Thanks, Pierre > On 12 Mar 2021, at 3:02 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > On Fri, Mar 12, 2021 at 7:29 AM Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: > On Thu, Mar 11, 2021 at 11:24 PM Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]>> wrote: > For forks - a member of the developer group needs to start a new pipeline. (after basic checks on the changes) > > The original pipeline just sat pending in the source check, so I cancelled it. > > I created a new pipeline, but it is just sitting pending in the source check > > https://gitlab.com/danfinn/petsc/-/pipelines/269297070 <https://gitlab.com/danfinn/petsc/-/pipelines/269297070> > > Why will this not run? > > Same problem for Connor's branch: https://gitlab.com/connorjward/petsc/-/pipelines/269584870 <https://gitlab.com/connorjward/petsc/-/pipelines/269584870> > > Matt > > Thanks, > > Matt > > Satish > > On Thu, 11 Mar 2021, Jed Brown wrote: > > > Says the pipeline was canceled. The branch comes from a fork so it should need approval to run. > > > > https://gitlab.com/petsc/petsc/-/merge_requests/3707 <https://gitlab.com/petsc/petsc/-/merge_requests/3707> > > > > Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> writes: > > > > > https://gitlab.com/danfinn/petsc/-/pipelines/269297070 <https://gitlab.com/danfinn/petsc/-/pipelines/269297070> > > > > > > Thanks, > > > > > > Matt > > > > > > -- > > > What most experimenters take for granted before they begin their > > > experiments is infinitely more interesting than any results to which their > > > experiments lead. > > > -- Norbert Wiener > > > > > > https://www.cse.buffalo.edu/~knepley/ <https://www.cse.buffalo.edu/~knepley/> <http://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>> > > > > > > -- > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/> > > > -- > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] Are pipelines down?
by Matthew Knepley 12 Mar '21

12 Mar '21

On Fri, Mar 12, 2021 at 7:29 AM Matthew Knepley <knepley(a)gmail.com> wrote: > On Thu, Mar 11, 2021 at 11:24 PM Satish Balay <balay(a)mcs.anl.gov> wrote: > >> For forks - a member of the developer group needs to start a new >> pipeline. (after basic checks on the changes) >> > > The original pipeline just sat pending in the source check, so I cancelled > it. > > I created a new pipeline, but it is just sitting pending in the source > check > > https://gitlab.com/danfinn/petsc/-/pipelines/269297070 > > Why will this not run? > Same problem for Connor's branch: https://gitlab.com/connorjward/petsc/-/pipelines/269584870 Matt > Thanks, > > Matt > > >> Satish >> >> On Thu, 11 Mar 2021, Jed Brown wrote: >> >> > Says the pipeline was canceled. The branch comes from a fork so it >> should need approval to run. >> > >> > https://gitlab.com/petsc/petsc/-/merge_requests/3707 >> > >> > Matthew Knepley <knepley(a)gmail.com> writes: >> > >> > > https://gitlab.com/danfinn/petsc/-/pipelines/269297070 >> > > >> > > Thanks, >> > > >> > > Matt >> > > >> > > -- >> > > What most experimenters take for granted before they begin their >> > > experiments is infinitely more interesting than any results to which >> their >> > > experiments lead. >> > > -- Norbert Wiener >> > > >> > > https://www.cse.buffalo.edu/~knepley/ < >> http://www.cse.buffalo.edu/~knepley/> >> > >> >> > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > <http://www.cse.buffalo.edu/~knepley/> > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] Are pipelines down?
by Matthew Knepley 12 Mar '21

12 Mar '21

On Thu, Mar 11, 2021 at 11:24 PM Satish Balay <balay(a)mcs.anl.gov> wrote: > For forks - a member of the developer group needs to start a new pipeline. > (after basic checks on the changes) > The original pipeline just sat pending in the source check, so I cancelled it. I created a new pipeline, but it is just sitting pending in the source check https://gitlab.com/danfinn/petsc/-/pipelines/269297070 Why will this not run? Thanks, Matt > Satish > > On Thu, 11 Mar 2021, Jed Brown wrote: > > > Says the pipeline was canceled. The branch comes from a fork so it > should need approval to run. > > > > https://gitlab.com/petsc/petsc/-/merge_requests/3707 > > > > Matthew Knepley <knepley(a)gmail.com> writes: > > > > > https://gitlab.com/danfinn/petsc/-/pipelines/269297070 > > > > > > Thanks, > > > > > > Matt > > > > > > -- > > > What most experimenters take for granted before they begin their > > > experiments is infinitely more interesting than any results to which > their > > > experiments lead. > > > -- Norbert Wiener > > > > > > https://www.cse.buffalo.edu/~knepley/ < > http://www.cse.buffalo.edu/~knepley/> > > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] Fortran macOS Linkage Warning
by Matthew Knepley 12 Mar '21

12 Mar '21

On Fri, Mar 12, 2021 at 3:44 AM Pierre Jolivet <pierre(a)joliv.et> wrote: > Sorry to dig up this old thread, but this is triggering false positives > while make checking for people who don’t want to toy around with > MACOSX_DEPLOYMENT_TARGET. > Could/should we filter this somehow, or have BuildSystem tinker with the > environment variable itself? > I worry about suppressing this warning because the variable has real consequences for linking (especially if CMake is somehow involved), and it might make it harder to debug. I would rather have a large warning suggesting people unset this. Thanks, Matt > Thanks, > Pierre > > $ make check > Running check examples to verify correct installation > Using PETSC_DIR=/Users/jolivet/repo/petsc and > PETSC_ARCH=arch-darwin-c-debug-real > *******************Error detected during compile or > link!******************* > See http://www.mcs.anl.gov/petsc/documentation/faq.html > /Users/jolivet/repo/petsc/src/snes/tutorials ex19 > > ********************************************************************************* > mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress > -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs > -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -g -Wall -g > -I/Users/jolivet/repo/petsc/include > -I/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/include > -I/opt/intel/mkl/include ex19.c > -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib > -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib > -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib > -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib > -Wl,-rpath,/opt/intel/mkl/lib -L/opt/intel/mkl/lib > -Wl,-rpath,/opt/intel/lib -L/opt/intel/lib > -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib > -L/usr/local/Cellar/mpich/3.4.1_1/lib > -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 > -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 > -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 > -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lpetsc -lHYPRE -lcmumps > -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmkl_scalapack_lp64 > -lmkl_blacs_mpich_lp64 -lEl -lElSuiteSparse -lpmrrr -lp4est -lsc -liomp5 > -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lparmmg -lmmg -lmmg3d > -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch > -lscotcherr -lparmetis -lmetis -ltriangle -ltet -lz -lX11 -lc++ -ldl > -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lc++ -ldl -o ex19 > ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) > was built for newer macOS version (11.1) than being linked (11.0) > ld: warning: dylib > (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for > newer macOS version (11.2) than being linked (11.0) > ld: warning: dylib > (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for > newer macOS version (11.2) than being linked (11.0) > ld: warning: dylib > (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built > for newer macOS version (11.2) than being linked (11.0) > ld: warning: object file > (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libcmumps.a(cana_aux.o)) > was built for newer macOS version (11.2) than being linked (11.0) > ld: warning: object file > (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libdmumps.a(dana_aux.o)) > was built for newer macOS version (11.2) than being linked (11.0) > ld: warning: object file > (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libsmumps.a(sana_aux.o)) > was built for newer macOS version (11.2) than being linked (11.0) > ld: warning: object file > (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libzmumps.a(zana_aux.o)) > was built for newer macOS version (11.2) than being linked (11.0) > ld: warning: object file > (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libmumps_common.a(front_data_mgt_m.o)) > was built for newer macOS version (11.2) than being linked (11.0) > C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process > > > On 15 Feb 2021, at 6:08 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com> > wrote: > > 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] <jacob.fai(a)gmail.com>>> 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] <balay(a)mcs.anl.gov>>> 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 > > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] Fortran macOS Linkage Warning
by Pierre Jolivet 12 Mar '21

12 Mar '21

Sorry to dig up this old thread, but this is triggering false positives while make checking for people who don’t want to toy around with MACOSX_DEPLOYMENT_TARGET. Could/should we filter this somehow, or have BuildSystem tinker with the environment variable itself? Thanks, Pierre $ make check Running check examples to verify correct installation Using PETSC_DIR=/Users/jolivet/repo/petsc and PETSC_ARCH=arch-darwin-c-debug-real *******************Error detected during compile or link!******************* See http://www.mcs.anl.gov/petsc/documentation/faq.html /Users/jolivet/repo/petsc/src/snes/tutorials ex19 ********************************************************************************* mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -g -Wall -g -I/Users/jolivet/repo/petsc/include -I/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/include -I/opt/intel/mkl/include ex19.c -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -Wl,-rpath,/opt/intel/mkl/lib -L/opt/intel/mkl/lib -Wl,-rpath,/opt/intel/lib -L/opt/intel/lib -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib -L/usr/local/Cellar/mpich/3.4.1_1/lib -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lpetsc -lHYPRE -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmkl_scalapack_lp64 -lmkl_blacs_mpich_lp64 -lEl -lElSuiteSparse -lpmrrr -lp4est -lsc -liomp5 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lparmmg -lmmg -lmmg3d -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -ltriangle -ltet -lz -lX11 -lc++ -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lc++ -ldl -o ex19 ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) was built for newer macOS version (11.1) than being linked (11.0) ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for newer macOS version (11.2) than being linked (11.0) ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for newer macOS version (11.2) than being linked (11.0) ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built for newer macOS version (11.2) than being linked (11.0) ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libcmumps.a(cana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libdmumps.a(dana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libsmumps.a(sana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libzmumps.a(zana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libmumps_common.a(front_data_mgt_m.o)) was built for newer macOS version (11.2) than being linked (11.0) C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process > On 15 Feb 2021, at 6:08 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com> wrote: > > 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 <mailto:[email protected]>> 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 <mailto:[email protected]>> 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] Are pipelines down?
by Satish Balay 11 Mar '21

11 Mar '21

For forks - a member of the developer group needs to start a new pipeline. (after basic checks on the changes) Satish On Thu, 11 Mar 2021, Jed Brown wrote: > Says the pipeline was canceled. The branch comes from a fork so it should need approval to run. > > https://gitlab.com/petsc/petsc/-/merge_requests/3707 > > Matthew Knepley <knepley(a)gmail.com> writes: > > > https://gitlab.com/danfinn/petsc/-/pipelines/269297070 > > > > Thanks, > > > > Matt > > > > -- > > What most experimenters take for granted before they begin their > > experiments is infinitely more interesting than any results to which their > > experiments lead. > > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/> >

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Re: [petsc-dev] Are pipelines down?
by Jed Brown 11 Mar '21

11 Mar '21

Says the pipeline was canceled. The branch comes from a fork so it should need approval to run. https://gitlab.com/petsc/petsc/-/merge_requests/3707 Matthew Knepley <knepley(a)gmail.com> writes: > https://gitlab.com/danfinn/petsc/-/pipelines/269297070 > > Thanks, > > Matt > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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