Fande, Before send the files I requested in my last email could you try with the branch barry/2021-03-10/handle-pie-flag-conda/release and send its configure.log if it fails.
Thanks Barry > On Mar 10, 2021, at 5:59 PM, Fande Kong <fdkong...@gmail.com> wrote: > > Do not know what the fix should look like, but this works for me > > > @staticmethod > @@ -1194,7 +1194,6 @@ class Configure(config.base.Configure): > output.find('unrecognized command line option') >= 0 or > output.find('unrecognized option') >= 0 or output.find('unrecognised option') > >= 0 or > output.find('not recognized') >= 0 or output.find('not recognised') >= 0 > or > output.find('unknown option') >= 0 or output.find('unknown flag') >= 0 > or output.find('Unknown switch') >= 0 or > - output.find('ignoring option') >= 0 or output.find('ignored') >= 0 or > output.find('argument unused') >= 0 or output.find('not supported') >= 0 > or > # When checking for the existence of 'attribute' > output.find('is unsupported and will be skipped') >= 0 or > > > > Thanks, > > Fande > > On Wed, Mar 10, 2021 at 4:21 PM Fande Kong <fdkong...@gmail.com > <mailto:fdkong...@gmail.com>> wrote: > > > On Wed, Mar 10, 2021 at 1:36 PM Satish Balay <ba...@mcs.anl.gov > <mailto:ba...@mcs.anl.gov>> wrote: > Can you use a different MPI for this conda install? > > We control how to build MPI. If I take "-pie" options out of LDFLAGS, conda > can not compile mpich. > > > > > Alternative: > > ./configure CC=x86_64-apple-darwin13.4.0-clang COPTFLAGS="-march=core2 > -mtune=haswell" CPPFLAGS=-I/Users/kongf/miniconda3/envs/testpetsc/include > LDFLAGS="-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs > -Wl,-commons,use_dylibs" > LIBS="-Wl,-rpath,/Users/kongf/miniconda3/envs/testpetsc/lib -lmpi -lpmpi" > > MPI can not generate an executable because we took out "-pie". > > Thanks, > > Fande > > > etc.. [don't know if you really need LDFLAGS options] > > Satish > > On Wed, 10 Mar 2021, Fande Kong wrote: > > > I guess it was encoded in mpicc > > > > petsc % mpicc -show > > x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -Wl,-pie > > -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs > > -Wl,-rpath,/Users/kongf/miniconda3/envs/testpetsc/lib > > -L/Users/kongf/miniconda3/envs/testpetsc/lib -Wl,-commons,use_dylibs > > -I/Users/kongf/miniconda3/envs/testpetsc/include > > -L/Users/kongf/miniconda3/envs/testpetsc/lib -lmpi -lpmpi > > > > > > Thanks, > > > > Fande > > > > On Wed, Mar 10, 2021 at 12:51 PM Satish Balay <ba...@mcs.anl.gov > > <mailto:ba...@mcs.anl.gov>> wrote: > > > > > > LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath > > > /Users/kongf/miniconda3/envs/testpetsc/lib > > > -L/Users/kongf/miniconda3/envs/testpetsc/lib > > > > > > Does conda compiler pick up '-pie' from this env variable? If so - perhaps > > > its easier to just modify it? > > > > > > Or is it encoded in mpicc wrapper? [mpicc -show] > > > > > > Satish > > > > > > On Wed, 10 Mar 2021, Fande Kong wrote: > > > > > > > Thanks Barry, > > > > > > > > Got the same result, but "-pie" was not filtered out somehow. > > > > > > > > I did changes like this: > > > > > > > > kongf@x86_64-apple-darwin13 petsc % git diff > > > > diff --git a/config/BuildSystem/config/framework.py > > > > b/config/BuildSystem/config/framework.py > > > > index beefe82956..c31fbeb95e 100644 > > > > --- a/config/BuildSystem/config/framework.py > > > > +++ b/config/BuildSystem/config/framework.py > > > > @@ -504,6 +504,8 @@ class Framework(config.base.Configure, > > > > script.LanguageProcessor): > > > > lines = [s for s in lines if s.find('Load a valid targeting module > > > > or > > > > set CRAY_CPU_TARGET') < 0] > > > > # pgi dumps filename on stderr - but returns 0 errorcode' > > > > lines = [s for s in lines if lines != 'conftest.c:'] > > > > + # in case -pie is always being passed to linker > > > > + lines = [s for s in lines if s.find('-pie being ignored. It is only > > > > used when linking a main executable') < 0] > > > > if lines: output = reduce(lambda s, t: s+t, lines, '\n') > > > > else: output = '' > > > > log.write("Linker stderr after filtering:\n"+output+":\n") > > > > > > > > The log was attached again. > > > > > > > > Thanks, > > > > > > > > Fande > > > > > > > > > > > > On Wed, Mar 10, 2021 at 12:05 PM Barry Smith <bsm...@petsc.dev > > > > <mailto:bsm...@petsc.dev>> wrote: > > > > > > > > > Fande, > > > > > > > > > > Please add in config/BuildSystem/config/framework.py line 528 two > > > new > > > > > lines > > > > > > > > > > # pgi dumps filename on stderr - but returns 0 errorcode' > > > > > lines = [s for s in lines if lines != 'conftest.c:'] > > > > > # in case -pie is always being passed to linker > > > > > lines = [s for s in lines if s.find('-pie being ignored. It is > > > only > > > > > used when linking a main executable') < 0] > > > > > > > > > > Barry > > > > > > > > > > You have (another of Conda's "take over the world my way" approach) > > > > > > > > > > LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs > > > -rpath > > > > > /Users/kongf/miniconda3/envs/testpetsc/lib > > > > > -L/Users/kongf/miniconda3/envs/testpetsc/lib > > > > > > > > > > Executing: mpicc -o > > > > > > > > /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/conftest > > > > > -dynamiclib -single_module > > > > > > > > /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/conftest.o > > > > > Possible ERROR while running linker: > > > > > stderr: > > > > > ld: warning: -pie being ignored. It is only used when linking a main > > > > > executable > > > > > Rejecting C linker flag -dynamiclib -single_module due to > > > > > > > > > > ld: warning: -pie being ignored. It is only used when linking a main > > > > > executable > > > > > > > > > > This is the correct link command for the Mac but it is being rejected > > > due > > > > > to the warning message. > > > > > > > > > > > > > > > On Mar 10, 2021, at 10:11 AM, Fande Kong <fdkong...@gmail.com > > > > > <mailto:fdkong...@gmail.com>> wrote: > > > > > > > > > > Thanks, Barry, > > > > > > > > > > It seems PETSc works fine with manually built compilers. We are pretty > > > > > much sure that the issue is related to conda. Conda might introduce > > > extra > > > > > flags. > > > > > > > > > > We still need to make it work with conda because we deliver our > > > > > package > > > > > via conda for users. > > > > > > > > > > > > > > > I unset all flags from conda, and got slightly different results this > > > > > time. The log was attached. Anyone could explain the motivation that > > > we > > > > > try to build executable without a main function? > > > > > > > > > > Thanks, > > > > > > > > > > Fande > > > > > > > > > > Executing: mpicc -c -o > > > > > > > > /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/conftest.o > > > > > > > > -I/var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers > > > > > -fPIC > > > > > > > > /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/conftest.c > > > > > > > > > > Successful compile: > > > > > Source: > > > > > #include "confdefs.h" > > > > > #include "conffix.h" > > > > > #include <stdio.h> > > > > > int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; > > > > > void foo(void){ > > > > > fprintf_ptr(stdout,"hello"); > > > > > return; > > > > > } > > > > > void bar(void){foo();} > > > > > Running Executable WITHOUT threads to time it out > > > > > Executing: mpicc -o > > > > > > > > /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/libconftest.so > > > > > -dynamic -fPIC > > > > > > > > /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/conftest.o > > > > > > > > > > Possible ERROR while running linker: exit code 1 > > > > > stderr: > > > > > Undefined symbols for architecture x86_64: > > > > > "_main", referenced from: > > > > > implicit entry/start for main executable > > > > > ld: symbol(s) not found for architecture x86_64 > > > > > clang-11: error: linker command failed with exit code 1 (use -v to see > > > > > invocation) > > > > > Rejected C compiler flag -fPIC because it was not compatible > > > > > with shared linker mpicc using flags ['-dynamic'] > > > > > > > > > > > > > > > On Mon, Mar 8, 2021 at 7:28 PM Barry Smith <bsm...@petsc.dev > > > > > <mailto:bsm...@petsc.dev>> wrote: > > > > > > > > > >> > > > > >> Fande, > > > > >> > > > > >> I see you are using CONDA, this can cause issues since it sticks > > > all > > > > >> kinds of things into the environment. PETSc tries to remove some of > > > them > > > > >> but perhaps not enough. If you run printenv you will see all the mess > > > it is > > > > >> dumping in. > > > > >> > > > > >> Can you trying the same build without CONDA environment? > > > > >> > > > > >> Barry > > > > >> > > > > >> > > > > >> On Mar 8, 2021, at 7:31 PM, Matthew Knepley <knep...@gmail.com > > > > >> <mailto:knep...@gmail.com>> > > > wrote: > > > > >> > > > > >> On Mon, Mar 8, 2021 at 8:23 PM Fande Kong <fdkong...@gmail.com > > > > >> <mailto:fdkong...@gmail.com>> > > > wrote: > > > > >> > > > > >>> Thanks Matthew, > > > > >>> > > > > >>> Hmm, we still have the same issue after shutting off all unknown > > > flags. > > > > >>> > > > > >> > > > > >> Oh, I was misinterpreting the error message: > > > > >> > > > > >> ld: can't link with a main executable file > > > > >> > > > '/var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-6v1w4q4u/config.setCompilers/libconftest.dylib' > > > > >> > > > > >> So clang did not _actually_ make a shared library, it made an > > > executable. > > > > >> Did clang-11 change the options it uses to build a shared library? > > > > >> > > > > >> Satish, do we test with clang-11? > > > > >> > > > > >> Thanks, > > > > >> > > > > >> Matt > > > > >> > > > > >> Thanks, > > > > >>> > > > > >>> Fande > > > > >>> > > > > >>> On Mon, Mar 8, 2021 at 6:07 PM Matthew Knepley <knep...@gmail.com > > > > >>> <mailto:knep...@gmail.com>> > > > > >>> wrote: > > > > >>> > > > > >>>> On Mon, Mar 8, 2021 at 7:55 PM Fande Kong <fdkong...@gmail.com > > > > >>>> <mailto:fdkong...@gmail.com>> > > > wrote: > > > > >>>> > > > > >>>>> Hi All, > > > > >>>>> > > > > >>>>> mpicc rejected "-fPIC". Anyone has a clue how to work around this > > > > >>>>> issue? > > > > >>>>> > > > > >>>> > > > > >>>> The failure is at the last step > > > > >>>> > > > > >>>> Executing: mpicc -o > > > > >>>> > > > /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-6v1w4q4u/config.setCompilers/conftest > > > > >>>> -fPIC > > > > >>>> > > > /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-6v1w4q4u/config.setCompilers/conftest.o > > > > >>>> > > > -L/var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-6v1w4q4u/config.setCompilers > > > > >>>> -lconftest > > > > >>>> Possible ERROR while running linker: exit code 1 > > > > >>>> stderr: > > > > >>>> ld: can't link with a main executable file > > > > >>>> > > > '/var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-6v1w4q4u/config.setCompilers/libconftest.dylib' > > > > >>>> for architecture x86_64 > > > > >>>> clang-11: error: linker command failed with exit code 1 (use -v to > > > see > > > > >>>> invocation) > > > > >>>> > > > > >>>> but you have some flags stuck in which may or may not affect this. > > > > >>>> I > > > > >>>> would try shutting them off: > > > > >>>> > > > > >>>> LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs > > > -rpath > > > > >>>> /Users/kongf/miniconda3/envs/moose/lib > > > > >>>> -L/Users/kongf/miniconda3/envs/moose/lib > > > > >>>> > > > > >>>> I cannot tell exactly why clang is failing because it does not > > > report a > > > > >>>> specific error. > > > > >>>> > > > > >>>> Thanks, > > > > >>>> > > > > >>>> Matt > > > > >>>> > > > > >>>> The log was attached. > > > > >>>>> > > > > >>>>> Thanks so much, > > > > >>>>> > > > > >>>>> Fande > > > > >>>>> > > > > >>>> > > > > >>>> > > > > >>>> -- > > > > >>>> 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/ > > > > >> <https://www.cse.buffalo.edu/~knepley/> > > > > >> <http://www.cse.buffalo.edu/~knepley/ > > > > >> <http://www.cse.buffalo.edu/~knepley/>> > > > > >> > > > > >> > > > > >> <configure.log> > > > > > > > > > > > > > > > > > > > > > > > > > > > >