[petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!
Satish Balay
balay at mcs.anl.gov
Wed Mar 10 14:35:59 CST 2021
Can you use a different MPI for this conda install?
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"
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 <balay at 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 at 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 <bsmith at 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.jd at 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 <bsmith at 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 <knepley at gmail.com>
> > wrote:
> > > >>
> > > >> On Mon, Mar 8, 2021 at 8:23 PM Fande Kong <fdkong.jd at 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 <knepley at gmail.com>
> > > >>> wrote:
> > > >>>
> > > >>>> On Mon, Mar 8, 2021 at 7:55 PM Fande Kong <fdkong.jd at 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/
> > > >>>> <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/>
> > > >>
> > > >>
> > > >> <configure.log>
> > > >
> > > >
> > > >
> > >
> >
> >
>
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