[petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!
Fande Kong
fdkong.jd at gmail.com
Wed Mar 10 12:15:22 CST 2021
On Wed, Mar 10, 2021 at 9:34 AM Satish Balay <balay at mcs.anl.gov> wrote:
> On Wed, 10 Mar 2021, Fande Kong 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?
>
> Its attempting to build a shared library - which shouldn't have a main.
>
> However - the primary issue is:
>
> >>>>>
> Executing: mpicc -o
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/conftest
>
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/conftest.o
> -L/var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/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-pkset22y/config.setCompilers/libconftest.dylib'
> for architecture x86_64
> clang-11: error: linker command failed with exit code 1 (use -v to see
> invocation)
> <<<
>
> Here its built a .dylib - and attempting to use it. But the compiler gives
> the above error.
>
> Can you build with conda compilers - but outside conda env? It appears to
> have:
>
I am already outside of conda (build), but in order to use conda compilers,
we need a few variables.
>
> AS=/Users/kongf/miniconda3/envs/testpetsc/bin/x86_64-apple-darwin13.4.0-as
> AR=/Users/kongf/miniconda3/envs/testpetsc/bin/x86_64-apple-darwin13.4.0-ar
>
> CXX_FOR_BUILD=/Users/kongf/miniconda3/envs/testpetsc/bin/x86_64-apple-darwin13.4.0-clang++
>
> INSTALL_NAME_TOOL=/Users/kongf/miniconda3/envs/testpetsc/bin/x86_64-apple-darwin13.4.0-install_name_tool
>
> CC_FOR_BUILD=/Users/kongf/miniconda3/envs/testpetsc/bin/x86_64-apple-darwin13.4.0-clang
> FC_FOR_BUILD=/Users/kongf/miniconda3/envs/testpetsc/bin/-gfortran
> LD=/Users/kongf/miniconda3/envs/testpetsc/bin/x86_64-apple-darwin13.4.0-ld
>
> Don't know if any one of them is making a difference.
>
I unset all these variables, and did not make a difference.
>
> Also you might want to comment out
> "self.executeTest(self.resetEnvCompilers)" in setCompilers.py to see if its
> making a difference [same with self.checkEnvCompilers?
>
Still the same issue. Might it is just a bad compiler
Thanks for your help
Fande,
>
>
> Satish
>
>
> >
> > 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/>
> > >
> > >
> > >
> >
>
>
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