[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 13:51:08 CST 2021 

> 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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