[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 17:59:21 CST 2021
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.jd at gmail.com> wrote:
>
>
> On Wed, Mar 10, 2021 at 1:36 PM Satish Balay <balay at 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 <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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