[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 20:46:23 CST 2021
Thanks Barry,
Your branch works very well. Thanks for your help!!!
Could you merge it to upstream?
Fande
On Wed, Mar 10, 2021 at 6:30 PM Barry Smith <bsmith at petsc.dev> wrote:
>
> 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.jd at 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.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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