subject:"\[petsc\-users\] Exhausted all shared linker guesses. Could not determine how to create a shared library\!"

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Barry Smith


  Excellent, thanks for letting me know. It is a bit miraculous since I could 
not reproduce your problem (and was not willing to install Conda myself).

  https://gitlab.com/petsc/petsc/-/merge_requests/3703



> On Mar 10, 2021, at 8:46 PM, Fande Kong  wrote:
> 
> 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  > 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 > > 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 > > wrote:
>> 
>> 
>> On Wed, Mar 10, 2021 at 1:36 PM Satish Balay > > 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 > > > 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@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

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Fande Kong

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  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  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  wrote:
>
>>
>>
>> On Wed, Mar 10, 2021 at 1:36 PM Satish Balay  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 
>>> 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@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 
>>> 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

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Barry Smith


  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  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  > wrote:
> 
> 
> On Wed, Mar 10, 2021 at 1:36 PM Satish Balay  > 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  > > 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@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  > > > > 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

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Barry Smith



> On Mar 10, 2021, at 5:59 PM, Fande Kong  wrote:
> 
> Do not know what the fix should look like, but this works for me

   Please clarify. 

   Is this using the mpicc that has a -pie in the show or not? 

   Is this using the first "fix" I sent you also?

  Please send your entire patch as an attachment and the successful 
configure.log 

  Barry

> 
> 
>  @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  > wrote:
> 
> 
> On Wed, Mar 10, 2021 at 1:36 PM Satish Balay  > 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  > > 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@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  > > > > 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

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Fande Kong

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  wrote:

>
>
> On Wed, Mar 10, 2021 at 1:36 PM Satish Balay  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 
>> 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@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 
>> 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
>> > > > >
>> > >
>>

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Fande Kong

On Wed, Mar 10, 2021 at 1:36 PM Satish Balay  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  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@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 
> 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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest
> > > > >  -dynamiclib -single_module
> > > > >
> > >
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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 
> 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

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Fande Kong

On Wed, Mar 10, 2021 at 12:05 PM Barry Smith  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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest
>  -dynamiclib -single_module
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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.
>

Could we somehow skip warning messages?



Fande


>
>
> On Mar 10, 2021, at 10:11 AM, 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?
>
> Thanks,
>
> Fande
>
> Executing: mpicc -c -o
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.o
> -I/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers
>  -fPIC
>  
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.c
>
> Successful compile:
> Source:
> #include "confdefs.h"
> #include "conffix.h"
> #include 
> 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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/libconftest.so
>  -dynamic  -fPIC
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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  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  wrote:
>>
>> On Mon, Mar 8, 2021 at 8:23 PM Fande Kong  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/ljnkj46x3nq45cp9tbkc000cgn/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 
>>> wrote:
>>>
 On Mon, Mar 8, 2021 at 7:55 PM Fande Kong  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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-6v1w4q4u/config.setCompilers/conftest
   -fPIC
 /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-6v1w4q4u/config.setCompilers/conftest.o
 -L/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-6v1w4q4u/config.setCompilers
 -lconftest

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Satish Balay via petsc-users

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  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@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  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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest
> > > >  -dynamiclib -single_module
> > > >
> > /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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  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
> > > >
> >

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Fande Kong

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  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@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  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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest
> > >  -dynamiclib -single_module
> > >
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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  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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.o
> > >
> -I/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers
> > >  -fPIC
> > >
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.c
> > >
> > > Successful compile:
> > > Source:
> > > #include "confdefs.h"
> > > #include "conffix.h"
> > > #include 
> > > 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
> > >
>

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Satish Balay via petsc-users

> 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@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  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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest
> >  -dynamiclib -single_module
> > /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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  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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.o
> > -I/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers
> >  -fPIC
> >  
> > /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.c
> >
> > Successful compile:
> > Source:
> > #include "confdefs.h"
> > #include "conffix.h"
> > #include 
> > 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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/libconftest.so
> >  -dynamic  -fPIC
> > /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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  wrote:
> >
> >>
> >>   Fande,
> >>
> >>  I see you are using

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Barry Smith

 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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest
  -dynamiclib -single_module   
/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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  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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.o
>  
> -I/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers
>   -fPIC  
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.c
>  
> Successful compile:
> Source:
> #include "confdefs.h"
> #include "conffix.h"
> #include 
> 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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/libconftest.so
>   -dynamic  -fPIC 
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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  > 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 > > wrote:
>> 
>> On Mon, Mar 8, 2021 at 8:23 PM Fande Kong > > 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/ljnkj46x3nq45cp9tbkc000cgn/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 > > wrote:
>> On Mon, Mar 8, 2021 at 7:55 PM Fande Kong > > 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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-6v1w4q4u/config.setCompilers/conftest
>> -fPIC 
>> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-6v1w4q4u/config.setCompilers/conftest.o
>>   
>> -L/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-6v1w4q4u/config.setCompilers
>>  -lconftest
>> Possible ERROR while running

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Satish Balay via petsc-users

On Wed, 10 Mar 2021, Fande Kong wrote:

> On Wed, Mar 10, 2021 at 9:34 AM Satish Balay  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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest
> >
> > /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.o
> > -L/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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/ljnkj46x3nq45cp9tbkc000cgn/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.

Can you send the configure.log for this build outside conda - but using conda 
tools.

And what do you get for:

/Users/kongf/miniconda3/envs/testpetsc/bin/mpicc -show
/Users/kongf/miniconda3/envs/testpetsc/bin/x86_64-apple-darwin13.4.0-clang -v 
src/benchmarks/sizeof.c

> >
> > 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

Perhaps you can try to reproduce the above test outside configure [i.e create a 
.dylib, and attempt to link to it] - and attempt to debug it further.

If its a broken conda compiler [or conda-ld] perhaps there is a way to use 
compilers/ld from outside conda - from this conda build.

Satish

- 

> 
> 
> Thanks for your help
> 
> Fande,
> 
> 
> >
> >
> > Satish
> >
> >
> > >
> > > Thanks,
> > >
> > > Fande
> > >
> > > Executing: mpicc -c -o
> > >
> > /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.o
> > >
> > -I/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers
> > >  -fPIC
> > >
> > /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.c
> > >
> > > Successful compile:
> > > Source:
> > > #include "confdefs.h"
> > > #include "conffix.h"
> > > #include 
> > > 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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/libconftest.so
> > >  -dynamic  -fPIC
> > >
> > /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-10 Thread Satish Balay via petsc-users

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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest

/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.o
  
-L/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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/ljnkj46x3nq45cp9tbkc000cgn/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:

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.

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?]

Satish


> 
> Thanks,
> 
> Fande
> 
> Executing: mpicc -c -o
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.o
> -I/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers
>  -fPIC
>  
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/conftest.c
> 
> Successful compile:
> Source:
> #include "confdefs.h"
> #include "conffix.h"
> #include 
> 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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-pkset22y/config.setCompilers/libconftest.so
>  -dynamic  -fPIC
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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  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  wrote:
> >
> > On Mon, Mar 8, 2021 at 8:23 PM Fande Kong  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/ljnkj46x3nq45cp9tbkc000cgn/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  wrote:
> >>
> >>> On Mon, Mar 8, 2021 at 7:55 PM Fande Kong  wrote:
> >>>
>  Hi All,
> 
>  mpicc rejected "-fPIC". Anyone has a clue how to work around this issue?
> 
> >>>
> >>> The failure is at the last

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-08 Thread Barry Smith


  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  wrote:
> 
> On Mon, Mar 8, 2021 at 8:23 PM Fande Kong  > 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/ljnkj46x3nq45cp9tbkc000cgn/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  > wrote:
> On Mon, Mar 8, 2021 at 7:55 PM Fande Kong  > 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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-6v1w4q4u/config.setCompilers/conftest
> -fPIC 
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-6v1w4q4u/config.setCompilers/conftest.o
>   
> -L/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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/ljnkj46x3nq45cp9tbkc000cgn/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/ 
> 
> 
> -- 
> 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/

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-08 Thread Matthew Knepley

On Mon, Mar 8, 2021 at 8:23 PM Fande Kong  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/ljnkj46x3nq45cp9tbkc000cgn/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  wrote:
>
>> On Mon, Mar 8, 2021 at 7:55 PM Fande Kong  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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-6v1w4q4u/config.setCompilers/conftest
>>   -fPIC
>> /var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-6v1w4q4u/config.setCompilers/conftest.o
>> -L/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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/ljnkj46x3nq45cp9tbkc000cgn/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/
>> 
>>
>

-- 
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/

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

2021-03-08 Thread Matthew Knepley

On Mon, Mar 8, 2021 at 7:55 PM Fande Kong  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/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-6v1w4q4u/config.setCompilers/conftest
  -fPIC
/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/T/petsc-6v1w4q4u/config.setCompilers/conftest.o
-L/var/folders/tv/ljnkj46x3nq45cp9tbkc000cgn/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/ljnkj46x3nq45cp9tbkc000cgn/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/

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

16 matches

Site Navigation

Mail list logo

Footer information