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 <[email protected]> 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 <[email protected]
> <mailto:[email protected]>> 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 <[email protected]
>> <mailto:[email protected]>> wrote:
>>
>> On Mon, Mar 8, 2021 at 8:23 PM Fande Kong <[email protected]
>> <mailto:[email protected]>> 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 <[email protected]
>> <mailto:[email protected]>> wrote:
>> On Mon, Mar 8, 2021 at 7:55 PM Fande Kong <[email protected]
>> <mailto:[email protected]>> 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>
