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
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
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
> 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
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
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
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
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
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
> 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
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
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
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
>
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
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
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
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