[petsc-users] problems with petsc4py on M1 mac when configuring PETSc

Fri Apr 8 08:47:34 CDT 2022

> On 8 Apr 2022, at 3:37 PM, Veronika Ulanova <19veronika97 at gmail.com> wrote:
> 
> 
> Thank you Blaise Bourdin, will try that !

Do not do that unless you know exactly what you are doing and the inner workings of Brew.
You are not doing a fresh build, so you need first to rm arch-darwin-c-debug. That’s why you have an error.

Thanks,
Pierre

>> On Fri, Apr 8, 2022 at 2:36 PM Veronika Ulanova <19veronika97 at gmail.com> wrote:
>> Here it is attached:
>> 
>>> On Fri, Apr 8, 2022 at 11:11 AM Satish Balay <balay at mcs.anl.gov> wrote:
>>> This is strange. We have a successful build on M1 - for ex: https://gitlab.com/petsc/petsc/-/jobs/2308081220
>>> 
>>> Can you send corresponding configure.log?
>>> 
>>> Satish
>>> 
>>> On Fri, 8 Apr 2022, Veronika Ulanova wrote:
>>> 
>>> > To get this error i run the following commands:
>>> > 
>>> > 1.
>>> > 
>>> > *➜ * *petsc **git:(**release**)** ✗ *./configure --with-cc=gcc
>>> > --with-cxx=g++ --with-petsc4py=1 --with-fc=gfortran --download-mpich
>>> > --download-fblaslapack
>>> > 
>>> > *➜ * *petsc **git:(**release**)** ✗ *   make
>>> > PETSC_DIR=/Users/veronikaulanova/Documents/documents/Oxford_work/petsc
>>> > PETSC_ARCH=arch-darwin-c-debug all
>>> > 
>>> > On Fri, Apr 8, 2022 at 10:41 AM Veronika Ulanova <19veronika97 at gmail.com>
>>> > wrote:
>>> > 
>>> > > I pulled the updated repo but now I get a different error also related to
>>> > > architecture:
>>> > >
>>> > > ld: file not found: @rpath/libgcc_s.1.1.dylib for architecture arm64
>>> > >
>>> > > clang: error: linker command failed with exit code 1 (use -v to see
>>> > > invocation)
>>> > >
>>> > > error: command
>>> > > '/Users/veronikaulanova/Documents/documents/Oxford_work/petsc/arch-darwin-c-debug/bin/mpicc'
>>> > > failed with exit code 1
>>> > >
>>> > > **************************ERROR*************************************
>>> > >
>>> > > Error building petsc4py.
>>> > >
>>> > > ********************************************************************
>>> > >
>>> > > make[2]: *** [petsc4pybuild] Error 1
>>> > >
>>> > > ***************************ERROR**************************************
>>> > >
>>> > > *  Error during compile, check arch-darwin-c-debug/lib/petsc/conf/make.log*
>>> > >
>>> > > *  Send it and arch-darwin-c-debug/lib/petsc/conf/configure.log to
>>> > > petsc-maint at mcs.anl.gov <petsc-maint at mcs.anl.gov>*
>>> > >
>>> > > **********************************************************************
>>> > >
>>> > >
>>> > > Any idea about this one? Thank you
>>> > >
>>> > > On Fri, Apr 8, 2022 at 10:09 AM Veronika Ulanova <19veronika97 at gmail.com>
>>> > > wrote:
>>> > >
>>> > >> Hello Satish,
>>> > >>
>>> > >> By the repo you mean the main PETSc repository?
>>> > >>
>>> > >> Thank you, Veronika
>>> > >>
>>> > >> On Fri, Apr 8, 2022 at 9:49 AM Satish Balay <balay at mcs.anl.gov> wrote:
>>> > >>
>>> > >>> A fix for M1 was recently pushed to the git repo.
>>> > >>>
>>> > >>> Can you try using it [with either release or main branches] - and see if
>>> > >>> that works?
>>> > >>>
>>> > >>> Satish
>>> > >>>
>>> > >>>
>>> > >>>
>>> > >>> On Fri, 8 Apr 2022, Veronika Ulanova wrote:
>>> > >>>
>>> > >>> > Hi,
>>> > >>> >
>>> > >>> > I have been trying to configure the petsc4py package along with my
>>> > >>> PETSc
>>> > >>> > installation for my research. I have searched for solutions on the
>>> > >>> internet
>>> > >>> > but there was no luck, this is the error I get when I am trying to
>>> > >>> > configure PETSC and use it to run examples of code that utilise the
>>> > >>> > petsc4py package...
>>> > >>> >
>>> > >>> >
>>> > >>> >
>>> > >>> >  File
>>> > >>> >
>>> > >>> "/Users/veronikaulanova/Documents/documents/Oxford_work/petsc/arch-darwin-c-debug/lib/petsc4py/PETSc.py",
>>> > >>> > line 3, in <module>
>>> > >>> >
>>> > >>> >     PETSc = ImportPETSc(ARCH)
>>> > >>> >
>>> > >>> >   File
>>> > >>> >
>>> > >>> "/Users/veronikaulanova/Documents/documents/Oxford_work/petsc/arch-darwin-c-debug/lib/petsc4py/lib/__init__.py",
>>> > >>> > line 29, in ImportPETSc
>>> > >>> >
>>> > >>> >     return Import('petsc4py', 'PETSc', path, arch)
>>> > >>> >
>>> > >>> >   File
>>> > >>> >
>>> > >>> "/Users/veronikaulanova/Documents/documents/Oxford_work/petsc/arch-darwin-c-debug/lib/petsc4py/lib/__init__.py",
>>> > >>> > line 73, in Import
>>> > >>> >
>>> > >>> >     module = import_module(pkg, name, path, arch)
>>> > >>> >
>>> > >>> >   File
>>> > >>> >
>>> > >>> "/Users/veronikaulanova/Documents/documents/Oxford_work/petsc/arch-darwin-c-debug/lib/petsc4py/lib/__init__.py",
>>> > >>> > line 58, in import_module
>>> > >>> >
>>> > >>> >     with f: return imp.load_module(fullname, f, fn, info)
>>> > >>> >
>>> > >>> >   File "/opt/homebrew/Cellar/python at 3.9
>>> > >>> /3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/imp.py",
>>> > >>> > line 242, in load_module
>>> > >>> >
>>> > >>> >     return load_dynamic(name, filename, file)
>>> > >>> >
>>> > >>> >   File "/opt/homebrew/Cellar/python at 3.9
>>> > >>> /3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/imp.py",
>>> > >>> > line 342, in load_dynamic
>>> > >>> >
>>> > >>> >     return _load(spec)
>>> > >>> >
>>> > >>> > ImportError:
>>> > >>> >
>>> > >>> dlopen(/Users/veronikaulanova/Documents/documents/Oxford_work/petsc/arch-darwin-c-debug/lib/petsc4py/lib/arch-darwin-c-debug/
>>> > >>> > PETSc.cpython-39-darwin.so <http://petsc.cpython-39-darwin.so/>, 2):
>>> > >>> no
>>> > >>> > suitable image found.  Did find:
>>> > >>> >
>>> > >>> >
>>> > >>> /Users/veronikaulanova/Documents/documents/Oxford_work/petsc/arch-darwin-c-debug/lib/petsc4py/lib/arch-darwin-c-debug/
>>> > >>> > PETSc.cpython-39-darwin.so <http://petsc.cpython-39-darwin.so/>:
>>> > >>> mach-o,
>>> > >>> > but wrong architecture
>>> > >>> >
>>> > >>> >
>>> > >>> /Users/veronikaulanova/Documents/documents/Oxford_work/petsc/arch-darwin-c-debug/lib/petsc4py/lib/arch-darwin-c-debug/
>>> > >>> > PETSc.cpython-39-darwin.so <http://petsc.cpython-39-darwin.so/>:
>>> > >>> stat()
>>> > >>> > failed with errno=25
>>> > >>> >
>>> > >>> >
>>> > >>> > As you can see I am using an M1 mac and therefore that causes the
>>> > >>> petsc4py
>>> > >>> > package to give me an error (highlighted above), but do you have any
>>> > >>> idea
>>> > >>> > of how I can solve it or why it is even there? I know that the new M1
>>> > >>> has a
>>> > >>> > different architecture to intel macs but I have no idea of where to
>>> > >>> > start with fixing this or how to make it work. Any help would be much
>>> > >>> > appreciated, thank you in advance.
>>> > >>> >
>>> > >>> > Kind Regards, Veronika
>>> > >>> >
>>> > >>>
>>> > >>>
>>> > 
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