[petsc-users] petsc4py --with-64-bit-indices

Sun Dec 18 14:00:36 CST 2016

On Sun, 18 Dec 2016, Aurelien Ponte wrote:

> Here is what I am trying now:
> 
> setenv MPICC mpiicc

Suggest not using intel compiler [petsc configure ignores MPICC env variable anyway]

> pip install --user --upgrade --ignore-installed --no-cache-dir mpi4py
> pip install --user --upgrade --ignore-installed --no-cache-dir numpy
> setenv PETSC_CONFIGURE_OPTIONS '--with-64-bit-indices --with-fc=mpif90

Also specify compatible mpicc,mpicxx [i.e ones that use gcc/g++/gfortran - so that they are compatible with python]

i.e --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90

> --download-fblaslapack'
> pip install --user --upgrade --ignore-installed --no-cache-dir petsc petsc4py
> 
> I get now the following error message (I'll send the logs to
> petsc-maint at mcs.anl.gov as suggested):
> 
>               CC arch-python-linux-x86_64/obj/src/vec/is/is/interface/index.o
>     Fatal Error: Reading module mpi at line 1 column 2: Unexpected EOF

Some fortran module issue - happens if the compile and mpi have a mismatch..

Satish

>     gmake[2]: *** 
> [arch-python-linux-x86_64/obj/src/sys/f90-mod/petscsysmod.o] Error 1
>     gmake[2]: *** Waiting for unfinished jobs....
>     /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/client.c(3): warning 
> #161: unrecognized #pragma
>       #pragma clang diagnostic ignored "-Wdeprecated-declarations"
>               ^
> 
>     /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/client.c(4): warning #161:
> unrecognized #pragma
>       #pragma gcc diagnostic ignored "-Wdeprecated-declarations"
>               ^
> 
>     /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/google.c(3): warning #161:
> unrecognized #pragma
>       #pragma clang diagnostic ignored "-Wdeprecated-declarations"
>               ^
> 
>     /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/google.c(4): warning #161:
> unrecognized #pragma
>       #pragma gcc diagnostic ignored "-Wdeprecated-declarations"
>               ^
> 
>     /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/box.c(3): warning #161:
> unrecognized #pragma
>       #pragma clang diagnostic ignored "-Wdeprecated-declarations"
>               ^
> 
>     /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/box.c(4): warning #161:
> unrecognized #pragma
>       #pragma gcc diagnostic ignored "-Wdeprecated-declarations"
>               ^
> 
>     /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/globus.c(2): warning #161:
> unrecognized #pragma
>       #pragma clang diagnostic ignored "-Wdeprecated-declarations"
>               ^
> 
>     /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/globus.c(3): warning #161:
> unrecognized #pragma
>       #pragma gcc diagnostic ignored "-Wdeprecated-declarations"
>               ^
> 
>     gmake[2]: Leaving directory `/tmp/pip-build-t7pV1u/petsc'
>     gmake[1]: *** [gnumake] Error 2
>     gmake[1]: Leaving directory `/tmp/pip-build-t7pV1u/petsc'
> **************************ERROR*************************************
>       Error during compile, check
> arch-python-linux-x86_64/lib/petsc/conf/make.log
>       Send it and arch-python-linux-x86_64/lib/petsc/conf/configure.log to
> petsc-maint at mcs.anl.gov
> ********************************************************************
>     make: *** [all] Error 1
>     Traceback (most recent call last):
>       File "<string>", line 1, in <module>
>       File "/tmp/pip-build-t7pV1u/petsc/setup.py", line 302, in <module>
>         **metadata)
>       File
> "/appli/python/2.7.10_gcc-4.9.2/python-2.7.10/lib/python2.7/distutils/core.py",
> line 151, in setup
>         dist.run_commands()
>       File
> "/appli/python/2.7.10_gcc-4.9.2/python-2.7.10/lib/python2.7/distutils/dist.py",
> line 953, in run_commands
>         self.run_command(cmd)
>       File
> "/appli/python/2.7.10_gcc-4.9.2/python-2.7.10/lib/python2.7/distutils/dist.py",
> line 972, in run_command
>         cmd_obj.run()
>       File "/tmp/pip-build-t7pV1u/petsc/setup.py", line 219, in run
>         build(self.dry_run)
>       File "/tmp/pip-build-t7pV1u/petsc/setup.py", line 164, in build
>         if status != 0: raise RuntimeError(status)
>     RuntimeError: 512
> 
>     ----------------------------------------
> Command "/appli/python/2.7.10_gcc-4.9.2/python-2.7.10/bin/python -u -c "import
> setuptools,
> tokenize;__file__='/tmp/pip-build-t7pV1u/petsc/setup.py';f=getattr(tokenize,
> 'open', open)(__file__);code=f.read().replace('\r\n',
> '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record
> /tmp/pip-ebXwB3-record/install-record.txt --single-version-externally-managed
> --compile --user --prefix=" failed with error code 1 in
> /tmp/pip-build-t7pV1u/petsc/
> 
> 
> 
> 
> Le 18/12/2016 à 16:52, Satish Balay a écrit :
> > How about using --download-fblaslapack instead of MKL?
> >
> > Satish
> >
> > On Sun, 18 Dec 2016, Aurelien Ponte wrote:
> >
> > > Allright I got the following to complete:
> > >
> > > ### install pip:
> > > module load python/2.7.10_gnu-4.9.2
> > > wget https://bootstrap.pypa.io/get-pip.py
> > > python get-pip.py --user
> > > # edit .cshrc: set path = ($path $home/.local/bin)  + setenv
> > > LD_LIBRARY_PATH
> > > /home1/caparmor/aponte/.local/lib:${LD_LIBRARY_PATH}
> > >
> > > #
> > > setenv MPICC mpiicc
> > > pip install --user --upgrade mpi4py
> > > pip install --user --upgrade numpy
> > > setenv PETSC_CONFIGURE_OPTIONS '--with-64-bit-indices
> > > --with-blas-lapack-dir=/appli/intel/Compiler/11.1/073/mkl/lib/em64t'
> > > pip install --user petsc petsc4py
> > >
> > > But now I get the following at run time:
> > > *** libmkl_mc3.so *** failed with error :
> > > /appli/intel/Compiler/11.1/073/mkl/lib/em64t/libmkl_mc3.so: undefined
> > > symbol:
> > > mkl_dft_commit_descriptor_s_c2c_md_omp
> > > *** libmkl_def.so *** failed with error :
> > > /appli/intel/Compiler/11.1/073/mkl/lib/em64t/libmkl_def.so: undefined
> > > symbol:
> > > mkl_dft_commit_descriptor_s_c2c_md_omp
> > > MKL FATAL ERROR: Cannot load neither libmkl_mc3.so nor libmkl_def.so
> > > MKL FATAL ERROR: Cannot load neither libmkl_mc3.so nor libmkl_def.so
> > >
> > >
> > > Any ideas?
> > >
> > > I will also try the other approach (from source).
> > >
> > > thanks
> > >
> > > aurelien
> > >
> > >
> > >
> > >
> > > Le 17/12/2016 à 22:36, Lawrence Mitchell a écrit :
> > > > > On 17 Dec 2016, at 19:19, Barry Smith <bsmith at mcs.anl.gov> wrote:
> > > > >
> > > > >    Looks like --install-option= are options for pip not the underlying
> > > > >    package.
> > > > >
> > > > >    Lisandro,  how does one do what seems to be a simple request?
> > > > Set PETSC_CONFIGURE_OPTIONS to any additional flags you want to pass to
> > > > configure during pip install
> > >
> > >
> 
> 
> 