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

Sun Dec 18 13:59:48 CST 2016

   Do you need Fortran? Since you are using PETSc from python. If you do not need it then change --with-fc=mpif90 to --with-fc=0

Looks like something is wrong with the mpi Fortran 90 module
> Fatal Error: Reading module mpi at line 1 column 2: Unexpected EOF

> On Dec 18, 2016, at 1:54 PM, Aurelien Ponte <aurelien.ponte at ifremer.fr> wrote:
> 
> Here is what I am trying now:
> 
> setenv MPICC mpiicc
> 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 --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
>    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
>>> 
>>> 
> 
> 
> -- 
> Aurélien Ponte
> Tel: (+33) 2 98 22 40 73
> Fax: (+33) 2 98 22 44 96
> UMR 6523, IFREMER
> ZI de la Pointe du Diable
> CS 10070
> 29280 Plouzané
> 