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

[Aurelien Ponte]

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
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