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

Sun Dec 18 14:22:02 CST 2016

I am trying now trying with:
setenv PETSC_CONFIGURE_OPTIONS '--with-64-bit-indices --with-fc=0 
--download-f2cblaslapack'

Unfortunately I believe there is only intel mpi on the cluster I am 
working on (judging from the module avail command).
Do you believe I should try to compile openmpi with gcc?

aurelien

Le 18/12/2016 à 21:00, Satish Balay a écrit :
> 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
>>>>
>>
>>

-- 
Aurélien Ponte
Tel: (+33) 2 98 22 40 73
Fax: (+33) 2 98 22 44 96
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