[petsc-users] petsc4py --with-64-bit-indices
Aurelien Ponte
aurelien.ponte at ifremer.fr
Sun Dec 18 14:35:45 CST 2016
All right, the build did succeed and I was able to perform the
computations that used to fail
without --with-64-bit-indices.
So to summarize:
setenv MPICC mpiicc (useless according to Satish)
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=0
--download-f2cblaslapack'
pip install --user --upgrade --ignore-installed --no-cache-dir petsc
petsc4py
thanks to all for your help,
aurelien
Le 18/12/2016 à 21:22, Aurelien Ponte a écrit :
> 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
UMR 6523, IFREMER
ZI de la Pointe du Diable
CS 10070
29280 Plouzané
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