[petsc-users] petsc4py --with-64-bit-indices
Barry Smith
bsmith at mcs.anl.gov
Sat Dec 17 16:35:59 CST 2016
> On Dec 17, 2016, at 3:42 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>
> self.gitcommit = '026d6fa' # maint/3.7 from may-21-2026
> self.download = ['git://https://bitbucket.org/petsc/petsc4py','https://bitbucket.org/petsc/petsc4py/get/'+self.gitcommit+'.tar.gz']
> self.downloaddirname = 'petsc-petsc4py'
>
> Configure is setup to use tarball that is obtained from the gitcommit - i.e not the petsc4py release tarball.
This is nuts, how is anyone suppose to know this obscure mis-feature? I have fixed it in the branch barry/allow-multiple-downloaddirnames so that it can use the petsc4py release tarball as well.
Barry
> i.e use:
>
> https://bitbucket.org/petsc/petsc4py/get/026d6fa.tar.gz
>
> [or let petsc configure download it for you - instead of wget]
>
> Also I think its best to use gnu/mpi to be compatible with gnu/python.
>
> Satish
>
> On Sat, 17 Dec 2016, Barry Smith wrote:
>
>>
>> Please do
>>
>> ls /home1/caparmor/aponte/petsc/petsc-3.7.4/linux-gnu-intel/externalpackages
>>
>> and send the results. It looks like we may have a bug in checking for the correct file.
>>
>> Sorry about this, it is not suppose to be this difficult.
>>
>> Barry
>>
>>
>>> On Dec 17, 2016, at 2:18 PM, Aurelien Ponte <aurelien.ponte at ifremer.fr> wrote:
>>>
>>> Ok, while waiting for an answer for the pip approach, I am trying another one:
>>>
>>> module load python/2.7.10_gnu-4.9.2
>>> setenv MPICC mpiicc
>>> setenv PETSC_DIR /home1/caparmor/aponte/petsc/petsc-3.7.4
>>> setenv PETSC_ARCH linux-gnu-intel
>>>
>>> wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.7.4.tar.gz
>>> wget https://bitbucket.org/petsc/petsc4py/downloads/petsc4py-3.7.0.tar.gz
>>> pip install --user --upgrade cython (not sure cython is required if not in dev mode)
>>> cd /home1/caparmor/aponte/petsc/petsc-3.7.4
>>> ./configure PETSC_ARCH=linux-gnu-intel --with-cc=mpiicc --with-fc=mpiifort --with-blas-lapack-dir=/appli/intel/Compiler/11.1/073/mkl --with-64-bit-indices --download-petsc4py=/home1/caparmor/aponte/petsc/petsc4py-3.7.0.tar.gz
>>>
>>> But the latter fails with the following message (which I do not understand as petsc4py-3.7.0.tar.gz is indeed in the right place):
>>>
>>> ================================================================================
>>> TEST configureLibrary from config.packages.petsc4py(/home1/caparmor/aponte/petsc/petsc-3.7.4/config/BuildSystem/config/packages/petsc4py.py:82)
>>> TESTING: configureLibrary from config.packages.petsc4py(config/BuildSystem/config/packages/petsc4py.py:82)
>>> Looking for PETSC4PY at git.petsc4py, hg.petsc4py or a directory starting with petsc-petsc4py
>>> Could not locate an existing copy of PETSC4PY:
>>> []
>>> Downloading petsc4py
>>> ===============================================================================
>>> Trying to download file:///home1/caparmor/aponte/petsc/petsc4py-3.7.0.tar.gz for PETSC4PY
>>> ===============================================================================
>>>
>>> Downloading file:///home1/caparmor/aponte/petsc/petsc4py-3.7.0.tar.gz to /home1/caparmor/aponte/petsc/petsc-3.7.4/linux-gnu-intel/externalpackages/_d_petsc4py-3.7.0.tar.gz
>>> Extracting /home1/caparmor/aponte/petsc/petsc-3.7.4/linux-gnu-intel/externalpackages/_d_petsc4py-3.7.0.tar.gz
>>> Executing: cd /home1/caparmor/aponte/petsc/petsc-3.7.4/linux-gnu-intel/externalpackages; chmod -R a+r petsc4py-3.7.0;find petsc4py-3.7.0 -type d -name "*" -exec chmod a+rx {} \;
>>> Looking for PETSC4PY at git.petsc4py, hg.petsc4py or a directory starting with petsc-petsc4py
>>> Could not locate an existing copy of PETSC4PY:
>>> ['petsc4py-3.7.0']
>>> ERROR: Failed to download PETSC4PY
>>> **** Configure header /tmp/petsc-ViI4NW/confdefs.h ****
>>>
>>>
>>> any ideas for this one?
>>> thanks
>>> aurelien
>>>
>>>
>>> Le 17/12/2016 à 20:19, Barry Smith a écrit :
>>>> Looks like --install-option= are options for pip not the underlying package.
>>>>
>>>> Lisandro, how does one do what seems to be a simple request?
>>>>
>>>>
>>>>> On Dec 17, 2016, at 9:00 AM, Aurelien Ponte <aurelien.ponte at ifremer.fr> wrote:
>>>>>
>>>>> Hi all,
>>>>>
>>>>> I am trying to install petsc4py and petsc with the --with-64-bit-indices option.
>>>>>
>>>>> I followed the pip install described on the petsc4py bitbucket with some slight modifications:
>>>>>
>>>>> module load python/2.7.10_gnu-4.9.2
>>>>> wget https://bootstrap.pypa.io/get-pip.py
>>>>> python get-pip.py --user
>>>>> setenv MPICC mpiicc
>>>>> pip install --user --upgrade mpi4py
>>>>> pip install --user --upgrade numpy
>>>>> pip install --user petsc petsc4py --install-option="--with-64-bit-indices"
>>>>>
>>>>> but I do get the error copied below.
>>>>>
>>>>> Any ideas on what I could do?
>>>>>
>>>>> Should I try to use a different method of install?
>>>>>
>>>>> thanks
>>>>>
>>>>> aurelien
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> service7>479% pip install --user petsc petsc4py --install-option="--with-64-bit-indices"
>>>>> /home1/caparmor/aponte/.local/lib/python2.7/site-packages/pip/commands/install.py:194: UserWarning: Disabling all use of wheels due to the use of --build-options / --global-options / --install-options.
>>>>> cmdoptions.check_install_build_global(options)
>>>>> Collecting petsc
>>>>> Downloading petsc-3.7.2.1.tar.gz (8.7MB)
>>>>> 100% |################################| 8.7MB 116kB/s
>>>>> Collecting petsc4py
>>>>> Downloading petsc4py-3.7.0.tar.gz (1.7MB)
>>>>> 100% |################################| 1.7MB 415kB/s
>>>>> Requirement already satisfied: numpy in /home1/caparmor/aponte/.local/lib/python2.7/site-packages (from petsc4py)
>>>>> Skipping bdist_wheel for petsc, due to binaries being disabled for it.
>>>>> Skipping bdist_wheel for petsc4py, due to binaries being disabled for it.
>>>>> Installing collected packages: petsc, petsc4py
>>>>> Running setup.py install for petsc ... error
>>>>> Complete output from 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-3C49gO/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-iuRtIV-record/install-record.txt --single-version-externally-managed --compile --with-64-bit-indices --user --prefix=:
>>>>> usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
>>>>> or: -c --help [cmd1 cmd2 ...]
>>>>> or: -c --help-commands
>>>>> or: -c cmd --help
>>>>>
>>>>> error: option --with-64-bit-indices not recognized
>>>>>
>>>>> ----------------------------------------
>>>>> 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-3C49gO/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-iuRtIV-record/install-record.txt --single-version-externally-managed --compile --with-64-bit-indices --user --prefix=" failed with error code 1 in /tmp/pip-build-3C49gO/petsc/
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>
>>>
>>> --
>>> 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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