[petsc-users] petsc4py Build Problem
Mikhail Khodak
mkhodak at princeton.edu
Tue Jun 23 12:15:59 CDT 2015
Thank you for reviewing this. The errors for the command 'pip2 install .'
inside the petsc4py directory are attached, along with the configure/make
logs for the PETSc build.
Best,
Mikhail Khodak
On Mon, Jun 22, 2015 at 12:25 PM, Lisandro Dalcin <dalcinl at gmail.com> wrote:
> Dear Mikhail, Satish helped me and we managed to get petsc4py working
> with static builds and Cygwin's Open MPI. Please git pull and try
> again.
>
> On 11 June 2015 at 14:13, Mikhail Khodak <mkhodak at princeton.edu> wrote:
> > I have attached the log files.
> > I tried using Open MPI before but received the same result. I will try a
> > static build later and otherwise will get a VM.
> > Thanks for looking at this,
> > Mikhail
> >
> >
> > On Thu, Jun 11, 2015 at 10:48 AM, Satish Balay <balay at mcs.anl.gov>
> wrote:
> >>
> >> Also - should mention:
> >>
> >> - cygwin has OpenMPI pacakged - so you could also try that.
> >> - most of my builds are static [so never tried dll builds]
> >>
> >> Satish
> >>
> >> On Thu, 11 Jun 2015, Satish Balay wrote:
> >>
> >> > If you get errors when running basic petsc examples - send us the
> >> > relavant petsc logs [configure.log, make.log, test.log etc..]
> >> >
> >> > Also - note that mpich is not supported on cygwin/windows [it
> >> > generally works for us - when we try the --download-mpich build].
> >> >
> >> > Unless you really need a cywin build/use of petsc4py - it might be
> >> > easier to install a linux VM - and use PETSc/petsc4py on it.
> >> >
> >> > Satish
> >> >
> >> > On Thu, 11 Jun 2015, Mikhail Khodak wrote:
> >> >
> >> > > I added these lines to the petsc4py test files (specifically
> >> > > test_comm.py)
> >> > > but the error remains the same. However, I have done the standard
> >> > > 'which
> >> > > mpiexec', 'which mpicc', 'which mpirun' and they are all in the same
> >> > > folder. In fact it is the only MPI installed.
> >> > > The reason I thought it might be a PETSc build problem is because
> one
> >> > > of
> >> > > the PETSc 'make test' tests (ex5f) fails with the same error, even
> >> > > though
> >> > > the 'make streams' test works fine with MPI processes.
> >> > > Thanks,
> >> > > Mikhail
> >> > >
> >> > > On Thu, Jun 11, 2015 at 4:21 AM, Matthew Knepley <knepley at gmail.com
> >
> >> > > wrote:
> >> > >
> >> > > > On Thu, Jun 11, 2015 at 5:07 AM, Mikhail Khodak
> >> > > > <mkhodak at princeton.edu>
> >> > > > wrote:
> >> > > >
> >> > > >> Thank you for your help - the install seems to work, apart from
> >> > > >> routines
> >> > > >> requiring MPI, which fail due to the "Attempting to use an MPI
> >> > > >> routine
> >> > > >> before initializing MPI" error. This seems to be an error in the
> >> > > >> PETSc
> >> > > >> build itself.
> >> > > >>
> >> > > >
> >> > > > The MPI routines will not work until after
> >> > > >
> >> > > > import petsc4py, sys
> >> > > > petsc4py.init(sys.argv)
> >> > > > from petsc4py import PETSc
> >> > > >
> >> > > > If they fail after this, it is usually a mismatch between the
> >> > > > mpiexec
> >> > > > being used and the MPI
> >> > > > libraries being linked.
> >> > > >
> >> > > > Thanks,
> >> > > >
> >> > > > Matt
> >> > > >
> >> > > > Thanks again,
> >> > > >> Mikhail Khodak
> >> > > >>
> >> > > >> On Mon, Jun 8, 2015 at 5:11 AM, Lisandro Dalcin <
> dalcinl at gmail.com>
> >> > > >> wrote:
> >> > > >>
> >> > > >>> On 8 June 2015 at 02:50, Mikhail Khodak <mkhodak at princeton.edu>
> >> > > >>> wrote:
> >> > > >>> > Hello, I am trying to build petsc4py-3.5.1 using Cygwin on
> >> > > >>> > 64-bit
> >> > > >>> Windows 7.
> >> > > >>> > I have built PETSc 3.5.4 with shared and dynamic libraries
> using
> >> > > >>> > mpich2-1.2.1 and successfully ran the installation tests. I am
> >> > > >>> > using
> >> > > >>> Python
> >> > > >>> > 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I
> >> > > >>> > attempt
> >> > > >>> to
> >> > > >>> > install petsc4py (both with pip and distutils) I get a mpicc
> >> > > >>> > compiler
> >> > > >>> error
> >> > > >>> > due to undefined references/symbols. I have attached the
> output
> >> > > >>> > of
> >> > > >>> running
> >> > > >>> >
> >> > > >>> > pip install petsc petsc4py --allow-external petsc
> >> > > >>> > --allow-external
> >> > > >>> petsc4py
> >> > > >>> >
> >> > > >>>
> >> > > >>> I've never ever built or test petsc4py under Cygwin. The errors
> >> > > >>> you
> >> > > >>> see are expected.
> >> > > >>> Perhaps you can manually workaround the issues following the
> >> > > >>> following
> >> > > >>> steps:
> >> > > >>>
> >> > > >>> 1) Download the petsc4py tarball and unpack it.
> >> > > >>> 2) Open the file "src/libpetsc4py/libpetsc4py.h", add remove all
> >> > > >>> occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just
> XYZ
> >> > > >>> 3) Use pip again:
> >> > > >>>
> >> > > >>> pip install petsc
> >> > > >>> pip install .
> >> > > >>>
> >> > > >>> The last line assumes your current working directory is the one
> >> > > >>> having
> >> > > >>> petsc4py's setup.py
> >> > > >>>
> >> > > >>> Finally, I do not guarantee this will work. I'm just guessing,
> >> > > >>> petsc4py never explicitly supported Windows and/or Cygwin.
> >> > > >>>
> >> > > >>>
> >> > > >>> --
> >> > > >>> Lisandro Dalcin
> >> > > >>> ============
> >> > > >>> Research Scientist
> >> > > >>> Computer, Electrical and Mathematical Sciences & Engineering
> >> > > >>> (CEMSE)
> >> > > >>> Numerical Porous Media Center (NumPor)
> >> > > >>> King Abdullah University of Science and Technology (KAUST)
> >> > > >>> http://numpor.kaust.edu.sa/
> >> > > >>>
> >> > > >>> 4700 King Abdullah University of Science and Technology
> >> > > >>> al-Khawarizmi Bldg (Bldg 1), Office # 4332
> >> > > >>> Thuwal 23955-6900, Kingdom of Saudi Arabia
> >> > > >>> http://www.kaust.edu.sa
> >> > > >>>
> >> > > >>> Office Phone: +966 12 808-0459
> >> > > >>>
> >> > > >>
> >> > > >>
> >> > > >
> >> > > >
> >> > > > --
> >> > > > What most experimenters take for granted before they begin their
> >> > > > experiments is infinitely more interesting than any results to
> which
> >> > > > their
> >> > > > experiments lead.
> >> > > > -- Norbert Wiener
> >> > > >
> >> > >
> >> >
> >> >
>
>
>
> --
> Lisandro Dalcin
> ============
> Research Scientist
> Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
> Numerical Porous Media Center (NumPor)
> King Abdullah University of Science and Technology (KAUST)
> http://numpor.kaust.edu.sa/
>
> 4700 King Abdullah University of Science and Technology
> al-Khawarizmi Bldg (Bldg 1), Office # 4332
> Thuwal 23955-6900, Kingdom of Saudi Arabia
> http://www.kaust.edu.sa
>
> Office Phone: +966 12 808-0459
>
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Processing /cygdrive/c/cygwin64/lib/python2.7/site-packages/petsc4py-3.5.1
Requirement already satisfied (use --upgrade to upgrade): numpy in /usr/lib/python2.7/site-packages (from petsc4py==3.6.0)
Building wheels for collected packages: petsc4py
Running setup.py bdist_wheel for petsc4py
Complete output from command /usr/bin/python -c "import setuptools;__file__='/tmp/pip-yBfOJT-build/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /tmp/tmpXdUvO2pip-wheel-:
running bdist_wheel
running build
running build_src
cythonizing 'petsc4py.PETSc.pyx' -> 'petsc4py.PETSc.c'
cythonizing 'libpetsc4py/libpetsc4py.pyx' -> 'libpetsc4py/libpetsc4py.c'
running build_py
creating build
creating build/lib.cygwin-2.0.4-i686-2.7
creating build/lib.cygwin-2.0.4-i686-2.7/petsc4py
copying src/PETSc.py -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py
copying src/__init__.py -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py
copying src/__main__.py -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py
creating build/lib.cygwin-2.0.4-i686-2.7/petsc4py/lib
copying src/lib/__init__.py -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py/lib
creating build/lib.cygwin-2.0.4-i686-2.7/petsc4py/include
creating build/lib.cygwin-2.0.4-i686-2.7/petsc4py/include/petsc4py
copying src/include/petsc4py/numpy.h -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py/include/petsc4py
copying src/include/petsc4py/petsc4py.h -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py/include/petsc4py
copying src/include/petsc4py/petsc4py.PETSc.h -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py/include/petsc4py
copying src/include/petsc4py/petsc4py.PETSc_api.h -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py/include/petsc4py
copying src/include/petsc4py/petsc4py.i -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py/include/petsc4py
copying src/include/petsc4py/PETSc.pxd -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py/include/petsc4py
copying src/include/petsc4py/__init__.pxd -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py/include/petsc4py
copying src/include/petsc4py/__init__.pyx -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py/include/petsc4py
copying src/lib/petsc.cfg -> build/lib.cygwin-2.0.4-i686-2.7/petsc4py/lib
running build_ext
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-yBfOJT-build/setup.py", line 266, in <module>
main()
File "/tmp/pip-yBfOJT-build/setup.py", line 263, in main
run_setup()
File "/tmp/pip-yBfOJT-build/setup.py", line 136, in run_setup
**setup_args)
File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/usr/lib/python2.7/site-packages/wheel/bdist_wheel.py", line 175, in run
self.run_command('build')
File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/usr/lib/python2.7/distutils/command/build.py", line 127, in run
self.run_command(cmd_name)
File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/usr/lib/python2.7/site-packages/setuptools/command/build_ext.py", line 50, in run
_build_ext.run(self)
File "/usr/lib/python2.7/distutils/command/build_ext.py", line 337, in run
self.build_extensions()
File "conf/baseconf.py", line 510, in build_extensions
_build_ext.build_extensions(self, *args,**kargs)
File "/usr/lib/python2.7/distutils/command/build_ext.py", line 446, in build_extensions
self.build_extension(ext)
File "conf/baseconf.py", line 495, in build_extension
config = self.get_config_arch(arch)
File "conf/baseconf.py", line 486, in get_config_arch
return config.Configure(self.petsc_dir, arch)
File "conf/baseconf.py", line 108, in __init__
self.language = language_map[self['PETSC_LANGUAGE']]
File "conf/baseconf.py", line 111, in __getitem__
return self.configdict[item]
KeyError: 'PETSC_LANGUAGE'
----------------------------------------
Failed to build petsc4py
Installing collected packages: petsc4py
Running setup.py install for petsc4py
Complete output from command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip-yBfOJT-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-0cQfDb-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_src
running build_py
running build_ext
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-yBfOJT-build/setup.py", line 266, in <module>
main()
File "/tmp/pip-yBfOJT-build/setup.py", line 263, in main
run_setup()
File "/tmp/pip-yBfOJT-build/setup.py", line 136, in run_setup
**setup_args)
File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "conf/baseconf.py", line 561, in run
_install.run(self)
File "/usr/lib/python2.7/site-packages/setuptools/command/install.py", line 61, in run
return orig.install.run(self)
File "/usr/lib/python2.7/distutils/command/install.py", line 563, in run
self.run_command('build')
File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/usr/lib/python2.7/distutils/command/build.py", line 127, in run
self.run_command(cmd_name)
File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/usr/lib/python2.7/site-packages/setuptools/command/build_ext.py", line 50, in run
_build_ext.run(self)
File "/usr/lib/python2.7/distutils/command/build_ext.py", line 337, in run
self.build_extensions()
File "conf/baseconf.py", line 510, in build_extensions
_build_ext.build_extensions(self, *args,**kargs)
File "/usr/lib/python2.7/distutils/command/build_ext.py", line 446, in build_extensions
self.build_extension(ext)
File "conf/baseconf.py", line 495, in build_extension
config = self.get_config_arch(arch)
File "conf/baseconf.py", line 486, in get_config_arch
return config.Configure(self.petsc_dir, arch)
File "conf/baseconf.py", line 108, in __init__
self.language = language_map[self['PETSC_LANGUAGE']]
File "conf/baseconf.py", line 111, in __getitem__
return self.configdict[item]
KeyError: 'PETSC_LANGUAGE'
----------------------------------------
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