[firedrake] error installing PyOP2
Justin Chang
jychang48 at gmail.com
Tue Jul 14 11:08:03 BST 2015
Actually, after running git pull in the PyOP2 directory, I ran this:
python setup.py build_ext --inplace
and got this after running 'make test' again:
cd test; py.test unit --backend=sequential
Segmentation fault (core dumped)
make: *** [unit_sequential] Error 139
should I have run something else?
Thanks,
Justin
On Tue, Jul 14, 2015 at 5:04 AM, Justin Chang <jychang48 at gmail.com> wrote:
> Lawrence,
>
> python -c "import petsc4py; petsc4py.init()" gives me no output, so I
> assume it's working?
>
> btw I installed petsc4py using:
>
> git clone .... && git checkout firedrake && sudo -E python setup.py
> install.
>
> So when I now run:
>
> pip show petsc4py
>
> gives me the following:
>
> ---
> Name: petsc4py
> Version: 3.5.1
> Location: /usr/local/lib/python2.7/dist-packages
> Requires:
>
> Doing the latest pull of PyOP2, I ran:
>
> make test
>
> And got these errors:
>
> cd test; py.test unit --backend=sequential
> Traceback (most recent call last):
> File "/usr/local/bin/py.test", line 11, in <module>
> sys.exit(main())
> File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 18, in
> main
> config = _prepareconfig(args, plugins)
> File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 62, in
> _prepareconfig
> pluginmanager=pluginmanager, args=args)
> File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 376, in
> __call__
> return self._docall(methods, kwargs)
> File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 387, in
> _docall
> res = mc.execute()
> File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 288, in
> execute
> res = method(**kwargs)
> File "/usr/lib/python2.7/dist-packages/_pytest/helpconfig.py", line 25,
> in pytest_cmdline_parse
> config = __multicall__.execute()
> File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 288, in
> execute
> res = method(**kwargs)
> File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 617, in
> pytest_cmdline_parse
> self.parse(args)
> File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 710, in
> parse
> self._preparse(args)
> File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 690, in
> _preparse
> args=args, parser=self._parser)
> File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 376, in
> __call__
> return self._docall(methods, kwargs)
> File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 387, in
> _docall
> res = mc.execute()
> File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 288, in
> execute
> res = method(**kwargs)
> File "/usr/lib/python2.7/dist-packages/_pytest/capture.py", line 42, in
> pytest_load_initial_conftests
> return __multicall__.execute()
> File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 288, in
> execute
> res = method(**kwargs)
> File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 673, in
> pytest_load_initial_conftests
> self._conftest.setinitial(args)
> File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 486, in
> setinitial
> self._try_load_conftest(anchor)
> File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 492, in
> _try_load_conftest
> self._path2confmods[None] = self.getconftestmodules(anchor)
> File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 511, in
> getconftestmodules
> clist.append(self.importconftest(conftestpath))
> File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 537, in
> importconftest
> self._conftestpath2mod[conftestpath] = mod = conftestpath.pyimport()
> File "/usr/lib/python2.7/dist-packages/py/_path/local.py", line 620, in
> pyimport
> __import__(modname)
> File "/home/justin/Software/firedrake-deps/PyOP2/test/conftest.py", line
> 40, in <module>
> from pyop2 import op2
> File "/home/justin/Software/firedrake-deps/PyOP2/pyop2/__init__.py",
> line 9, in <module>
> from op2 import *
> File "/home/justin/Software/firedrake-deps/PyOP2/pyop2/op2.py", line 39,
> in <module>
> import base
> File "/home/justin/Software/firedrake-deps/PyOP2/pyop2/base.py", line
> 56, in <module>
> from sparsity import build_sparsity
> ImportError: No module named sparsity
> make: *** [unit_sequential] Error 1
>
> This is a different error now. Do you know what the problem is now?
>
> Thanks,
> Justin
>
> On Tue, Jul 14, 2015 at 4:14 AM, Lawrence Mitchell <
> lawrence.mitchell at imperial.ac.uk> wrote:
>
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> On 14/07/15 09:57, Justin Chang wrote:
>> > Hi everyone,
>> >
>> > I am trying to installing firedrake on my Ubuntu machine. Following
>> > the instructions for PyOP2, I get this error when I run "make
>> > test"
>> >
>> > cd test; py.test unit --backend=sequential Segmentation fault (core
>> > dumped) make: *** [unit_sequential] Error 139
>> >
>> > I have installed everything via sudo pip install ... with the
>> > exception of petsc4py which was installed via pip install --user -U
>> > --no-deps ...
>> >
>> > python -c 'from pprint import pprint; import sys; pprint(sys.path)'
>> > gives the following:
>> >
>> > ['', '/usr/lib/python2.7/dist-packages',
>> > '/home/justin/.local/lib/python2.7/site-packages',
>> > '/home/justin/Software/firedrake-deps/PyOP2',
>> > '/home/justin/Software/firedrake-deps/firedrake',
>> > '/home/justin/.local/lib/python2.7/dist-packages',
>> > '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu',
>> > '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old',
>> > '/usr/lib/python2.7/lib-dynload',
>> > '/usr/local/lib/python2.7/dist-packages',
>> > '/usr/lib/python2.7/dist-packages/PILcompat',
>> > '/usr/lib/python2.7/dist-packages/gtk-2.0',
>> > '/usr/lib/pymodules/python2.7',
>> > '/usr/lib/python2.7/dist-packages/ubuntu-sso-client']
>> >
>> > and py.test test/unit -vsx --tb=short --backend=sequential gives
>> > the following:
>> >
>> > [pacotaco-xps:29386] *** Process received signal ***
>> > [pacotaco-xps:29386] Signal: Segmentation fault (11)
>> > [pacotaco-xps:29386] Signal code: Address not mapped (1)
>> > [pacotaco-xps:29386] Failing at address: 0x44000098
>> > [pacotaco-xps:29386] [ 0]
>> > /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7f7eafdd8340]
>> > [pacotaco-xps:29386] [ 1]
>> > /usr/lib/libmpi.so.1(MPI_Comm_set_errhandler+0x4d)
>> > [0x7f7ead7fca1d] [pacotaco-xps:29386] [ 2]
>> >
>> /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libpetsc.so.3.06(PetscInitialize+0x2a7)
>> > [0x7f7e9063f6b6] [pacotaco-xps:29386] [ 3]
>> >
>> /home/justin/.local/lib/python2.7/site-packages/petsc4py/lib/arch-linux2-c-opt/PETSc.so(+0x11d3e8)
>> > [0x7f7e8e33c3e8] [pacotaco-xps:29386] [ 4]
>> > /usr/bin/python(PyEval_EvalFrameEx+0x40d) [0x49968d]
>> > [pacotaco-xps:29386] [ 5] /usr/bin/python(PyEval_EvalCodeEx+0x2ac)
>> > [0x4a090c] [pacotaco-xps:29386] [ 6]
>> > /usr/bin/python(PyEval_EvalCode+0x32) [0x588d42]
>> > [pacotaco-xps:29386] [ 7]
>> > /usr/bin/python(PyImport_ExecCodeModuleEx+0xaa) [0x588dfa]
>> > [pacotaco-xps:29386] [ 8] /usr/bin/python() [0x5b1f0f]
>> > [pacotaco-xps:29386] [ 9] /usr/bin/python() [0x540948]
>> > [pacotaco-xps:29386] [10] /usr/bin/python() [0x540d08]
>> > [pacotaco-xps:29386] [11] /usr/bin/python() [0x541510]
>> > [pacotaco-xps:29386] [12] /usr/bin/python() [0x51dd20]
>> > [pacotaco-xps:29386] [13] /usr/bin/python(PyObject_Call+0x36)
>> > [0x505f96] [pacotaco-xps:29386] [14] /usr/bin/python() [0x536095]
>> > [pacotaco-xps:29386] [15]
>> > /usr/bin/python(PyObject_CallFunction+0xa5) [0x4ca095]
>> > [pacotaco-xps:29386] [16] /usr/bin/python(PyImport_Import+0xdd)
>> > [0x525e8d] [pacotaco-xps:29386] [17]
>> > /home/justin/Software/firedrake-deps/PyOP2/pyop2/sparsity.so(+0x770a)
>> > [0x7f7e915de70a] [pacotaco-xps:29386] [18]
>> >
>> /home/justin/Software/firedrake-deps/PyOP2/pyop2/sparsity.so(initsparsity+0x1244)
>> > [0x7f7e915f91a4] [pacotaco-xps:29386] [19]
>> > /usr/bin/python(_PyImport_LoadDynamicModule+0x9b) [0x42266c]
>> > [pacotaco-xps:29386] [20] /usr/bin/python() [0x540948]
>> > [pacotaco-xps:29386] [21] /usr/bin/python() [0x540d08]
>> > [pacotaco-xps:29386] [22] /usr/bin/python() [0x54111b]
>> > [pacotaco-xps:29386] [23] /usr/bin/python() [0x51dd20]
>> > [pacotaco-xps:29386] [24]
>> > /usr/bin/python(PyEval_CallObjectWithKeywords+0x6b) [0x4dc9cb]
>> > [pacotaco-xps:29386] [25]
>> > /usr/bin/python(PyEval_EvalFrameEx+0x25fe) [0x49b87e]
>> > [pacotaco-xps:29386] [26] /usr/bin/python(PyEval_EvalCodeEx+0x2ac)
>> > [0x4a090c] [pacotaco-xps:29386] [27]
>> > /usr/bin/python(PyEval_EvalCode+0x32) [0x588d42]
>> > [pacotaco-xps:29386] [28]
>> > /usr/bin/python(PyImport_ExecCodeModuleEx+0xaa) [0x588dfa]
>> > [pacotaco-xps:29386] [29] /usr/bin/python() [0x5b1f0f]
>> > [pacotaco-xps:29386] *** End of error message *** Segmentation
>> > fault (core dumped)
>> >
>> > Any idea what's going on?
>>
>> This doesn't immediately look like a PyOP2 related problem. Rather
>> some mismatch between MPI pieces.
>>
>> Does the following work?
>>
>> python -c "import petsc4py; petsc4py.init()"
>>
>> If not, can you compile and run C-based PETSc programs (using the same
>> PETSC_DIR/PETSC_ARCH combo) ?
>>
>> Cheers,
>>
>> Lawrence
>>
>> -----BEGIN PGP SIGNATURE-----
>> Version: GnuPG v1
>>
>> iQEcBAEBAgAGBQJVpNL7AAoJECOc1kQ8PEYvoC4H/iqMGswugo73P8MoJQiHGZ9j
>> IsmvwD2TxXqf52eBWkZ+GEbYjp4p6HTRWARe5/ib9WD+Et6qD3aUeeu5aXNwnEFF
>> PGPeJ4tWD0usYwqzgtY/Rh1g7JfoQxR5fSq9vTpjTFheUHZLUOHEbUz8ZAPE+MQ+
>> Oke+GbQZvg5fm4ddBwrQP8ramPIBnrszs4hG8Jelc+/Dp3950Iyeqd7PhBHGjLtK
>> 0rHzVDWgTodlj6jdCT942BdOQpsEzbDayRXgbt/ivaGDOxPszbWIxHB8k1BvJT2g
>> Y8z6zqB0pQNb05Wi0fcnagHSk/9nOdBREv3wqgqlfO9SYvd7T5uBV9oJwLEfOSw=
>> =hXpq
>> -----END PGP SIGNATURE-----
>>
>> _______________________________________________
>> firedrake mailing list
>> firedrake at imperial.ac.uk
>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>
>
>
-------------- next part --------------
HTML attachment scrubbed and removed
More information about the firedrake
mailing list