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@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

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