[firedrake] error installing PyOP2
Justin Chang
jychang48 at gmail.com
Tue Jul 14 11:04:48 BST 2015
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
>
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