[firedrake] problems with notebook

[Francis Poulin]

Hello again,

I was looking over the firedrake notebooks (thanks for putting those together!) and decided to try running the one that involves adjoint.

https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/master/docs/notebooks/example-stokes-bc-control.ipynb

I did install scipy and adjoint, as requested, but get an error when I try plotting u_init


axes = plot(u_init);

The error is copied below.  Is there something else that I need to install for this to work?

Cheers, Francis


---------------------------------------------------------------------------
CompilationError                          Traceback (most recent call last)
<ipython-input-11-ab90b4141777> in <module>()
      1 u_init, p_init = w.split()
----> 2 axes = plot(u_init);
      3 #axes.set_aspect("equal")
      4 #axes.set_title("Velocity")
      5 #axes = plot(p_init)

/home/fpoulin/software/firedrake/src/firedrake/firedrake/plot.pyc in plot(function_or_mesh, num_sample_points, axes, plot3d, **kwargs)
    293             coords = function.ufl_domain().coordinates.dat.data_ro
    294             X, Y = coords.T
--> 295             vals = np.asarray(function.at(coords))
    296             C = np.linalg.norm(vals, axis=1)
    297             U, V = vals.T

/home/fpoulin/software/firedrake/src/firedrake/firedrake/function.pyc in at(self, arg, *args, **kwargs)
    532                 else:
    533                     p_result = np.empty(value_shape, dtype=float)
--> 534                     single_eval(points[i:i+1], p_result)
    535                     l_result.append((i, p_result))
    536             except PointNotInDomainError:

/home/fpoulin/software/firedrake/src/firedrake/firedrake/function.pyc in single_eval(x, buf)
    510         def single_eval(x, buf):
    511             """Helper function to evaluate at a single point."""
--> 512             err = self._c_evaluate(self._ctypes,
    513                                    x.ctypes.data_as(POINTER(c_double)),
    514                                    buf.ctypes.data_as(POINTER(c_double)))

/home/fpoulin/software/firedrake/src/PyOP2/pyop2/utils.pyc in __get__(self, obj, cls)
     62         if obj is None:
     63             return self
---> 64         obj.__dict__[self.__name__] = result = self.fget(obj)
     65         return result
     66

/home/fpoulin/software/firedrake/src/firedrake/firedrake/function.pyc in _c_evaluate(self)
    460     @utils.cached_property
    461     def _c_evaluate(self):
--> 462         result = make_c_evaluate(self)
    463         result.argtypes = [POINTER(_CFunction), POINTER(c_double), POINTER(c_double)]
    464         result.restype = c_int

/home/fpoulin/software/firedrake/src/firedrake/firedrake/function.pyc in make_c_evaluate(function, c_name, ldargs)
    610                             ["-I%s/include" % d for d in get_petsc_dir()],
    611                             ldargs=ldargs,
--> 612                             comm=function.comm)

/home/fpoulin/software/firedrake/src/PyOP2/pyop2/compilation.pyc in load(src, extension, fn_name, cppargs, ldargs, argtypes, restype, compiler, comm)
    328         raise CompilationError("Don't know what compiler to use for platform '%s'" %
    329                                platform)
--> 330     dll = compiler.get_so(src, extension)
    331
    332     fn = getattr(dll, fn_name)

/home/fpoulin/software/firedrake/src/PyOP2/pyop2/compilation.pyc in get_so(self, src, extension)
    166 Unable to compile code
    167 Compile log in %s
--> 168 Compile errors in %s""" % (e.cmd, e.returncode, logfile, errfile))
    169                     else:
    170                         cc = [self._cc] + self._cppargs + \

CompilationError: Command "['mpicc', '-std=c99', '-fPIC', '-Wall', '-march=native', '-O3', '-fno-ivopts', '-I/home/fpoulin/software/firedrake/src/firedrake/firedrake', '-I/usr/include', '-I/home/fpoulin/software/firedrake/lib/python2.7/site-packages/petsc/include', '-o', '/tmp/pyop2-cache-uid1000/7137338dc043a2dcfd35bcc4ecc64e90_p6844.so.tmp', '/tmp/pyop2-cache-uid1000/7137338dc043a2dcfd35bcc4ecc64e90_p6844.c', '-shared', '-L/usr/lib', '-lspatialindex_c', '-Wl,-rpath,/usr/lib']" return error status 1.
Unable to compile code
Compile log in /tmp/pyop2-cache-uid1000/7137338dc043a2dcfd35bcc4ecc64e90_p6844.log
Compile errors in /tmp/pyop2-cache-uid1000/7137338dc043a2dcfd35bcc4ecc64e90_p6844.err



------------------
Francis Poulin
Associate Professor
Department of Applied Mathematics
University of Waterloo

email:           fpoulin at uwaterloo.ca
Web:            https://uwaterloo.ca/poulin-research-group/
Telephone:  +1 519 888 4567 x32637

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