Hi,
I have installed firedrake under Windows Subsystem Linux (Ubuntu 18.04). I get the following error and segmentation fault. Kindly, could you let me know what the instructions are?
Thanks
Jagir
firedrake:WARNING Your kernel body contains a double indirection.
You should update it to single indirections.
Mail firedrake@imperial.ac.uk for advice.
firedrake:WARNING Your kernel body contains a double indirection.
You should update it to single indirections.
Mail firedrake@imperial.ac.uk for advice.
Traceback (most recent call last):
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/caching.py", line 197, in __new__
return cls._cache_lookup(key)
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/caching.py", line 205, in _cache_lookup
return cls._cache[key]
KeyError: ('c9930cddd7d7e4db4562d4b34b0960db', <class 'pyop2.base.Set'>, False, False, True, <class 'pyop2.base.Arg'>, Access('WRITE'), (<class 'pyop2.petsc_base.Dat'>, dtype('float64'), (<class 'pyop2.petsc_base.DataSet'>,
(1,), (<class 'pyop2.base.Set'>,))), ((<class 'pyop2.base.Map'>, 1, None),), False, 0, None, <class 'pyop2.sequential.JITModule'>, 4)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/compilation.py", line 263, in get_so
return ctypes.CDLL(soname)
File "/usr/lib/python3.6/ctypes/__init__.py", line 348, in __init__
self._handle = _dlopen(self._name, mode)
OSError: /home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b.so: cannot open shared object file: No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/compilation.py", line 293, in get_so
stdout=log)
File "/usr/lib/python3.6/subprocess.py", line 291, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['mpicc', '-std=c99', '-fPIC', '-Wall', '-march=native', '-O3', '-ffast-math', '-I/home/ftest/firedrake/firedrake/lib/python3.6/site-packages/petsc/include', '-I/home/ftest/firedrake/firedrake/src/PyOP2/pyop2',
'-o', '/home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b_p524.so.tmp', '/home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b_p524.c', '-shared', '-L/home/ftest/firedrake/firedrake/lib/python3.6/site-packages/petsc/lib',
'-Wl,-rpath,/home/ftest/firedrake/firedrake/lib/python3.6/site-packages/petsc/lib', '-lpetsc', '-lm']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "start_computation.py", line 12, in <module>
fn.time_evolution(parameters.parameters)
File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/functions.py", line 88, in time_evolution
CS = coupled_system.CoupledSystem(prm)
File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/coupled_system.py", line 25, in __init__
self.W = water_mixed.Water_mixed( self.mesh, **parameters )
File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/water_mixed.py", line 13, in __init__
super(Water_mixed, self).__init__(**kwargs)
File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/water.py", line 28, in __init__
self.initialize()
File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/water_mixed.py", line 19, in initialize
self.beyond_fluid_BCs()
File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/water_mixed.py", line 57, in beyond_fluid_BCs
self.BC_exclude_beyond_fluid = MyBC( self.V, 0, self.I_cg )
File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/water_mixed.py", line 53, in __init__
self.nodes = np.unique(np.where(markers.dat.data_ro_with_halos == 0)[0])
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/base.py", line 1683, in data_ro_with_halos
_trace.evaluate(set([self]), set())
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/base.py", line 192, in evaluate
comp._run()
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/base.py", line 3740, in _run
return self.compute()
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/base.py", line 3786, in compute
fun = self._jitmodule
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/utils.py", line 62, in __get__
obj.__dict__[self.__name__] = result = self.fget(obj)
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/sequential.py", line 207, in _jitmodule
pass_layer_arg=self._pass_layer_arg)
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/caching.py", line 199, in __new__
obj = make_obj()
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/caching.py", line 189, in make_obj
obj.__init__(*args, **kwargs)
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/sequential.py", line 101, in __init__
self.compile()
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/sequential.py", line 159, in compile
comm=self.comm)
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/compilation.py", line 475, in load
dll = compiler.get_so(code, extension)
File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/compilation.py", line 299, in get_so
Compile errors in %s""" % (e.cmd, e.returncode, logfile, errfile))
pyop2.exceptions.CompilationError: Command "['mpicc', '-std=c99', '-fPIC', '-Wall', '-march=native', '-O3', '-ffast-math', '-I/home/ftest/firedrake/firedrake/lib/python3.6/site-packages/petsc/include', '-I/home/ftest/firedrake/firedrake/src/PyOP2/pyop2',
'-o', '/home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b_p524.so.tmp', '/home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b_p524.c', '-shared', '-L/home/ftest/firedrake/firedrake/lib/python3.6/site-packages/petsc/lib',
'-Wl,-rpath,/home/ftest/firedrake/firedrake/lib/python3.6/site-packages/petsc/lib', '-lpetsc', '-lm']" return error status 1.
Unable to compile code
Compile log in /home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b_p524.log
Compile errors in /home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b_p524.err