Hi every one
Ihave installed fenics with anaconda. but when i use Fonctionspace, in jupyter notebook,
i have this error:
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Moving new file over differing existing file:
src: /home/sambou/Documents/jitfailure-ffc_element_2a4ec0e3cf61cfa91bc23fa17689ebd036afdff2/error.log.398d84c0e48b427d9f7119e8e3186c6d
dst: /home/sambou/Documents/jitfailure-ffc_element_2a4ec0e3cf61cfa91bc23fa17689ebd036afdff2/error.log
backup: /home/sambou/Documents/jitfailure-ffc_element_2a4ec0e3cf61cfa91bc23fa17689ebd036afdff2/error.log.old
Backup file exists, overwriting.
------------------- Start compiler output ------------------------
In file included from /home/sambou/anaconda3/envs/fenicsproject/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/sys/types.h:136:0,
from /home/sambou/anaconda3/envs/fenicsproject/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/stdlib.h:320,
from /home/sambou/anaconda3/envs/fenicsproject/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cstdlib:75,
from /home/sambou/anaconda3/envs/fenicsproject/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/stl_algo.h:59,
from /home/sambou/anaconda3/envs/fenicsproject/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/algorithm:62,
from /tmp/tmpzkc83y_i/ffc_element_2a4ec0e3cf61cfa91bc23fa17689ebd036afdff2.h:31,
from /tmp/tmpzkc83y_i/ffc_element_2a4ec0e3cf61cfa91bc23fa17689ebd036afdff2.cpp:29:
/usr/include/time.h:37:10: fatal error: bits/types/clock_t.h: No such file or directory
#include <bits/types/clock_t.h>
^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
------------------- End compiler output ------------------------
Compilation failed! Sources, command, and errors have been written to: /home/sambou/Documents/jitfailure-ffc_element_2a4ec0e3cf61cfa91bc23fa17689ebd036afdff2
DijitsoError Traceback (most recent call last)
in
----> 1 W = FunctionSpace(mesh, TH)
/usr/lib/python3/dist-packages/dolfin/function/functionspace.py in init(self, *args, **kwargs)
29 pass
30 elif len(args) == 2:
—> 31 self._init_from_ufl(*args, **kwargs)
32 else:
33 self._init_convenience(*args, **kwargs)
/usr/lib/python3/dist-packages/dolfin/function/functionspace.py in _init_from_ufl(self, mesh, element, constrained_domain)
41 # Compile dofmap and element
42 ufc_element, ufc_dofmap = ffc_jit(element, form_compiler_parameters=None,
—> 43 mpi_comm=mesh.mpi_comm())
44 ufc_element = cpp.fem.make_ufc_finite_element(ufc_element)
45
/usr/lib/python3/dist-packages/dolfin/jit/jit.py in mpi_jit(*args, **kwargs)
45 # Just call JIT compiler when running in serial
46 if MPI.size(mpi_comm) == 1:
—> 47 return local_jit(*args, **kwargs)
48
49 # Default status (0 == ok, 1 == fail)
/usr/lib/python3/dist-packages/dolfin/jit/jit.py in ffc_jit(ufl_form, form_compiler_parameters)
95 p.update(dict(parameters[“form_compiler”]))
96 p.update(form_compiler_parameters or {})
—> 97 return ffc.jit(ufl_form, parameters=p)
98
99
/usr/lib/python3/dist-packages/ffc/jitcompiler.py in jit(ufl_object, parameters, indirect)
215
216 # Inspect cache and generate+build if necessary
–> 217 module = jit_build(ufl_object, module_name, parameters)
218
219 # Raise exception on failure to build or import module
/usr/lib/python3/dist-packages/ffc/jitcompiler.py in jit_build(ufl_object, module_name, parameters)
131 name=module_name,
132 params=params,
–> 133 generate=jit_generate)
134 return module
135
/usr/lib/python3/dist-packages/dijitso/jit.py in jit(jitable, name, params, generate, send, receive, wait)
163 elif generate:
164 # 1) Generate source code
–> 165 header, source, dependencies = generate(jitable, name, signature, params[“generator”])
166 # Ensure we got unicode from generate
167 header = as_unicode(header)
/usr/lib/python3/dist-packages/ffc/jitcompiler.py in jit_generate(ufl_object, module_name, signature, parameters)
74 dependencies = []
75 for dep in dependent_ufl_objects[“element”]:
—> 76 dep_module_name = jit(dep, parameters, indirect=True)
77 dependencies.append(dep_module_name)
78 for dep in dependent_ufl_objects[“coordinate_mapping”]:
/usr/lib/python3/dist-packages/ffc/jitcompiler.py in jit(ufl_object, parameters, indirect)
215
216 # Inspect cache and generate+build if necessary
–> 217 module = jit_build(ufl_object, module_name, parameters)
218
219 # Raise exception on failure to build or import module
/usr/lib/python3/dist-packages/ffc/jitcompiler.py in jit_build(ufl_object, module_name, parameters)
131 name=module_name,
132 params=params,
–> 133 generate=jit_generate)
134 return module
135
/usr/lib/python3/dist-packages/dijitso/jit.py in jit(jitable, name, params, generate, send, receive, wait)
215 # TODO: Parse output to find error(s) for better error messages
216 raise DijitsoError(“Dijitso JIT compilation failed, see ‘%s’ for details”
–> 217 % err_info[‘fail_dir’], err_info)
218
219 # Return built library and its signature
DijitsoError: Dijitso JIT compilation failed, see ‘/home/sambou/Documents/jitfailure-ffc_element_2a4ec0e3cf61cfa91bc23fa17689ebd036afdff2’ for details