running a code


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7 months ago by
Hi There
I am trying to run below code via docker in win7. but there is several error:

http://www.ifm.tuberlin.de/fileadmin/fg49/CompReal/supply/Abali_2015_Supply_Code_of_Strain_gradient_elasticity_with_geometric_nonlinearities.py



Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
--- Instant: compiling ---
--- Instant: compiling ---
Notation dx[meshfunction] is deprecated. Please use dx(subdomain_data=meshfuncti
on) instead.
Notation dx[meshfunction] is deprecated. Please use dx(subdomain_data=meshfuncti
on) instead.
--- Instant: compiling ---
time 0.2
Calling FFC just-in-time (JIT) compiler, this may take some time.
Ignoring precision in integral metadata compiled using quadrature representati
on. Not implemented.
Ignoring precision in integral metadata compiled using quadrature representati
on. Not implemented.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
/usr/local/lib/python3.5/dist-packages/ffc/quadrature/quadraturerepresentation.p
y:59: QuadratureRepresentationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
/usr/local/lib/python3.5/dist-packages/ffc/quadrature/quadraturerepresentation.p
y:59: QuadratureRepresentationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
------------------- Start compiler output ------------------------
c++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-5/README.Bugs> for instructions.

------------------- End compiler output ------------------------
Compilation failed! Sources, command, and errors have been written to: /home/fen
ics/shared/jitfailure-ffc_element_ec694fc2ff0bf3bb1faee89b545d26f1a31824a3
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/jit.py", line 142,
in jit
result = ffc.jit(ufl_object, parameters=p)
File "/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py", line 218, in
jit
module = jit_build(ufl_object, module_name, parameters)
File "/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py", line 134, in
jit_build
generate=jit_generate)
File "/usr/local/lib/python3.5/dist-packages/dijitso/jit.py", line 167, in jit
header, source, dependencies = generate(jitable, name, signature, params["ge
nerator"])
File "/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py", line 77, in
jit_generate
dep_module_name = jit(dep, parameters, indirect=True)
File "/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py", line 218, in
jit
module = jit_build(ufl_object, module_name, parameters)
File "/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py", line 134, in
jit_build
generate=jit_generate)
File "/usr/local/lib/python3.5/dist-packages/dijitso/jit.py", line 219, in jit
% err_info['fail_dir'], err_info)
dijitso.jit.DijitsoError: Dijitso JIT compilation failed, see '/home/fenics/shar
ed/jitfailure-ffc_element_ec694fc2ff0bf3bb1faee89b545d26f1a31824a3' for details

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "Abali.py", line 155, in <module>
u, plotu_norm, plotu, plotx_norm, plotx, E_ = compute(xlength,ylength,zlengt
h,mesh,F,alpha,beta,gamma,'shear')
File "Abali.py", line 121, in compute
form_compiler_parameters={"cpp_optimize": True, "representation": "quadratur
e", "quadrature_degree": 2} )
File "/usr/lib/python3/dist-packages/dolfin/fem/solving.py", line 300, in solv
e
_solve_varproblem(*args, **kwargs)
File "/usr/lib/python3/dist-packages/dolfin/fem/solving.py", line 344, in _sol
ve_varproblem
form_compiler_parameters=form_compiler_parameters)
File "/usr/lib/python3/dist-packages/dolfin/fem/solving.py", line 149, in __in
it__
F = Form(F, form_compiler_parameters=form_compiler_parameters)
File "/usr/lib/python3/dist-packages/dolfin/fem/form.py", line 92, in __init__
mpi_comm=mesh.mpi_comm())
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/jit.py", line 70, i
n mpi_jit
return local_jit(*args, **kwargs)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/jit.py", line 147,
in jit
"ffc.jit failed with message:\n%s" % (tb_text,))
File "/usr/lib/python3/dist-packages/dolfin/cpp/common.py", line 2739, in dolf
in_error
return _common.dolfin_error(location, task, reason)
RuntimeError:

*** -------------------------------------------------------------------------
*** DOLFIN encountered an error. If you are not able to resolve this issue
*** using the information listed below, you can ask for help at
***
*** fenics-support@googlegroups.com
***
*** Remember to include the error message listed below and, if possible,
*** include a *minimal* running example to reproduce the error.
***
*** -------------------------------------------------------------------------
*** Error: Unable to perform just-in-time compilation of form.
*** Reason: ffc.jit failed with message:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/jit.py", line 142,
in jit
result = ffc.jit(ufl_object, parameters=p)
File "/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py", line 218, in
jit
module = jit_build(ufl_object, module_name, parameters)
File "/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py", line 134, in
jit_build
generate=jit_generate)
File "/usr/local/lib/python3.5/dist-packages/dijitso/jit.py", line 167, in jit
header, source, dependencies = generate(jitable, name, signature, params["ge
nerator"])
File "/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py", line 77, in
jit_generate
dep_module_name = jit(dep, parameters, indirect=True)
File "/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py", line 218, in
jit
module = jit_build(ufl_object, module_name, parameters)
File "/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py", line 134, in
jit_build
generate=jit_generate)
File "/usr/local/lib/python3.5/dist-packages/dijitso/jit.py", line 219, in jit
5.386570e-316rr_info['fail_dir'], err_info)
dijitso.jit.DijitsoError: Dijitso JIT compilation failed, see '/home/fenics/shar
ed/jitfailure-ffc_element_ec694fc2ff0bf3bb1faee89b545d26f1a31824a3' for details
.
*** Where: This error was encountered inside jit.py.
*** Process: 0
***
*** DOLFIN version: 2017.2.0
*** Git changeset: 0baf73825079a581e43ab1705370043040aa213d
*** -------------------------------------------------------------------------
Community: FEniCS Project
2
to install FEniCS stable 1.6.0 in docker you can use the following command:-

docker run -ti -v $(pwd):/home/fenics/shared quay.io/fenicsproject/stable:1.6.0
written 7 months ago by Ovais  
Hi Thanks. But there are errors still abut FFC: quadrature representation is deprecated! It will:

-----------------------------shear
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
--- Instant: compiling ---
--- Instant: compiling ---
Notation dx[meshfunction] is deprecated. Please use dx(subdomain_data=meshfuncti
on) instead.
Notation dx[meshfunction] is deprecated. Please use dx(subdomain_data=meshfuncti
on) instead.
--- Instant: compiling ---
time 0.2
Calling FFC just-in-time (JIT) compiler, this may take some time.
/usr/local/lib/python3.5/dist-packages/ffc/quadrature/quadraturerepresentation.p
y:59: QuadratureRepresentationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
/usr/local/lib/python3.5/dist-packages/ffc/quadrature/quadraturerepresentation.p
y:59: QuadratureRepresentationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
Ignoring precision in integral metadata compiled using quadrature representati
on. Not implemented.
Ignoring precision in integral metadata compiled using quadrature representati
on. Not implemented.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py:235: QuadratureReprese
ntationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
Calling FFC just-in-time (JIT) compiler, this may take some time.
/usr/local/lib/python3.5/dist-packages/ffc/quadrature/quadraturerepresentation.p
y:59: QuadratureRepresentationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
Ignoring precision in integral metadata compiled using quadrature representati
on. Not implemented.
/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py:235: QuadratureReprese
ntationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
time 0.4
/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py:235: QuadratureReprese
ntationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py:235: QuadratureReprese
ntationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
time 0.6000000000000001
/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py:235: QuadratureReprese
ntationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py:235: QuadratureReprese
ntationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
time 0.8
/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py:235: QuadratureReprese
ntationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py:235: QuadratureReprese
ntationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
time 1.0
/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py:235: QuadratureReprese
ntationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py:235: QuadratureReprese
ntationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
shear displacement: 0.0498778982343
181.687852045 sec
Notation dx[meshfunction] is deprecated. Please use dx(subdomain_data=meshfuncti
on) instead.
Notation dx[meshfunction] is deprecated. Please use dx(subdomain_data=meshfuncti
on) instead.
time 0.2
Calling FFC just-in-time (JIT) compiler, this may take some time.
/usr/local/lib/python3.5/dist-packages/ffc/quadrature/quadraturerepresentation.p
y:59: QuadratureRepresentationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
/usr/local/lib/python3.5/dist-packages/ffc/quadrature/quadraturerepresentation.p
y:59: QuadratureRepresentationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
Ignoring precision in integral metadata compiled using quadrature representati
on. Not implemented.
Ignoring precision in integral metadata compiled using quadrature representati
on. Not implemented.
/usr/local/lib/python3.5/dist-packages/ffc/jitcompiler.py:235: QuadratureReprese
ntationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
Calling FFC just-in-time (JIT) compiler, this may take some time.
/usr/local/lib/python3.5/dist-packages/ffc/quadrature/quadraturerepresentation.p
y:59: QuadratureRepresentationDeprecationWarning:
*** ===================================================== ***
*** FFC: quadrature representation is deprecated! It will ***
*** likely be removed in 2018.1.0 release. Use uflacs ***
*** representation instead. ***
*** ===================================================== ***
issue_deprecation_warning()
Ignoring precision in integral metadata compiled using quadrature representati
on. Not implemented.
Killed
fenics@7e45aa3c83de:~/shared$
written 7 months ago by MMZ1992  
Note: Answers should respond to the original question at the top of this page.

Use the comments to discuss the post, ask for clarifications, request more information.
written 7 months ago by Jan Blechta  
-1
I am using docker on windows 7. These errors will not occur in FEniCS version of 2016. The code runs till end. To install FEnics version through which you would be able to run the code ... consult this web page , install the stable version of 2016 and then ammend the code.

Here is the link : https://bitbucket.org/fenics-project/docker


written 7 months ago by Ovais  
Note: Answers should respond to the original question at the top of this page.

Use the comments to discuss the post, ask for clarifications, request more information.
written 7 months ago by Jan Blechta  

1 Answer


2
7 months ago by
Ovais  
I have tried running the code in FEniCS stable 1.6.0. You can run the code  after following changes:-


line 35: mesh = BoxMesh(Point(0, -ylength/2., -zlength/2.), Point(xlength,ylength/2.,zlength/2.), 30*non,1*non,1*non)

line 26: #pwd = '/calcul/straingrad09/'    
(you dont need this unless you want your output to be saved at this specific path)

line: 176,182,188,194,204,210,216,222,232,239,246 and 252 (instead of previous , change to the following)
file_u = File('displ_tensile_0_0_1_.pvd')     
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