So I have some follow-up issues, maybe because there are some dependencies and FEnics is not able to detect. I am getting the following error
`cylinder in cross-flow mesh has been created
meshcells 176360
Moving new file over differing existing file:
src: /home/nanand/source/FEniCSLab_Arthur/work/cylinder_cross_flow/jitfailure-dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f/error.log.a3d3a4f1b6d849d397366cb94925a5e1
dst: /home/nanand/source/FEniCSLab_Arthur/work/cylinder_cross_flow/jitfailure-dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f/error.log
backup: /home/nanand/source/FEniCSLab_Arthur/work/cylinder_cross_flow/jitfailure-dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f/error.log.old
Backup file exists, overwriting.
------------------- Start compiler output ------------------------
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp: In member function ‘void dolfin::FilterWindow::set_ref_point(Eigen::Ref<const Eigen::Matrix<double, -1, 1> >)’:
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:213:16: warning: comparison of integer expressions of different signedness: ‘Eigen::EigenBase<Eigen::Ref<const Eigen::Matrix<double, -1, 1> > >::Index’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
213 | if(znew.size()<=_gdim){
| ~^
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:214:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Ref<const Eigen::Matrix<double, -1, 1> > >::Index’ {aka ‘long int’} [-Wsign-compare]
214 | for (std::size_t i = 0; i < znew.size(); i++){
| ^
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp: In member function ‘virtual void dolfin::DoubleBoxAverage::eval(Eigen::Ref<Eigen::Matrix<double, -1, 1> >, Eigen::Ref<const Eigen::Matrix<double, -1, 1> >) const’:
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:741:10: warning: unused variable ‘y2’ [-Wunused-variable]
741 | double y2 = x[2] - z[2];
| ^~
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp: At global scope:
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:3409:8: error: ‘void filterformtrianglecg1_cell_integral_0_1::tabulate_tensor(double*, const double* const*, const double*, int) const’ marked ‘final’, but is not virtual
3409 | void tabulate_tensor(double * A,
| ^~~~~~~~~~~~~~~
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:3409:8: error: ‘void filterformtrianglecg1_cell_integral_0_1::tabulate_tensor(double*, const double* const*, const double*, int) const’ marked ‘override’, but does not override
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp: In member function ‘virtual ufc::cell_integral* filterformtrianglecg1_form_0::create_cell_integral(std::size_t) const’:
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:3642:60: error: invalid new-expression of abstract class type ‘filterformtrianglecg1_cell_integral_0_1’
3642 | return new filterformtrianglecg1_cell_integral_0_1();
| ^
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:3389:7: note: because the following virtual functions are pure within ‘filterformtrianglecg1_cell_integral_0_1’:
3389 | class filterformtrianglecg1_cell_integral_0_1: public ufc::cell_integral
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/dolfin/function/Expression.h:25,
from /tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:426:
/usr/lib/python3/dist-packages/ffc/backends/ufc/ufc.h:607:18: note: ‘virtual void ufc::cell_integral::tabulate_tensor(double*, const double* const*, const double*, int, std::size_t) const’
607 | virtual void tabulate_tensor(double * A,
| ^~~~~~~~~~~~~~~
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp: At global scope:
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:8157:8: error: ‘void filterformtrianglecg2_cell_integral_0_1::tabulate_tensor(double*, const double* const*, const double*, int) const’ marked ‘final’, but is not virtual
8157 | void tabulate_tensor(double * A,
| ^~~~~~~~~~~~~~~
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:8157:8: error: ‘void filterformtrianglecg2_cell_integral_0_1::tabulate_tensor(double*, const double* const*, const double*, int) const’ marked ‘override’, but does not override
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp: In member function ‘virtual ufc::cell_integral* filterformtrianglecg2_form_0::create_cell_integral(std::size_t) const’:
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:8393:60: error: invalid new-expression of abstract class type ‘filterformtrianglecg2_cell_integral_0_1’
8393 | return new filterformtrianglecg2_cell_integral_0_1();
| ^
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:8137:7: note: because the following virtual functions are pure within ‘filterformtrianglecg2_cell_integral_0_1’:
8137 | class filterformtrianglecg2_cell_integral_0_1: public ufc::cell_integral
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/dolfin/function/Expression.h:25,
from /tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:426:
/usr/lib/python3/dist-packages/ffc/backends/ufc/ufc.h:607:18: note: ‘virtual void ufc::cell_integral::tabulate_tensor(double*, const double* const*, const double*, int, std::size_t) const’
607 | virtual void tabulate_tensor(double * A,
| ^~~~~~~~~~~~~~~
In file included from /tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:8843:
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTriangleDG0.h: At global scope:
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTriangleDG0.h:3123:8: error: ‘void filterformtriangledg0_cell_integral_0_1::tabulate_tensor(double*, const double* const*, const double*, int) const’ marked ‘final’, but is not virtual
3123 | void tabulate_tensor(double * A,
| ^~~~~~~~~~~~~~~
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTriangleDG0.h:3123:8: error: ‘void filterformtriangledg0_cell_integral_0_1::tabulate_tensor(double*, const double* const*, const double*, int) const’ marked ‘override’, but does not override
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTriangleDG0.h: In member function ‘virtual ufc::cell_integral* filterformtriangledg0_form_0::create_cell_integral(std::size_t) const’:
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTriangleDG0.h:3343:60: error: invalid new-expression of abstract class type ‘filterformtriangledg0_cell_integral_0_1’
3343 | return new filterformtriangledg0_cell_integral_0_1();
| ^
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTriangleDG0.h:3103:7: note: because the following virtual functions are pure within ‘filterformtriangledg0_cell_integral_0_1’:
3103 | class filterformtriangledg0_cell_integral_0_1: public ufc::cell_integral
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/dolfin/function/Expression.h:25,
from /tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:426:
/usr/lib/python3/dist-packages/ffc/backends/ufc/ufc.h:607:18: note: ‘virtual void ufc::cell_integral::tabulate_tensor(double*, const double* const*, const double*, int, std::size_t) const’
607 | virtual void tabulate_tensor(double * A,
| ^~~~~~~~~~~~~~~
In file included from /tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:8846:
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronDG0.h: At global scope:
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronDG0.h:4612:8: error: ‘void filterformtetrahedrondg0_cell_integral_0_1::tabulate_tensor(double*, const double* const*, const double*, int) const’ marked ‘final’, but is not virtual
4612 | void tabulate_tensor(double * A,
| ^~~~~~~~~~~~~~~
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronDG0.h:4612:8: error: ‘void filterformtetrahedrondg0_cell_integral_0_1::tabulate_tensor(double*, const double* const*, const double*, int) const’ marked ‘override’, but does not override
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronDG0.h: In member function ‘virtual ufc::cell_integral* filterformtetrahedrondg0_form_0::create_cell_integral(std::size_t) const’:
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronDG0.h:4848:63: error: invalid new-expression of abstract class type ‘filterformtetrahedrondg0_cell_integral_0_1’
4848 | return new filterformtetrahedrondg0_cell_integral_0_1();
| ^
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronDG0.h:4592:7: note: because the following virtual functions are pure within ‘filterformtetrahedrondg0_cell_integral_0_1’:
4592 | class filterformtetrahedrondg0_cell_integral_0_1: public ufc::cell_integral
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/dolfin/function/Expression.h:25,
from /tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:426:
/usr/lib/python3/dist-packages/ffc/backends/ufc/ufc.h:607:18: note: ‘virtual void ufc::cell_integral::tabulate_tensor(double*, const double* const*, const double*, int, std::size_t) const’
607 | virtual void tabulate_tensor(double * A,
| ^~~~~~~~~~~~~~~
In file included from /tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:8847:
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronCG1.h: At global scope:
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronCG1.h:4116:8: error: ‘void filterformtetrahedroncg1_cell_integral_0_1::tabulate_tensor(double*, const double* const*, const double*, int) const’ marked ‘final’, but is not virtual
4116 | void tabulate_tensor(double * A,
| ^~~~~~~~~~~~~~~
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronCG1.h:4116:8: error: ‘void filterformtetrahedroncg1_cell_integral_0_1::tabulate_tensor(double*, const double* const*, const double*, int) const’ marked ‘override’, but does not override
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronCG1.h: In member function ‘virtual ufc::cell_integral* filterformtetrahedroncg1_form_0::create_cell_integral(std::size_t) const’:
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronCG1.h:4366:63: error: invalid new-expression of abstract class type ‘filterformtetrahedroncg1_cell_integral_0_1’
4366 | return new filterformtetrahedroncg1_cell_integral_0_1();
| ^
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronCG1.h:4096:7: note: because the following virtual functions are pure within ‘filterformtetrahedroncg1_cell_integral_0_1’:
4096 | class filterformtetrahedroncg1_cell_integral_0_1: public ufc::cell_integral
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/dolfin/function/Expression.h:25,
from /tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:426:
/usr/lib/python3/dist-packages/ffc/backends/ufc/ufc.h:607:18: note: ‘virtual void ufc::cell_integral::tabulate_tensor(double*, const double* const*, const double*, int, std::size_t) const’
607 | virtual void tabulate_tensor(double * A,
| ^~~~~~~~~~~~~~~
In file included from /tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:8848:
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronCG2.h: At global scope:
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronCG2.h:4116:8: error: ‘void filterformtetrahedroncg2_cell_integral_0_1::tabulate_tensor(double*, const double* const*, const double*, int) const’ marked ‘final’, but is not virtual
4116 | void tabulate_tensor(double * A,
| ^~~~~~~~~~~~~~~
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronCG2.h:4116:8: error: ‘void filterformtetrahedroncg2_cell_integral_0_1::tabulate_tensor(double*, const double* const*, const double*, int) const’ marked ‘override’, but does not override
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronCG2.h: In member function ‘virtual ufc::cell_integral* filterformtetrahedroncg2_form_0::create_cell_integral(std::size_t) const’:
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronCG2.h:4366:63: error: invalid new-expression of abstract class type ‘filterformtetrahedroncg2_cell_integral_0_1’
4366 | return new filterformtetrahedroncg2_cell_integral_0_1();
| ^
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/Filter/FilterFormTetrahedronCG2.h:4096:7: note: because the following virtual functions are pure within ‘filterformtetrahedroncg2_cell_integral_0_1’:
4096 | class filterformtetrahedroncg2_cell_integral_0_1: public ufc::cell_integral
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/dolfin/function/Expression.h:25,
from /tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:426:
/usr/lib/python3/dist-packages/ffc/backends/ufc/ufc.h:607:18: note: ‘virtual void ufc::cell_integral::tabulate_tensor(double*, const double* const*, const double*, int, std::size_t) const’
607 | virtual void tabulate_tensor(double * A,
| ^~~~~~~~~~~~~~~
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp: In lambda function:
/tmp/tmp4wa23a1g/dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f.cpp:9318:4: warning: control reaches end of non-void function [-Wreturn-type]
9318 | }))
| ^
------------------- End compiler output ------------------------
Compilation failed! Sources, command, and errors have been written to: /home/nanand/source/FEniCSLab_Arthur/work/cylinder_cross_flow/jitfailure-dolfin_cpp_module_1b6a5de17bcd8bde62970d7c62135a7f
/home/nanand/source/FEniCSLab_Arthur/fenicslab/filters/init.py:6: UserWarning: filters/Filter/BoxFilterWindow/BoxAverage/CompiledDoubleBoxAverage not installed
warnings.warn(“filters/Filter/BoxFilterWindow/BoxAverage/CompiledDoubleBoxAverage not installed”)
/home/nanand/source/FEniCSLab_Arthur/fenicslab/fenicstools/init.py:7: UserWarning: Probe/Probes/StatisticsProbe/StatisticsProbes not installed
warnings.warn(“Probe/Probes/StatisticsProbe/StatisticsProbes not installed”)
/home/nanand/source/FEniCSLab_Arthur/fenicslab/fenicstools/init.py:13: UserWarning: interpolate_nonmatching_mesh/interpolate_nonmatching_mesh_any not installed
warnings.warn(“interpolate_nonmatching_mesh/interpolate_nonmatching_mesh_any not installed”)
Traceback (most recent call last):
File “solveCasedef.py”, line 6, in
from generateCasedef import mycasedef
File “/home/nanand/source/FEniCSLab_Arthur/work/cylinder_cross_flow/generateCasedef.py”, line 10, in
from fenicslab.common.distributions import nu_expression
File “/home/nanand/source/FEniCSLab_Arthur/fenicslab/common/distributions.py”, line 52, in
nu_expression = compile_cpp_code(viscositycode).Viscosity()
File “/usr/lib/petsc/lib/python3/dist-packages/dolfin/jit/pybind11jit.py”, line 95, in compile_cpp_code
module, signature = dijitso_jit(cpp_code, module_name, params,
File “/usr/lib/petsc/lib/python3/dist-packages/dolfin/jit/jit.py”, line 50, in mpi_jit
return local_jit(*args, **kwargs)
File “/usr/lib/petsc/lib/python3/dist-packages/dolfin/jit/jit.py”, line 106, in dijitso_jit
return dijitso.jit(*args, **kwargs)
File “/usr/lib/python3/dist-packages/dijitso/jit.py”, line 153, in jit
lib = lookup_lib(signature, cache_params)
File “/usr/lib/python3/dist-packages/dijitso/cache.py”, line 391, in lookup_lib
lib = load_library(lib_signature, cache_params)
File “/usr/lib/python3/dist-packages/dijitso/cache.py”, line 363, in load_library
lib = import(signature)
ImportError: libpetsc.so.3.11: cannot open shared object file: No such file or directory`
I have eigen installed, also the libpetsc.so.3.11 is available in the dist-package/petsc/ folder. So I am a bit lost so as to what is actually going wrong.
Obviosuly, I have done this already…
sudo apt-get install --no-install-recommends software-properties-common sudo add-apt-repository ppa:fenics-packages/fenics sudo apt-get update sudo apt-get install --no-install-recommends fenics
Any lead will be appreciated @dparsons !
