Hello Roshan Suresh Kumar,
Thanks for the report. This problem started appearing a few weeks ago. It occurs only on some platforms and not always. I suspect a multiprocessing package related problem - sometimes the example hangs on a poll function there, but there might be another issue. We are looking into that.
r.
On 9/5/19 4:48 AM, Roshan Suresh Kumar wrote:
Hi,
During my installation of the latest version of sfepy from source (GitHub repo) in Windows, I ran the command to test the various modules. I found that one test had failed, the one for test_homogenization_perfusion.py. I ran the test in raise mode and the output is show below.
P.S.: I installed all of the optional dependencies except igakit, petsc4py, slepc4py, pymetis, scikits.umfpack and pysparse.
I hope this helps. Let me know if you need any other details.
Thanks. Roshan Suresh Kumar
<<< directory: tests, test files: 1 <<< [1] tests\test_homogenization_perfusion.py [1] sfepy: left over: ['__name__', '__doc__', '__package__', '__loader__', '__spec__', '__file__', '__cached__', '__builtins__', 'print_function', 'absolute_import', 'six', 'input_name', 'TestCommon', 'verbose', '_filename']
test instance prepared (1 test(s)) run_tests.py:105: DeprecationWarning: time.clock has been deprecated in Python 3.3 and will be removed from Python 3.8: use time.perf_counter or time.process_time instead tt = time.clock() ../examples/homogenization/perfusion_micro.py [1] sfepy: left over: ['__name__', '__doc__', '__package__', '__loader__', '__spec__', '__file__', '__cached__', '__builtins__', 'absolute_import', 'match_x_plane', 'match_y_plane', 'cb', 'nm', 'data_dir', 'six', 'range', 'get_mats', 'recovery_perf', 'geoms', 'pb_def', 'eps0', 'param_h', 'aux', 'ch', 'val', 'all_periodicYM', 'all_periodicY', 'reg_io', 'ebcs_eta', 'ebcs_gamma', 'ch2', 'val2', 'aux_bY', 'i_io', 'io', 'ion', 'matk1', 'matk2', 'ipm', 'ireg', 'coefs', 'requirements', 'ipm2', 'get_channel', 'set_corrpis', 'set_corr_S', 'set_corr_cc', 'i_io2', 'io2', 'io12', 'verbose', '_filename'] homogen: reading mesh [line2, tri3, quad4, tetra4, hexa8] (C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\meshes\3d\perfusion_micro3d.mesh)... homogen: ...done in 0.12 s homogen: creating regions... homogen: Y homogen: YM homogen: Pl homogen: Pr homogen: Pn homogen: Pf homogen: bYm homogen: bYp homogen: YA homogen: fixedYA homogen: YB homogen: fixedYB homogen: PlYM homogen: PrYM homogen: PnYM homogen: PfYM homogen: bYMA homogen: PlYA homogen: PrYA homogen: PnYA homogen: PfYA homogen: bYA_1 homogen: bYA_2 homogen: bYA_3 homogen: bYMB homogen: PlYB homogen: PrYB homogen: PnYB homogen: PfYB homogen: bYB_1 homogen: bYB_2 homogen: bYB_3 homogen: bYMp homogen: bYMm homogen: bYA homogen: bYB homogen: bYMpm homogen: bYMchs homogen: bYA_n1 homogen: bYA_n2 homogen: bYA_n3 homogen: bYB_n1 homogen: bYB_n2 homogen: bYB_n3 homogen: YMmchs homogen: ...done in 0.25 s homogen: using solvers: ts: no ts nls: newton ls: ls he: computing dependency corrs_gamma_m... he: equation "eq_gamma_pm": he: dw_diffusion.iV.YM(mat2M.k, qM, pM) = 1.000000e+00 * dw_surface_integrate.iS.bYMm(qM) he: updating variables... he: ...done he: setting up dof connectivities... he: ...done in 0.01 s he: matrix shape: (1992, 1992) he: assembling matrix graph... he: ...done in 0.01 s he: matrix structural nonzeros: 25154 (6.34e-03% fill) he: updating materials... he: mat2M he: ...done in 0.03 s he: using solvers: ts: no ts nls: newton ls: ls he: updating variables... he: ...done he: updating variables... he: ...done he: updating materials... he: mat2M he: ...done in 0.00 s he: nls: iter: 0, residual: 6.480876e-02 (rel: 1.000000e+00) he: residual: 0.04 [s] he: matrix: 0.03 [s] he: solve: 0.09 [s] he: nls: iter: 1, residual: 3.816937e-16 (rel: 5.889539e-15) he: solved in 1 steps in 0.38 seconds he: ...done he: computing Volume_total... he: equation "tmp": he: d_volume.iV.Y(vol_all) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_one... he: ...done he: computing Volume_bYMp... he: equation "tmp": he: d_surface.iS.bYMp(pM) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYp... he: equation "tmp": he: d_surface.iS.bYp(vol_all) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYMm... he: equation "tmp": he: d_surface.iS.bYMm(pM) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYm... he: equation "tmp": he: d_surface.iS.bYm(vol_all) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYA_1... he: equation "tmp": he: d_surface.iS.bYA_1(pA) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYA_2... he: equation "tmp": he: d_surface.iS.bYA_2(pA) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYA_3... he: equation "tmp": he: d_surface.iS.bYA_3(pA) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYB_1... he: equation "tmp": he: d_surface.iS.bYB_1(pB) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYB_2... he: equation "tmp": he: d_surface.iS.bYB_2(pB) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYB_3... he: equation "tmp": he: d_surface.iS.bYB_3(pB) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Hmp... he: equation "tmp": he: ev_surface_integrate.iS.bYMp(corr_M) he: updating materials... he: ...done in 0.00 s he: ...done he: computing dependency corrs_gamma_p... he: equation "eq_gamma_pm": he: dw_diffusion.iV.YM(mat2M.k, qM, pM) = 1.000000e+00 * dw_surface_integrate.iS.bYMp(qM) he: updating variables... he: ...done he: setting up dof connectivities... he: ...done in 0.00 s he: matrix shape: (1992, 1992) he: assembling matrix graph... he: ...done in 0.01 s he: matrix structural nonzeros: 25154 (6.34e-03% fill) he: updating materials... he: mat2M he: ...done in 0.03 s he: using solvers: ts: no ts nls: newton ls: ls he: updating variables... he: ...done he: updating variables... he: ...done he: updating materials... he: mat2M he: ...done in 0.00 s he: nls: iter: 0, residual: 7.140562e-02 (rel: 1.000000e+00) he: residual: 0.01 [s] he: matrix: 0.04 [s] he: solve: 0.09 [s] he: nls: iter: 1, residual: 3.887365e-16 (rel: 5.444059e-15) he: solved in 1 steps in 0.37 seconds he: ...done he: computing Hpm... he: equation "tmp": he: ev_surface_integrate.iS.bYMm(corr_M) he: updating materials... he: ...done in 0.00 s he: ...done he: computing dependency corrs_etaA... he: equation "eq_eta": he: dw_diffusion.iV.YM(mat2M.k, qM, pM) = 0 he: updating variables... he: ...done he: setting up dof connectivities... he: ...done in 0.00 s he: matrix shape: (1992, 1992) he: assembling matrix graph... he: ...done in 0.01 s he: matrix structural nonzeros: 25154 (6.34e-03% fill) he: updating materials... he: mat2M he: ...done in 0.02 s he: using solvers: ts: no ts nls: newton ls: ls he: updating variables... he: ...done he: updating variables... he: ...done he: updating materials... he: mat2M he: ...done in 0.00 s he: nls: iter: 0, residual: 1.862908e-01 (rel: 1.000000e+00) he: residual: 0.01 [s] he: matrix: 0.03 [s] he: solve: 0.09 [s] he: nls: iter: 1, residual: 4.052551e-16 (rel: 2.175390e-15) he: solved in 1 steps in 0.35 seconds he: ...done he: computing EmA... he: equation "tmp": he: ev_surface_integrate.iS.bYMm(corr_M) he: updating materials... he: ...done in 0.00 s he: ...done he: computing dependency corrs_gamma_B_1... he: equation "eq_gamma": he: dw_diffusion.iV.YB(mat2B.k, qB, pB) + dw_volume_dot.iV.YB(qB, lsB) = 1.000000e+00 * dw_surface_integrate.iS.bYB_1(qB) he: equation "eq_imv": he: dw_volume_dot.iV.YB(lvB, pB) = 0 he: updating variables... he: ...done he: setting up dof connectivities... he: ...done in 0.00 s he: lcbc: imvB he: dofs: total 1406, free 694, constrained 712, new 1 he: -> active 695 he: matrix shape: (1406, 1406) he: assembling matrix graph... he: ...done in 0.01 s he: matrix structural nonzeros: 22052 (1.12e-02% fill) he: updating materials... he: mat2B he: ...done in 0.01 s he: using solvers: ts: no ts nls: newton ls: ls he: updating variables... he: ...done he: lcbc: imvB he: dofs: total 1406, free 694, constrained 712, new 1 he: -> active 695 he: updating variables... he: ...done he: lcbc: imvB he: dofs: total 1406, free 694, constrained 712, new 1 he: -> active 695 he: updating materials... he: mat2B he: ...done in 0.00 s he: nls: iter: 0, residual: 9.945233e-03 (rel: 1.000000e+00) he: residual: 0.01 [s] he: matrix: 0.01 [s] he: solve: 0.01 [s] he: nls: iter: 1, residual: 2.133885e-16 (rel: 2.145636e-14) he: solved in 1 steps in 0.13 seconds he: ...done he: computing RB_2_1... he: equation "tmp": he: ev_surface_integrate.iS.bYB_2(corr1_B) he: updating materials... he: ...done in 0.00 s he: ...done he: computing dependency corrs_oneB... he: ...done he: computing dependency corrs_etaB... he: equation "eq_eta": he: dw_diffusion.iV.YM(mat2M.k, qM, pM) = 0
Traceback (most recent call last): File "run_tests.py", line 234, in <module> sys.exit(main()) File "run_tests.py", line 223, in main run_tests(stats, dirname, [filename]) File "run_tests.py", line 144, in run_tests stats[0] + 1) File "run_tests.py", line 108, in run_test ifile=ifile) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\base\testing.py", line 67, in run ret = test_method() File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\tests\test_homogenization_perfusion.py", line 51, in test_solution coefs = app() File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\applications\application.py", line 29, in call_basic return self.call(**kwargs) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\homogen_app.py", line 174, in call aux = self.he(ret_all=ret_all, time_tag=time_tag) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\applications\application.py", line 29, in call_basic return self.call(**kwargs) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\engine.py", line 729, in call self.app_options.store_micro_idxs, time_tag) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\engine.py", line 107, in __call__ time_tag) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\engine.py", line 281, in calculate_req chunk_tab, 'reqs', proc_id) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\engine.py", line 149, in calculate val = mini_app(data=data) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\coefs_base.py", line 459, in __call__ problem.set_equations(self.equations) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\discrete\problem.py", line 525, in set_equations user=user) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\discrete\equations.py", line 66, in from_conf materials, integrals, user=user) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\discrete\equations.py", line 772, in from_desc terms.assign_args(variables, materials, user) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\terms\terms.py", line 299, in assign_args term.assign_args(variables, materials, user) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\terms\terms.py", line 512, in assign_args raise ValueError('argument %s not found!' % arg_name) ValueError: argument qM not found! Sent from Mail for Windows 10
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