# CADET does not run with a specific version with CADET-Python on Linux **URL:** \ **Category:** CADET Troubleshooting\ **Created:** [February 11, 2025, 10:31am UTC](https://forum.cadet-web.de/t/cadet-does-not-run-with-a-specific-version-with-cadet-python-on-linux/1158 "2025-02-11T10:31:28Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Flynn](https://forum.cadet-web.de/user_avatar/forum.cadet-web.de/flynn/32/1045_2.png) [@Flynn](https://forum.cadet-web.de/u/Flynn)\ **Post date:** [February 11, 2025, 10:31am UTC](https://forum.cadet-web.de/t/cadet-does-not-run-with-a-specific-version-with-cadet-python-on-linux/1158/1 "2025-02-11T10:31:28Z")
### Expected behavior. Simulation runs with no errors. ### Actual behavior Simulation failed and returned message: CompletedProcess(args=[‘/home/zhangwx37/.conda/pkgs/cadet-5.0.0-hbe33008\_0/bin/cadet-cli’, ‘8f7380c7-4926-4668-aa1e-59be173593e3.h5’], returncode=127, stdout=b’‘, stderr=b’/home/zhangwx37/.conda/pkgs/cadet-5.0.0-hbe33008\_0/bin/cadet-cli: error while loading shared libraries: libhdf5.so.310: cannot open shared object file: No such file or directory\n’) ### How to produce bug (including a minimal reproducible example) System: Linux (Red Hat) CADET: 5.0.0 CADET-Python: 0.14.1 Python: 3.12.8 ## Example code: ```auto from cadet import Cadet import numpy as np Cadet.cadet_path = r"/home/zhangwx37/.conda/pkgs/cadet-5.0.0-hbe33008_0/bin/cadet-cli" ## fixed params n_sites = 2 n_x = 1 model = Cadet() # number of unit operations model.root.input.model.nunits = 3 #inlet model model.root.input.model.unit_000.unit_type = 'INLET' model.root.input.model.unit_000.ncomp = n_x model.root.input.model.unit_000.inlet_type = 'PIECEWISE_CUBIC_POLY' #time sections model.root.input.solver.sections.nsec = 1 model.root.input.solver.sections.section_times = [0.0, 7500.0,] # s model.root.input.solver.sections.section_continuity = [] model.root.input.model.unit_000.sec_000.const_coeff = n_x*[0.0,] model.root.input.model.unit_000.sec_000.lin_coeff = n_x*[0.0,] model.root.input.model.unit_000.sec_000.quad_coeff = n_x*[0.0,] model.root.input.model.unit_000.sec_000.cube_coeff = n_x*[0.0,] model.root.input.model.unit_001.unit_type = 'GENERAL_RATE_MODEL' model.root.input.model.unit_001.ncomp = 1 ## Geometry model.root.input.model.unit_001.col_length = 1.0 # m model.root.input.model.unit_001.cross_section_area = 36/1e6 # m^2, length x area should be the reactor volume model.root.input.model.unit_001.col_porosity = 0.33 # 1 model.root.input.model.unit_001.par_porosity = 0.97 # 1 model.root.input.model.unit_001.par_radius = 0.045/1e3 # m ## Transport model.root.input.model.unit_001.col_dispersion = 0.0 # m^2/s model.root.input.model.unit_001.film_diffusion = [1.48e-5,] # m/s, 1.35e-5, no film diffusion resistances model.root.input.model.unit_001.par_diffusion = [1e-12,] # m^2/s model.root.input.model.unit_001.par_surfdiffusion = n_sites * [0.0,] model.root.input.model.unit_001.adsorption_model = 'MULTI_COMPONENT_BILANGMUIR' model.root.input.model.unit_001.adsorption.is_kinetic = 1 model.root.input.model.unit_001.adsorption.mcbl_ka = [2.0, 2.0] ## m^3 mobile phase / mol protein / s ml/mg=m^3/kg 1 kda = 1 kg/mol model.root.input.model.unit_001.adsorption.mcbl_kd = n_sites * [1.0,] ## 1/s model.root.input.model.unit_001.adsorption.mcbl_qmax = [5.0, 5.0] ## mol protein / m^3 solid phase (not resin) model.root.input.model.unit_001.init_c = [5/150,] ## mg/ml=kg/m^3, kg/mol, mol/m^3 model.root.input.model.unit_001.init_q = n_sites * [0.0,] ### Grid cells model.root.input.model.unit_001.discretization.ncol = 1 ## make sure this is 1 model.root.input.model.unit_001.discretization.npar = 100 ### Bound states model.root.input.model.unit_001.discretization.nbound = [n_sites,] ### Other options model.root.input.model.unit_001.discretization.par_disc_type = 'EQUIDISTANT_PAR' model.root.input.model.unit_001.discretization.use_analytic_jacobian = 1 model.root.input.model.unit_001.discretization.reconstruction = 'WENO' model.root.input.model.unit_001.discretization.gs_type = 1 model.root.input.model.unit_001.discretization.max_krylov = 0 model.root.input.model.unit_001.discretization.max_restarts = 10 model.root.input.model.unit_001.discretization.schur_safety = 1.0e-8 model.root.input.model.unit_001.discretization.weno.boundary_model = 0 model.root.input.model.unit_001.discretization.weno.weno_eps = 1e-10 model.root.input.model.unit_001.discretization.weno.weno_order = 2 ## Outlet model.root.input.model.unit_002.unit_type = 'OUTLET' model.root.input.model.unit_002.ncomp = n_x # Connections Q = 0 # volumetric flow rate model.root.input.model.connections.nswitches = 1 model.root.input.model.connections.switch_000.section = 0 model.root.input.model.connections.switch_000.connections = [ 0, 1, -1, -1, Q, 1, 2, -1, -1, Q, ] # Q, volumetric flow rate # numerical solver configuration model.root.input.model.solver.gs_type = 1 model.root.input.model.solver.max_krylov = 0 model.root.input.model.solver.max_restarts = 10 model.root.input.model.solver.schur_safety = 1e-8 # Number of cores for parallel simulation model.root.input.solver.nthreads = 1 # Tolerances for the time integrator model.root.input.solver.time_integrator.abstol = 1e-5 model.root.input.solver.time_integrator.algtol = 1e-8 model.root.input.solver.time_integrator.reltol = 1e-5 model.root.input.solver.time_integrator.init_step_size = 1e-18 model.root.input.solver.time_integrator.max_steps = 1000000 # Return data model.root.input['return'].split_components_data = 0 model.root.input['return'].split_ports_data = 0 model.root.input['return'].unit_000.write_solution_bulk = 0 model.root.input['return'].unit_000.write_solution_inlet = 0 model.root.input['return'].unit_000.write_solution_outlet = 1 model.root.input['return'].unit_000.write_sens_outlet=0 model.root.input['return'].unit_000.write_sens_bulk=0 # Copy settings to the other unit operations model.root.input['return'].unit_001 = model.root.input['return'].unit_000 model.root.input['return'].unit_002 = model.root.input['return'].unit_000 # Solution times model.root.input.solver.user_solution_times = np.linspace(0, 7250.0, 100) model.filename = 'test.h5' model.save() data = model.run() model.load() print(data) tl = model.root.input.solver.user_solution_times cl = model.root.output.solution.unit_001.solution_outlet*150 ``` ### File produced by `conda env export > environment.yml` [environment.yml](https://forum.cadet-web.de/uploads/short-url/kjdOcvGvXOEpXOWnNtLs4m0fuKo.yml) (7.93 KB) ---
**Author:** ![j.schmoelder](https://forum.cadet-web.de/user_avatar/forum.cadet-web.de/j.schmoelder/32/93_2.png) [@j.schmoelder](https://forum.cadet-web.de/u/j.schmoelder)\ **Post date:** [February 11, 2025, 10:41am UTC](https://forum.cadet-web.de/t/cadet-does-not-run-with-a-specific-version-with-cadet-python-on-linux/1158/2 "2025-02-11T10:41:36Z")
Hi Flynn, thanks for reporting the issue. Unfortunately, I cannot reproduce the issue, but I have a couple of questions / ideas: - Is the `cadet_path` in the same conda environment as you’re running the code from? - If so, it’s actually no longer required to set the install path if you use the “standard” installation; it should be autodetected. - Update CADET-Core to v5.0.3 - Setup a new (clean) environment and try again. Let us know if this helped. ---
**Author:** ![Flynn](https://forum.cadet-web.de/user_avatar/forum.cadet-web.de/flynn/32/1045_2.png) [@Flynn](https://forum.cadet-web.de/u/Flynn)\ **Post date:** [February 11, 2025, 3:01pm UTC](https://forum.cadet-web.de/t/cadet-does-not-run-with-a-specific-version-with-cadet-python-on-linux/1158/3 "2025-02-11T15:01:54Z")
Hi Johannes, thanks for your reply! Is there a method we can call in CADET for older versions like above to find the `cadet_path` from standard installation? ---
**Author:** ![j.schmoelder](https://forum.cadet-web.de/user_avatar/forum.cadet-web.de/j.schmoelder/32/93_2.png) [@j.schmoelder](https://forum.cadet-web.de/u/j.schmoelder)\ **Post date:** [February 12, 2025, 12:29pm UTC](https://forum.cadet-web.de/t/cadet-does-not-run-with-a-specific-version-with-cadet-python-on-linux/1158/4 "2025-02-12T12:29:08Z")
You can specify the path to a separate version just the way you did it. However, if this is in another conda environment, there might be issues with dependencies. Maybe in your case, the `cadet-cli` was dynamically linked against a specific version of HDF5 which is then not used in the environment you’re currently on. Just out of curiosity, why don’t you update to the latest CADET-Core version? ---
**Author:** ![Flynn](https://forum.cadet-web.de/user_avatar/forum.cadet-web.de/flynn/32/1045_2.png) [@Flynn](https://forum.cadet-web.de/u/Flynn)\ **Post date:** [February 13, 2025, 12:52am UTC](https://forum.cadet-web.de/t/cadet-does-not-run-with-a-specific-version-with-cadet-python-on-linux/1158/5 "2025-02-13T00:52:01Z")
Hello Jo, I think this is not about CADET but rather CADET-Python. 1. I updated CADET to 5.0.3. If I don’t specify the path to `cadet_cli`, it gives an error: ![image](https://forum.cadet-web.de/uploads/default/original/2X/9/9f2d2ae79b5925097afdc65c635515dc69276443.png) 2. If I specify the following path: `"/home/zhangwx37/.conda/pkgs/cadet-5.0.3-hbe33008_0/bin/cadet-cli" `, it gives the same error: ![image](https://forum.cadet-web.de/uploads/default/optimized/2X/5/50068c21728a6c210cc6445652700a4bf0b68029_2_690x12.png) However, I did realize I was specifying the wrong path… Inside the .conda/ folder there are two folders, one is `pkgs` and the other is `env`. I can find `cadet_cli` in both of them. However, only the one in `env` works. Anyway, problem solved. Another quick question, for newer versions, I still define `cadet_path` to specify customized `cadet_cli`? Would this cause any problems regarding dynamic links? ---
**Author:** ![h.lanzrath](https://forum.cadet-web.de/user_avatar/forum.cadet-web.de/h.lanzrath/32/1186_2.png) [@h.lanzrath](https://forum.cadet-web.de/u/h.lanzrath)\ **Post date:** [January 27, 2026, 11:41am UTC](https://forum.cadet-web.de/t/cadet-does-not-run-with-a-specific-version-with-cadet-python-on-linux/1158/6 "2026-01-27T11:41:34Z")