Error when trying to run demo problem
AudreyDemafo opened this issue · 9 comments
AudreyDemafo commented
Hi everyone,
I am encountering an issue while solving the optimal control problem for the Poisson. I reproduced the the same code that is in the cashocs tutorial and I am getting the following error:
"TypeError: Cannot convert float to petsc4py.PETSc.Vec". This is what the erro looks like:
> ---------------------------------------------------------------------------
> TypeError Traceback (most recent call last)
> Cell In[10], line 23
> 18 J = cashocs.IntegralFunctional(
> 19 Constant(0.5) * (y - y_d) * (y - y_d) * dx + Constant(0.5 * alpha) * u * u * dx
> 20 )
> 22 ocp = cashocs.OptimalControlProblem(e, bcs, J, y, u, p, config=config)
> ---> 23 ocp.solve()
> File ~/yes/envs/fenicsproject/lib/python3.9/site-packages/cashocs/_optimization/optimal_control/optimal_control_problem.py:382, in > OptimalControlProblem.solve(self, algorithm, rtol, atol, max_iter)
> 379 self._setup_control_bcs()
> 381 self.solver = self._setup_solver()
> --> 382 self.solver.run()
> 383 self.solver.post_processing()
> File ~/yes/envs/fenicsproject/lib/python3.9/site-packages/cashocs/_optimization/optimization_algorithms/l_bfgs.py:128, in
> LBFGSMethod.run(self)
> 125 if self.convergence_test():
> 126 break
> --> 128 self.update_hessian_approximation()
>File ~/yes/envs/fenicsproject/lib/python3.9/site-packages/cashocs/_optimization/optimization_algorithms/l_bfgs.py:243, in > >LBFGSMethod.update_hessian_approximation(self)
> 235 self.y_k[i].vector().vec().aypx(
> 236 0.0,
> 237 self.gradient[i].vector().vec()
> 238 - self.gradient_prev[i].vector().vec(),
> 239 )
> 240 self.y_k[i].vector().apply("")
> 241 self.s_k[i].vector().vec().aypx(
> 242 0.0,
>--> 243 self.stepsize * self.search_direction[i].vector().vec(),
> 244 )
> 245 self.s_k[i].vector().apply("")
> 247 self.optimization_variable_abstractions.restrict_to_inactive_set(
> 248 self.y_k, self.y_k
> 249 )
> File petsc4py/PETSc/Vec.pyx:90, in petsc4py.PETSc.Vec.__mul__()
> TypeError: Cannot convert float to petsc4py.PETSc.Vec"
Here is the code
from fenics imort*
import cashocs
from dolfin import*
cashocs.set_log_level(cashocs.LogLevel.INFO)
config = cashocs.load_config("config.ini")
mesh, subdomains, boundaries, dx, ds, dS = cashocs.regular_mesh(25)
V = FunctionSpace(mesh, "CG", 1)
u = Function(V)
y = Function(V)
p = Function(V)
Function(V)
e = inner(grad(y), grad(p)) * dx - u * p * dx
bcs = cashocs.create_dirichlet_bcs(V, Constant(0), boundaries, [1, 2, 3, 4])
y_d = Expression("sin(2*pi*x[0])*sin(2*pi*x[1])", degree=1)
alpha = 1e-6
J = cashocs.IntegralFunctional(
Constant(0.5) * (y - y_d) * (y - y_d) * dx + Constant(0.5 * alpha) * u * u * dx
)
ocp = cashocs.OptimalControlProblem(e, bcs, J, y, u, p, config=config)
ocp.solve()
Appearently, it looks like the error comes from the solve function but I have no idea on how to fix it. @sblauth any help on the issue would be very much appreciated.
I am using python 3.9.12. I install cashocs within the fenicsproject environment.
Thank you in advance.
sblauth commented
I cannot reproduce the problem. First, you have a typo in your code, the first line should be
from fenics import *
So please make sure that you copy the actual code you are using, so that reproduction is possible.
As you have not specified your config.ini file, I have tried running your code with all solvers, and it worked without any problems.
Could you post your config.ini file, so I can try to reproduce the problem?
Also, please provide the version of cashocs you are using. You can show this with the lines
import cashocs
print(cashocs.__version__)
AudreyDemafo commented
Thank you very much your reply. I have copied exactly the same code from my jupyter notebook and this is what it looks like. I have tried to check whether the space between import and the star changes anything in the code and both syntaxes work well for me.
Here is the code and the config.ini file as well
from fenics import*
from dolfin import*
import cashocs
cashocs.set_log_level(cashocs.LogLevel.INFO)
config = cashocs.load_config("config.ini")
mesh, subdomains, boundaries, dx, ds, dS = cashocs.regular_mesh(25)
V = FunctionSpace(mesh, "CG", 1)
u = Function(V)
y = Function(V)
p = Function(V)
Function(V)
e = inner(grad(y), grad(p)) * dx - u * p * dx
bcs = cashocs.create_dirichlet_bcs(V, Constant(0), boundaries, [1, 2, 3, 4])
y_d = Expression("sin(2*pi*x[0])*sin(2*pi*x[1])", degree=1)
alpha = 1e-6
J = cashocs.IntegralFunctional(
Constant(0.5) * (y - y_d) * (y - y_d) * dx + Constant(0.5 * alpha) * u * u * dx
)
ocp = cashocs.OptimalControlProblem(e, bcs, J, y, u, p, config=config)
ocp.solve()
And here is the config.ini file
#[Mesh]
#mesh_file = ../mesh/mesh.xdmf
[StateSystem]
is_linear = True
newton_rtol = 1e-11
newton_atol = 1e-13
newton_iter = 50
newton_damped = True
newton_inexact = False
newton_verbose = False
picard_iteration = False
picard_rtol = 1e-10
picard_atol = 1e-12
picard_iter = 10
picard_verbose = False
[OptimizationRoutine]
algorithm = lbfgs
rtol = 1e-3
atol = 0.0
max_iter = 100
gradient_method = direct
gradient_tol = 1e-9
soft_exit = False
[LineSearch]
initial_stepsize = 1.0
safeguard_stepsize = True
epsilon_armijo = 1e-4
beta_armijo = 2
[AlgoLBFGS]
bfgs_memory_size = 3
use_bfgs_scaling = True
[AlgoCG]
cg_method = PR
cg_periodic_restart = False
cg_periodic_its = 5
cg_relative_restart = False
cg_restart_tol = 0.5
[AlgoTNM]
inner_newton = cg
max_it_inner_newton = 100
inner_newton_rtol = 1e-15
inner_newton_atol = 0.0
[Output]
verbose = True
save_results = True
save_txt = True
save_state = False
save_adjoint = False
save_gradient = False
result_dir = ./
precision = 3
time_suffix = False
I am using the version 2.0.11 of cashocs. Thank you
sblauth commented
I am sorry, but I still cannot replicate your problem. I just copied the files and got the following results with v2.0.11 of cashocs:
cashocs - INFO - Generating mesh.
cashocs - INFO - Done generating mesh. Elapsed time: 0.01 s.
cashocs - INFO - Successfully generated 2-dimensional mesh on 1 CPU(s).
cashocs - INFO - Mesh contains 676 vertices and 1,250 cells of type triangle.
iter, cost function, rel. grad. norm, abs. grad. norm, step size
0, 1.224e-01, 1.000e+00, 6.169e-03,
1, 1.224e-01, 9.998e-01, 6.168e-03, 1.000e+00
2, 4.065e-02, 2.308e+00, 1.424e-02, 1.000e+00
3, 8.569e-03, 4.848e-01, 2.991e-03, 5.000e-01
4, 7.846e-04, 2.605e-03, 1.607e-05, 1.000e+00
5, 7.842e-04, 2.149e-03, 1.326e-05, 1.000e+00
6, 7.831e-04, 1.065e-03, 6.568e-06, 1.000e+00
7, 7.831e-04, 6.823e-03, 4.209e-05, 1.000e+00
8, 7.828e-04, 1.588e-03, 9.797e-06, 1.000e+00
9, 7.827e-04, 7.597e-04, 4.687e-06, 1.000e+00
Optimization was successful.
Statistics:
total iterations: 9
final objective value: 7.827e-04
final gradient norm: 7.597e-04
total number of state systems solved: 11
total number of adjoint systems solved: 10
You said you installed cashocs in the fenicsproject environment? Are you using conda? If so, could you please provide the list of installed packages with conda list?
Have you tried creating a new environment with a clean installation of cashocs, as suggested in https://cashocs.readthedocs.io/en/stable/about/installation/#installation-instructions ?
AudreyDemafo commented
Thanks. I am using conda indeed. here is the list of installed package in the fenicsproject environment that I have:
# packages in environment at /home/audreydemafo/yes/envs/fenicsproject:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.10 hd590300_0 conda-forge
anyio 4.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39hd1e30aa_4 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
binutils_impl_linux-64 2.40 hf600244_0 conda-forge
binutils_linux-64 2.40 hbdbef99_2 conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.5 h0f2a231_0 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py39h3d6467e_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.26.0 hd590300_0 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
cashocs 2.0.11 pyhd8ed1ab_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py39h7a31438_0 conda-forge
cftime 1.6.3 py39h44dd56e_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
cmake 3.28.3 hcfe8598_0 conda-forge
comm 0.2.1 pyhd8ed1ab_0 conda-forge
contourpy 1.2.0 py39h7633fee_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.8.1 py39h3d6467e_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
eigen 3.4.0 h00ab1b0_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fenics 2019.1.0 py39hcaacaa7_42 conda-forge
fenics-dijitso 2019.1.0 pyhd8ed1ab_39 conda-forge
fenics-dolfin 2019.1.0 py39h3ef2b04_42 conda-forge
fenics-ffc 2019.1.0 pyhd8ed1ab_39 conda-forge
fenics-fiat 2019.1.0 pyhd8ed1ab_39 conda-forge
fenics-libdolfin 2019.1.0 h05c4287_42 conda-forge
fenics-ufl 2019.1.0 py39hf3d152e_38 conda-forge
fftw 3.3.10 mpi_mpich_h5537406_8 conda-forge
fltk 1.3.7 h83e168f_1 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.49.0 py39hd1e30aa_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freeimage 3.18.0 hca5c823_12 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
gcc_impl_linux-64 12.3.0 he2b93b0_5 conda-forge
gcc_linux-64 12.3.0 h76fc315_2 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
glib 2.78.4 hfc55251_0 conda-forge
glib-tools 2.78.4 hfc55251_0 conda-forge
gmp 6.3.0 h59595ed_0 conda-forge
gmpy2 2.1.2 py39h376b7d2_1 conda-forge
gmsh 4.11.1 h51d60e7_3 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gst-plugins-base 1.22.9 h8e1006c_0 conda-forge
gstreamer 1.22.9 h98fc4e7_0 conda-forge
gxx_impl_linux-64 12.3.0 he2b93b0_5 conda-forge
gxx_linux-64 12.3.0 h8a814eb_2 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h2 4.1.0 py39hf3d152e_0 conda-forge
h5py 3.10.0 nompi_py39h2c511df_101 conda-forge
harfbuzz 8.3.0 h3d44ed6_0 conda-forge
hdf4 4.2.15 h9772cbc_5 conda-forge
hdf5 1.14.3 mpi_mpich_ha2c2bf8_0 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
httpcore 1.0.3 pyhd8ed1ab_0 conda-forge
httpx 0.26.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
hypre 2.28.0 mpi_mpich_h716cb5e_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
imath 3.1.6 h6239696_1 conda-forge
importlib-metadata 7.0.1 pyha770c72_0 conda-forge
importlib-resources 6.1.1 pyhd8ed1ab_0 conda-forge
importlib_metadata 7.0.1 hd8ed1ab_0 conda-forge
importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.2 pyhd33586a_0 conda-forge
ipython 8.18.1 pyh707e725_3 conda-forge
ipywidgets 8.1.2 pyhd8ed1ab_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.3 pyhd8ed1ab_0 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
json5 0.9.17 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py39hf3d152e_3 conda-forge
jsonschema 4.21.1 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.21.1 pyhd8ed1ab_0 conda-forge
jupyter 1.0.0 pyhd8ed1ab_10 conda-forge
jupyter-lsp 2.2.2 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.0 pyhd8ed1ab_0 conda-forge
jupyter_console 6.6.3 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.1 py39hf3d152e_0 conda-forge
jupyter_events 0.9.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.12.5 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.5.2 pyhd8ed1ab_0 conda-forge
jupyterlab 4.1.2 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge
jupyterlab_server 2.25.3 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.10 pyhd8ed1ab_0 conda-forge
jxrlib 1.1 hd590300_3 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_17 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py39h7633fee_1 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.15 hfd0df8a_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.1.2 h59595ed_1 conda-forge
libblas 3.9.0 21_linux64_openblas conda-forge
libboost 1.82.0 h6fcfa73_6 conda-forge
libboost-headers 1.84.0 ha770c72_1 conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 21_linux64_openblas conda-forge
libcbor 0.10.2 hcb278e6_0 conda-forge
libclang 15.0.7 default_hb11cfb5_4 conda-forge
libclang13 15.0.7 default_ha2b6cf4_4 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.5.0 hca28451_0 conda-forge
libdeflate 1.17 h0b41bf4_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libfido2 1.14.0 h4446dcb_0 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-devel_linux-64 12.3.0 h8bca6fd_105 conda-forge
libgcc-ng 13.2.0 h807b86a_5 conda-forge
libgcrypt 1.10.3 hd590300_0 conda-forge
libgfortran-ng 13.2.0 h69a702a_5 conda-forge
libgfortran5 13.2.0 ha4646dd_5 conda-forge
libglib 2.78.4 h783c2da_0 conda-forge
libglu 9.0.0 hac7e632_1003 conda-forge
libgomp 13.2.0 h807b86a_5 conda-forge
libgpg-error 1.47 h71f35ed_0 conda-forge
libhwloc 2.9.3 default_h554bfaf_1009 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 21_linux64_openblas conda-forge
libllvm15 15.0.7 hb3ce162_4 conda-forge
libnetcdf 4.9.2 nompi_h9612171_113 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.26 pthreads_h413a1c8_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.42 h2797004_0 conda-forge
libpq 16.2 h33b98f1_0 conda-forge
libraw 0.21.1 h89bc310_0 conda-forge
libsanitizer 12.3.0 h0f45ef3_5 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsqlite 3.45.1 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-devel_linux-64 12.3.0 h8bca6fd_105 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
libsystemd0 255 h3516f8a_0 conda-forge
libtiff 4.6.0 ha9c0a0a_2 conda-forge
libudev1 255 h3f72095_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.47.0 hd590300_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.6.0 hd429924_1 conda-forge
libxml2 2.12.5 h232c23b_0 conda-forge
libzip 1.10.1 h2629f0a_3 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py39hd1e30aa_0 conda-forge
matplotlib 3.8.3 py39hf3d152e_0 conda-forge
matplotlib-base 3.8.3 py39he9076e7_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
meshio 5.3.5 pyhd8ed1ab_0 conda-forge
metis 5.1.0 h59595ed_1007 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
mpc 1.3.1 hfe3b2da_0 conda-forge
mpfr 4.2.1 h9458935_0 conda-forge
mpg123 1.32.4 h59595ed_0 conda-forge
mpi 1.0 mpich conda-forge
mpi4py 3.1.5 py39h6cbbaa3_0 conda-forge
mpich 4.2.0 h846660c_100 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
mumps-include 5.2.1 ha770c72_11 conda-forge
mumps-mpi 5.2.1 h7ee95aa_11 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.33 hf1915f5_6 conda-forge
mysql-libs 8.0.33 hca2cd23_6 conda-forge
nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
nbconvert 7.16.1 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.16.1 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.16.1 pyhd8ed1ab_0 conda-forge
nbformat 5.9.2 pyhd8ed1ab_0 conda-forge
ncurses 6.4 h59595ed_2 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
netcdf4 1.6.5 nompi_py39h4282601_100 conda-forge
notebook 7.1.0 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.98 h1d7d5a4_0 conda-forge
numpy 1.26.4 py39h474f0d3_0 conda-forge
occt 7.7.2 novtk_h130ccc2_101 conda-forge
openexr 3.1.5 h0cdce71_2 conda-forge
openjpeg 2.5.0 h488ebb8_3 conda-forge
openssh 9.6p1 h2d3b35a_0 conda-forge
openssl 3.2.1 hd590300_0 conda-forge
overrides 7.7.0 pyhd8ed1ab_0 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pandoc 3.1.12.1 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parmetis 4.0.3 h2a9763c_1005 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pcre2 10.42 hcad00b1_0 conda-forge
petsc 3.20.2 real_h622a54c_100 conda-forge
petsc4py 3.20.2 real_hbc6119c_100 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.2.0 py39had0adad_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
pkg-config 0.29.2 h36c2ea0_1008 conda-forge
pkgconfig 1.5.5 pyhd8ed1ab_4 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.2.0 pyhd8ed1ab_0 conda-forge
ply 3.11 py_1 conda-forge
prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.42 pyha770c72_0 conda-forge
prompt_toolkit 3.0.42 hd8ed1ab_0 conda-forge
psutil 5.9.8 py39hd1e30aa_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptscotch 6.0.9 hb499603_2 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulseaudio-client 16.1 hb77b528_5 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pybind11 2.11.1 py39h7633fee_2 conda-forge
pybind11-global 2.11.1 py39h7633fee_2 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py39h52134e7_5 conda-forge
pyqt5-sip 12.12.2 py39h3d6467e_5 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.9.18 h0755675_1_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.19.1 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python_abi 3.9 4_cp39 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py39hd1e30aa_1 conda-forge
pyzmq 25.1.2 py39h8c080ef_0 conda-forge
qt-main 5.15.8 h5810be5_19 conda-forge
qtconsole-base 5.5.1 pyha770c72_0 conda-forge
qtpy 2.4.1 pyhd8ed1ab_0 conda-forge
rapidjson 1.1.0 he1b5a44_1002 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.33.0 pyhd8ed1ab_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rhash 1.4.4 hd590300_0 conda-forge
rich 13.7.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.18.0 py39h9fdd4d6_0 conda-forge
scalapack 2.2.0 hd931219_1 conda-forge
scotch 6.0.9 hb2e6521_2 conda-forge
send2trash 1.8.2 pyh41d4057_0 conda-forge
setuptools 69.1.0 pyhd8ed1ab_1 conda-forge
sip 6.7.12 py39h3d6467e_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
slepc 3.20.1 real_hac23e11_100 conda-forge
slepc4py 3.20.1 real_hab767b8_100 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
suitesparse 5.10.1 h5a4f163_3 conda-forge
superlu 5.2.2 h00795ac_0 conda-forge
superlu_dist 7.2.0 h25dcc4a_0 conda-forge
sympy 1.12 pypyh9d50eac_103 conda-forge
sysroot_linux-64 2.12 he073ed8_17 conda-forge
tbb 2021.11.0 h00ab1b0_1 conda-forge
terminado 0.18.0 pyh0d859eb_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.4 py39hd1e30aa_0 conda-forge
traitlets 5.14.1 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.8.19.20240106 pyhd8ed1ab_0 conda-forge
typing-extensions 4.9.0 hd8ed1ab_0 conda-forge
typing_extensions 4.9.0 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
unicodedata2 15.1.0 py39hd1e30aa_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.7.0 pyhd8ed1ab_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.10 pyhd8ed1ab_0 conda-forge
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xkeyboard-config 2.41 hd590300_0 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.7 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxmu 1.1.3 h7f98852_0 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zeromq 4.3.5 h59595ed_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
Note: you may need to restart the kernel to use updated packages.
I am trying to do the installation in a new conda environment as suggested in https://cashocs.readthedocs.io/en/stable/about/installation/#installation-instructions. The process is not yet complete.
sblauth commented
Regarding your packages: You have installed PETSc 3.20.2 - cashocs currently has issues when using PETSc 3.20, as explained in #320
The issue I discovered does not come from cashocs, but from FEniCS itself. However, there could be other issues (as the one you are describing) which I have not yet been able to test rigorously. Based on my testing with PETSc 3.20 it should not be an issue, but I would suggest installing cashocs to a new enviroment - if you follow the instructions then a version of PETSc < 3.20 will be used automatically.
I think that this issue was fixed in #321, so the new cashocs version 2.1.0 should also work with PETSc 3.20, at least as far as your code goes.
I think the easiest solution is to update the cashocs package with conda, this should fix your problem.
AudreyDemafo commented
I have created a new environment in which I installed cashocs. Within the new environment the version changed to 1.8.12 and the code still gives me the sane error. I have tried to update the version with the syntax
conda update cashocs
but it seems not to be working.
sblauth commented
This won't happen. My nightly tests show what happens when you create a new conda environment with cashocs using
conda create -n test -c conda-forge cashocs python=3.11.
Output is
package | build
---------------------------|-----------------
brotli-1.1.0 | h0dc2134_1 19 KB conda-forge
brotli-bin-1.1.0 | h0dc2134_1 16 KB conda-forge
bzip2-1.0.8 | h10d778d_5 125 KB conda-forge
c-ares-1.26.0 | h10d778d_0 144 KB conda-forge
ca-certificates-2024.2.2 | h8857fd0_0 152 KB conda-forge
cached-property-1.5.2 | hd8ed1ab_1 4 KB conda-forge
cached_property-1.5.2 | pyha770c72_1 11 KB conda-forge
cairo-1.18.0 | h99e66fa_0 865 KB conda-forge
cashocs-2.1.0 | pyhd8ed1ab_0 202 KB conda-forge
certifi-2024.2.2 | pyhd8ed1ab_0 157 KB conda-forge
cftime-1.6.3 | py311hc9a392d_0 207 KB conda-forge
cmake-3.28.3 | h7c85d92_0 15.8 MB conda-forge
contourpy-1.2.0 | py311h7bea37d_0 242 KB conda-forge
curl-8.5.0 | h726d00d_0 150 KB conda-forge
cycler-0.12.1 | pyhd8ed1ab_0 13 KB conda-forge
eigen-3.4.0 | h1c7c39f_0 1.0 MB conda-forge
expat-2.5.0 | hf0c8a7f_1 118 KB conda-forge
fenics-2019.1.0 | py311h1768d6d_39 24 KB conda-forge
fenics-dijitso-2019.1.0 | pyhd8ed1ab_39 41 KB conda-forge
fenics-dolfin-2019.1.0 | py311he8092e6_39 1.0 MB conda-forge
fenics-ffc-2019.1.0 | pyhd8ed1ab_39 238 KB conda-forge
fenics-fiat-2019.1.0 | pyhd8ed1ab_39 75 KB conda-forge
fenics-libdolfin-2019.1.0 | h01bef3c_39 2.0 MB conda-forge
fenics-ufl-2019.1.0 | py311h6eed73b_38 456 KB conda-forge
fftw-3.3.10 |mpi_mpich_h4a8b384_7 1.8 MB conda-forge
fltk-1.3.8 | h299f19b_2 1.2 MB conda-forge
font-ttf-dejavu-sans-mono-2.37| hab24e00_0 388 KB conda-forge
font-ttf-inconsolata-3.000 | h77eed37_0 94 KB conda-forge
font-ttf-source-code-pro-2.038| h77eed37_0 684 KB conda-forge
font-ttf-ubuntu-0.83 | h77eed37_1 1.5 MB conda-forge
fontconfig-2.14.2 | h5bb23bf_0 232 KB conda-forge
fonts-conda-ecosystem-1 | 0 4 KB conda-forge
fonts-conda-forge-1 | 0 4 KB conda-forge
fonttools-4.49.0 | py311he705e18_0 2.6 MB conda-forge
freeimage-3.18.0 | h29db62a_17 411 KB conda-forge
freetype-2.12.1 | h60636b9_2 585 KB conda-forge
gettext-0.21.1 | h8a4c099_0 4.0 MB conda-forge
gmp-6.3.0 | h93d8f39_0 509 KB conda-forge
gmpy2-2.1.2 | py311hc5b4402_1 166 KB conda-forge
gmsh-4.11.1 | h92d8eba_5 11.1 MB conda-forge
h5py-3.8.0 |nompi_py311h777de7a_100 1.0 MB conda-forge
hdf4-4.2.15 | h9804679_6 708 KB conda-forge
hdf5-1.12.2 |mpi_mpich_hc154f39_0 3.9 MB conda-forge
hypre-2.27.0 |mpi_mpich_h5eb2ec2_0 1.8 MB conda-forge
icu-73.2 | hf5e326d_0 11.2 MB conda-forge
imath-3.1.9 | h7d26f99_0 152 KB conda-forge
importlib-metadata-7.0.1 | pyha770c72_0 26 KB conda-forge
importlib_metadata-7.0.1 | hd8ed1ab_0 9 KB conda-forge
jxrlib-1.1 | h10d778d_3 215 KB conda-forge
kiwisolver-1.4.5 | py311h5fe6e05_1 59 KB conda-forge
krb5-1.21.2 | hb884880_0 1.1 MB conda-forge
lcms2-2.15 | ha53face_2 220 KB conda-forge
lerc-4.0.0 | hb486fe8_0 284 KB conda-forge
libblas-3.9.0 |21_osx64_openblas 14 KB conda-forge
libboost-1.82.0 | h99d8d82_6 1.9 MB conda-forge
libboost-headers-1.84.0 | h694c41f_1 13.2 MB conda-forge
libbrotlicommon-1.1.0 | h0dc2134_1 66 KB conda-forge
libbrotlidec-1.1.0 | h0dc2134_1 30 KB conda-forge
libbrotlienc-1.1.0 | h0dc2134_1 292 KB conda-forge
libcblas-3.9.0 |21_osx64_openblas 14 KB conda-forge
libcbor-0.10.2 | hf0c8a7f_0 35 KB conda-forge
libcurl-8.5.0 | h726d00d_0 359 KB conda-forge
libcxx-16.0.6 | hd57cbcb_0 1.1 MB conda-forge
libdeflate-1.19 | ha4e1b8e_0 67 KB conda-forge
libedit-3.1.20191231 | h0678c8f_2 103 KB conda-forge
libev-4.33 | h10d778d_2 104 KB conda-forge
libexpat-2.5.0 | hf0c8a7f_1 68 KB conda-forge
libffi-3.4.2 | h0d85af4_5 50 KB conda-forge
libfido2-1.14.0 | h3cbcf74_0 261 KB conda-forge
libgfortran-5.0.0 |13_2_0_h97931a8_3 108 KB conda-forge
libgfortran5-13.2.0 | h2873a65_3 1.5 MB conda-forge
libglib-2.78.4 | hab64008_0 2.4 MB conda-forge
libhwloc-2.9.3 |default_h24e0189_1009 2.4 MB conda-forge
libiconv-1.17 | hd75f5a5_2 651 KB conda-forge
libjpeg-turbo-2.1.5.1 | h0dc2134_1 446 KB conda-forge
liblapack-3.9.0 |21_osx64_openblas 14 KB conda-forge
libnetcdf-4.9.1 |mpi_mpich_hbde6a2f_2 708 KB conda-forge
libnghttp2-1.58.0 | h64cf6d3_1 586 KB conda-forge
libopenblas-0.3.26 |openmp_hfef2a42_0 5.8 MB conda-forge
libpng-1.6.42 | h92b6c6a_0 263 KB conda-forge
libraw-0.21.1 | h9804679_1 574 KB conda-forge
libsqlite-3.45.1 | h92b6c6a_0 881 KB conda-forge
libssh2-1.11.0 | hd019ec5_0 253 KB conda-forge
libtiff-4.6.0 | haeeb97c_1 254 KB conda-forge
libuv-1.47.0 | h67532ce_0 395 KB conda-forge
libwebp-base-1.3.2 | h0dc2134_0 338 KB conda-forge
libxcb-1.15 | hb7f2c08_0 306 KB conda-forge
libxml2-2.12.5 | hc0ae0f7_0 605 KB conda-forge
libzip-1.10.1 | hc158999_3 125 KB conda-forge
libzlib-1.2.13 | h8a1eda9_5 58 KB conda-forge
llvm-openmp-17.0.6 | hb6ac08f_0 293 KB conda-forge
markdown-it-py-3.0.0 | pyhd8ed1ab_0 63 KB conda-forge
matplotlib-base-3.8.3 | py311h6ff1f5f_0 7.4 MB conda-forge
mdurl-0.1.2 | pyhd8ed1ab_0 14 KB conda-forge
meshio-5.3.5 | pyhd8ed1ab_0 374 KB conda-forge
metis-5.1.0 | he965462_1007 3.7 MB conda-forge
mpc-1.3.1 | h81bd1dd_0 107 KB conda-forge
mpfr-4.2.1 | h0c69b56_0 368 KB conda-forge
mpi-1.0 | mpich 4 KB conda-forge
mpi4py-3.1.4 | py311hbdc7f45_0 535 KB conda-forge
mpich-4.0.3 | hd33e60e_100 5.4 MB conda-forge
mpmath-1.3.0 | pyhd8ed1ab_0 428 KB conda-forge
mumps-include-5.2.1 | h694c41f_11 24 KB conda-forge
mumps-mpi-5.2.1 | h690e093_11 3.2 MB conda-forge
munkres-1.1.4 | pyh9f0ad1d_0 12 KB conda-forge
ncurses-6.4 | h93d8f39_2 803 KB conda-forge
netcdf4-1.6.3 |nompi_py311he6f34b2_100 437 KB conda-forge
numpy-1.26.4 | py311hc43a94b_0 7.2 MB conda-forge
occt-7.7.2 |novtk_h0a0d97a_101 24.3 MB conda-forge
openexr-3.2.1 | h747cbf1_0 1.3 MB conda-forge
openjpeg-2.5.0 | ha4da562_3 328 KB conda-forge
openssh-9.6p1 | h6dd4ff7_0 904 KB conda-forge
openssl-3.2.1 | hd75f5a5_0 2.4 MB conda-forge
packaging-23.2 | pyhd8ed1ab_0 48 KB conda-forge
parmetis-4.0.3 | hb7fa8f8_1005 295 KB conda-forge
pcre2-10.42 | h0ad2156_0 879 KB conda-forge
petsc-3.18.4 |real_h238465a_100 9.3 MB conda-forge
petsc4py-3.18.4 |real_h4c46328_100 1.0 MB conda-forge
pillow-10.0.1 | py311hd5308a1_1 44.0 MB conda-forge
pip-24.0 | pyhd8ed1ab_0 1.3 MB conda-forge
pixman-0.43.2 | h73e2aa4_0 317 KB conda-forge
pkg-config-0.29.2 | ha3d46e9_1008 263 KB conda-forge
pkgconfig-1.5.5 | pyhd8ed1ab_4 10 KB conda-forge
pthread-stubs-0.4 | hc929b4f_1001 6 KB conda-forge
ptscotch-6.0.9 | h4f3afa6_2 1.5 MB conda-forge
pybind11-2.11.1 | py311h5fe6e05_2 184 KB conda-forge
pybind11-global-2.11.1 | py311h5fe6e05_2 169 KB conda-forge
pygments-2.17.2 | pyhd8ed1ab_0 840 KB conda-forge
pyparsing-3.1.1 | pyhd8ed1ab_0 87 KB conda-forge
python-3.11.8 |h9f0c242_0_cpython 13.4 MB conda-forge
python-dateutil-2.8.2 | pyhd8ed1ab_0 240 KB conda-forge
python_abi-3.11 | 4_cp311 6 KB conda-forge
rapidjson-1.1.0 | hb1e8313_1002 104 KB conda-forge
readline-8.2 | h9e318b2_1 250 KB conda-forge
rhash-1.4.4 | h0dc2134_0 173 KB conda-forge
rich-13.7.0 | pyhd8ed1ab_0 180 KB conda-forge
scalapack-2.2.0 | hc746714_1 2.1 MB conda-forge
scotch-6.0.9 | h3da7401_2 1.2 MB conda-forge
setuptools-69.1.0 | pyhd8ed1ab_1 459 KB conda-forge
six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge
slepc-3.18.2 |real_ha03fd1b_100 3.5 MB conda-forge
slepc4py-3.18.2 |real_h5730752_100 311 KB conda-forge
suitesparse-5.10.1 | h4bf45ed_3 1.4 MB conda-forge
superlu-5.2.2 | h1f0f902_0 330 KB conda-forge
superlu_dist-7.2.0 | h4bb6bf2_0 1.1 MB conda-forge
sympy-1.12 | pypyh9d50eac_103 4.1 MB conda-forge
tbb-2021.11.0 | h7728843_1 169 KB conda-forge
tk-8.6.13 | h1abcd95_1 3.1 MB conda-forge
typing_extensions-4.9.0 | pyha770c72_0 35 KB conda-forge
tzdata-2024a | h0c530f3_0 117 KB conda-forge
wheel-0.42.0 | pyhd8ed1ab_0 56 KB conda-forge
xorg-fixesproto-5.0 | h0d85af4_1002 9 KB conda-forge
xorg-kbproto-1.0.7 | h35c211d_1002 27 KB conda-forge
xorg-libice-1.1.1 | h0dc2134_0 48 KB conda-forge
xorg-libsm-1.2.4 | h0dc2134_0 24 KB conda-forge
xorg-libx11-1.8.7 | hbd0b022_0 760 KB conda-forge
xorg-libxau-1.0.11 | h0dc2134_0 13 KB conda-forge
xorg-libxdmcp-1.1.3 | h35c211d_0 17 KB conda-forge
xorg-libxext-1.3.4 | hb7f2c08_2 42 KB conda-forge
xorg-libxfixes-5.0.3 | h0d85af4_1004 15 KB conda-forge
xorg-libxrender-0.9.11 | h0dc2134_0 28 KB conda-forge
xorg-renderproto-0.11.1 | h0d85af4_1002 9 KB conda-forge
xorg-xextproto-7.3.0 | hb7f2c08_1003 30 KB conda-forge
xorg-xproto-7.0.31 | h35c211d_1007 73 KB conda-forge
xz-5.2.6 | h775f41a_0 233 KB conda-forge
yaml-0.2.5 | h0d85af4_2 82 KB conda-forge
zipp-3.17.0 | pyhd8ed1ab_0 19 KB conda-forge
zlib-1.2.13 | h8a1eda9_5 89 KB conda-forge
zstd-1.5.5 | h829000d_0 488 KB conda-forge
------------------------------------------------------------
So cashocs 2.1.0 with PETSc 3.18 will be installed. Regarding conda update: I have found that for complex environments this is usually not working so well. For your fenicsproject environment, you could also just uninstall cashocs and reinstall it with pip, that should get you to the latest version, too.
AudreyDemafo commented
Thank you very much @sblauth . I was able to fix the problem by installing the python 3.11 version in the new environment that I created and the code works fine now. Thank you very much for your help on the issue.
sblauth commented
Okay, I'm glad to hear that. If you have any further issues, please let me know.