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mdolab / pyspline

pySpline produces B-spline curves, surfaces, and volumes
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Building error: Undefined symbol: Npy__PyLong_AsInt #61

Closed ekremekc closed 1 year ago

ekremekc commented 1 year ago

Hi,

I am trying to install the main branch of the pysplines into my Ubuntu 20.04 OS.

when I copy the config and run make, I got this error;

mkdir -p obj
ln -sf config/config.mk config.mk
making module in src/

make[2]: Entering directory '/home/ee331/Dev/pyspline/src'
make precision.o adtProjections.o
make[3]: Entering directory '/home/ee331/Dev/pyspline/src'
gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c precision.f90 -o ..//obj/precision.o

        --- Compiled precision.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c adtProjections.F90 -o ..//obj/adtProjections.o

        --- Compiled adtProjections.F90 successfully ---

make[3]: Leaving directory '/home/ee331/Dev/pyspline/src'
cp -f *.mod ../mod
make evaluations.o basis.o knots.o insertKnot.o getBasisPt.o parameterizations.o findSpan.o compute_curve.o compute_surface.o compute_volume.o eval_curve.o eval_surface.o eval_volume.o projections.o tfi2d.o 
make[3]: Entering directory '/home/ee331/Dev/pyspline/src'
gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c evaluations.f90 -o ..//obj/evaluations.o

        --- Compiled evaluations.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c basis.f90 -o ..//obj/basis.o

        --- Compiled basis.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c knots.f90 -o ..//obj/knots.o

        --- Compiled knots.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c insertKnot.f90 -o ..//obj/insertKnot.o

        --- Compiled insertKnot.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c getBasisPt.f90 -o ..//obj/getBasisPt.o

        --- Compiled getBasisPt.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c parameterizations.f90 -o ..//obj/parameterizations.o
parameterizations.f90:37:64:

   37 |                          (X(3, K, J, I) - X(3, K, J, I - 1))**2)
      |                                                                1
Warning: Obsolescent feature: Statement function at (1)
parameterizations.f90:41:64:

   41 |                          (X(3, K, J, I) - X(3, K, J - 1, I))**2)
      |                                                                1
Warning: Obsolescent feature: Statement function at (1)
parameterizations.f90:45:64:

   45 |                          (X(3, K, J, I) - X(3, K - 1, J, I))**2)
      |                                                                1
Warning: Obsolescent feature: Statement function at (1)

        --- Compiled parameterizations.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c findSpan.f90 -o ..//obj/findSpan.o

        --- Compiled findSpan.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c compute_curve.f90 -o ..//obj/compute_curve.o

        --- Compiled compute_curve.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c compute_surface.f90 -o ..//obj/compute_surface.o

        --- Compiled compute_surface.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c compute_volume.f90 -o ..//obj/compute_volume.o

        --- Compiled compute_volume.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c eval_curve.f90 -o ..//obj/eval_curve.o

        --- Compiled eval_curve.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c eval_surface.f90 -o ..//obj/eval_surface.o

        --- Compiled eval_surface.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c eval_volume.f90 -o ..//obj/eval_volume.o

        --- Compiled eval_volume.f90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c projections.F90 -o ..//obj/projections.o

        --- Compiled projections.F90 successfully ---

gfortran -I..//mod -fdefault-real-8 -O2 -fPIC -std=f2008 -c tfi2d.f90 -o ..//obj/tfi2d.o

        --- Compiled tfi2d.f90 successfully ---

make[3]: Leaving directory '/home/ee331/Dev/pyspline/src'
make[2]: Leaving directory '/home/ee331/Dev/pyspline/src'
(cd lib && make)
make[2]: Entering directory '/home/ee331/Dev/pyspline/lib'
        creating library ...

ar -rvs libspline.a ../obj/*.o
ar: creating libspline.a
a - ../obj/adtProjections.o
a - ../obj/basis.o
a - ../obj/compute_curve.o
a - ../obj/compute_surface.o
a - ../obj/compute_volume.o
a - ../obj/eval_curve.o
a - ../obj/eval_surface.o
a - ../obj/eval_volume.o
a - ../obj/evaluations.o
a - ../obj/findSpan.o
a - ../obj/getBasisPt.o
a - ../obj/insertKnot.o
a - ../obj/knots.o
a - ../obj/parameterizations.o
a - ../obj/precision.o
a - ../obj/projections.o
a - ../obj/tfi2d.o

        library libspline.a created.

make[2]: Leaving directory '/home/ee331/Dev/pyspline/lib'
(cd src/f2py && make)
make[2]: Entering directory '/home/ee331/Dev/pyspline/src/f2py'
#------------------------------------------------------#
Python Inclue Flags -I/usr/include/python3.8 -I/usr/include/python3.8
#------------------------------------------------------#
#------------------------------------------------------#
Numpy Include Directory: /home/ee331/Dev/Venvs/v060/lib/python3.8/site-packages/numpy/core/include
#------------------------------------------------------#
#------------------------------------------------------#
f2py root directory: /home/ee331/Dev/Venvs/v060/lib/python3.8/site-packages/numpy/f2py
#------------------------------------------------------#
cp f2py_f2cmap.ref .f2py_f2cmap
f2py pyspline.pyf
Reading f2cmap from '.f2py_f2cmap' ...
    Mapping "real(kind=realtype)" to "double"
Successfully applied user defined f2cmap changes
Reading fortran codes...
    Reading file 'pyspline.pyf' (format:free)
Post-processing...
    Block: libspline
            Block: knots_interp
            Block: knots_lms
            Block: insertknot
            Block: curve_jacobian_wrap
            Block: constr_jac
            Block: poly_length
            Block: curve_para_corr
            Block: surface_jacobian_wrap
            Block: para3d
            Block: tfi2d
            Block: volume_jacobian_wrap
            Block: eval_curve
            Block: eval_curve_deriv
            Block: eval_curve_deriv2
            Block: eval_curve_c
            Block: eval_curve_deriv_c
            Block: eval_curve_deriv2_c
            Block: eval_surface
            Block: eval_surface_deriv
            Block: eval_surface_deriv2
            Block: eval_volume
            Block: eval_volume_deriv
            Block: eval_volume_deriv2
            Block: point_curve
            Block: point_surface
            Block: point_volume
            Block: curve_curve
            Block: curve_surface
            Block: point_curve_start
            Block: point_surface_start
            Block: point_volume_start
            Block: curve_curve_start
            Block: curve_surface_start
            Block: line_plane
            Block: plane_line
            Block: point_plane
            Block: getbasisptsurface
            Block: getbasisptvolume
            Block: basis
            Block: derivbasis
            Block: findspan
            Block: adtprojections
                Block: searchquads
Applying post-processing hooks...
  character_backward_compatibility_hook
Post-processing (stage 2)...
    Block: libspline
        Block: unknown_interface
            Block: knots_interp
            Block: knots_lms
            Block: insertknot
            Block: curve_jacobian_wrap
            Block: constr_jac
            Block: poly_length
            Block: curve_para_corr
            Block: surface_jacobian_wrap
            Block: para3d
            Block: tfi2d
            Block: volume_jacobian_wrap
            Block: eval_curve
            Block: eval_curve_deriv
            Block: eval_curve_deriv2
            Block: eval_curve_c
            Block: eval_curve_deriv_c
            Block: eval_curve_deriv2_c
            Block: eval_surface
            Block: eval_surface_deriv
            Block: eval_surface_deriv2
            Block: eval_volume
            Block: eval_volume_deriv
            Block: eval_volume_deriv2
            Block: point_curve
            Block: point_surface
            Block: point_volume
            Block: curve_curve
            Block: curve_surface
            Block: point_curve_start
            Block: point_surface_start
            Block: point_volume_start
            Block: curve_curve_start
            Block: curve_surface_start
            Block: line_plane
            Block: plane_line
            Block: point_plane
            Block: getbasisptsurface
            Block: getbasisptvolume
            Block: basis
            Block: derivbasis
            Block: findspan
            Block: adtprojections
                Block: searchquads
Building modules...
    Building module "libspline"...
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "knots_interp"...
          t = knots_interp(x,deriv_ptr,k,[n,nd])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "knots_lms"...
          t = knots_lms(x,nctl,k,[n])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "insertknot"...
          r,t_new,coef_new,ileft = insertknot(u,r,t,k,coef,[nctl,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "curve_jacobian_wrap"...
          vals,row_ptr,col_ind = curve_jacobian_wrap(s,sd,t,k,nctl,vals,row_ptr,col_ind,[n,nd])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "constr_jac"...
          j_val,j_col_ind,j_row_ptr = constr_jac(a_val,a_row_ptr,a_col_ind,b_val,b_row_ptr,b_col_ind,c_val,c_row_ptr,c_col_ind,an,[am,cm,annz,bnnz,cnnz])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "poly_length"...
          length = poly_length(x,[n,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "curve_para_corr"...
          curve_para_corr(t,k,s,coef,length,x,[nctl,ndim,n])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "surface_jacobian_wrap"...
          vals,row_ptr,col_ind = surface_jacobian_wrap(u,v,tu,tv,ku,kv,nctlu,nctlv,[nu,nv])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "para3d"...
          s,u,v,w = para3d(x,[n,m,l,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "tfi2d"...
          x = tfi2d(e0,e1,e2,e3,[nu,nv])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "volume_jacobian_wrap"...
          vals,row_ptr,col_ind = volume_jacobian_wrap(u,v,w,tu,tv,tw,ku,kv,kw,nctlu,nctlv,nctlw,[nu,nv,nw])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "eval_curve"...
          val = eval_curve(s,t,k,coef,[nctl,ndim,n])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "eval_curve_deriv"...
          val = eval_curve_deriv(s,t,k,coef,[nctl,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "eval_curve_deriv2"...
          val = eval_curve_deriv2(s,t,k,coef,[nctl,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "eval_curve_c"...
          val = eval_curve_c(s,t,k,coef,[nctl,ndim,n])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "eval_curve_deriv_c"...
          val = eval_curve_deriv_c(s,t,k,coef,[nctl,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "eval_curve_deriv2_c"...
          val = eval_curve_deriv2_c(s,t,k,coef,[nctl,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "eval_surface"...
          val = eval_surface(u,v,tu,tv,ku,kv,coef,[nctlu,nctlv,ndim,n,m])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "eval_surface_deriv"...
          val = eval_surface_deriv(u,v,tu,tv,ku,kv,coef,[nctlu,nctlv,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "eval_surface_deriv2"...
          val = eval_surface_deriv2(u,v,tu,tv,ku,kv,coef,[nctlu,nctlv,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "eval_volume"...
          val = eval_volume(u,v,w,tu,tv,tw,ku,kv,kw,coef,[nctlu,nctlv,nctlw,ndim,n,m,l])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "eval_volume_deriv"...
          val = eval_volume_deriv(u,v,w,tu,tv,tw,ku,kv,kw,coef,[nctlu,nctlv,nctlw,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "eval_volume_deriv2"...
          val = eval_volume_deriv2(u,v,w,tu,tv,tw,ku,kv,kw,coef,[nctlu,nctlv,nctlw,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "point_curve"...
          s,diff = point_curve(x0,t,k,coef,niter,eps,s,[nctl,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "point_surface"...
          u,v,diff = point_surface(x0,tu,tv,ku,kv,coef,niter,eps,u,v,[nctlu,nctlv,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "point_volume"...
          u,v,w,diff = point_volume(x0,tu,tv,tw,ku,kv,kw,coef,niter,eps,u,v,w,[nctlu,nctlv,nctlw,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "curve_curve"...
          s,t,diff = curve_curve(t1,k1,coef1,t2,k2,coef2,niter,eps,s,t,[n1,n2,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "curve_surface"...
          u,v,s,diff = curve_surface(tc,kc,coefc,tu,tv,ku,kv,coefs,niter,eps,u,v,s,[nctlc,nctlu,nctlv,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "point_curve_start"...
          u = point_curve_start(x0,uu,data,[nu,ndim,n])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "point_surface_start"...
          u,v = point_surface_start(x0,uu,vv,data,[nu,nv,ndim,n])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "point_volume_start"...
          u,v,w = point_volume_start(x0,uu,vv,ww,data,[nu,nv,nw,ndim,n])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "curve_curve_start"...
          s1,s2 = curve_curve_start(data1,uu1,data2,uu2,[nu1,nu2,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "curve_surface_start"...
          s,u,v = curve_surface_start(data1,uu1,data2,uu2,vv2,[nu1,nu2,nv2,ndim])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "line_plane"...
          sol,pid,n_sol = line_plane(ia,vc,p0,v1,v2,[n])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "plane_line"...
          sol,n_sol = plane_line(ia,vc,p0,v1,v2,[n])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "point_plane"...
          sol,n_sol,best_sol = point_plane(pt,p0,v1,v2,[n])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "getbasisptsurface"...
          vals,col_ind = getbasisptsurface(u,v,tu,tv,ku,kv,vals,col_ind,istart,l_index,[nctlu,nctlv,nnz])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "getbasisptvolume"...
          vals,col_ind = getbasisptvolume(u,v,w,tu,tv,tw,ku,kv,kw,vals,col_ind,istart,l_index,[nctlu,nctlv,nctlw,nnz])
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "basis"...
          b = basis(t,nctl,k,u,ind)
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "derivbasis"...
          bd = derivbasis(t,nctl,ku,u,ind,n)
    Generating possibly empty wrappers"
    Maybe empty "libspline-f2pywrappers.f"
        Constructing wrapper function "findspan"...
          ind = findspan(u,k,t,nctl)
        Constructing F90 module support for "adtprojections"...
            Constructing wrapper function "adtprojections.searchquads"...
              faceid,uv = searchquads(pts,conn,searchpts,[npts,nconn,nsearchpts])
    Wrote C/API module "libspline" to file "./libsplinemodule.c"
    Fortran 90 wrappers are saved to "./libspline-f2pywrappers2.f90"

gcc -O2 -fPIC -I/usr/include/python3.8 -I/usr/include/python3.8 -I/home/ee331/Dev/Venvs/v060/lib/python3.8/site-packages/numpy/core/include \
-I/home/ee331/Dev/Venvs/v060/lib/python3.8/site-packages/numpy/f2py/src -c libsplinemodule.c
libsplinemodule.c: In function ‘int_from_pyobj’:
libsplinemodule.c:118:14: warning: implicit declaration of function ‘Npy__PyLong_AsInt’ [-Wimplicit-function-declaration]
  118 |         *v = Npy__PyLong_AsInt(obj);
      |              ^~~~~~~~~~~~~~~~~
libsplinemodule.c: In function ‘PyInit_libspline’:
libsplinemodule.c:10081:5: warning: implicit declaration of function ‘Py_SET_TYPE’; did you mean ‘Py_TYPE’? [-Wimplicit-function-declaration]
10081 |     Py_SET_TYPE(&PyFortran_Type, &PyType_Type);
      |     ^~~~~~~~~~~
      |     Py_TYPE
gcc -O2 -fPIC -I/usr/include/python3.8 -I/usr/include/python3.8 -I/home/ee331/Dev/Venvs/v060/lib/python3.8/site-packages/numpy/core/include -c \
/home/ee331/Dev/Venvs/v060/lib/python3.8/site-packages/numpy/f2py/src/fortranobject.c -o fortranobject.o
gfortran -I../../mod -fdefault-real-8 -O2 -fPIC -std=f2008 -I./ -c libspline-f2pywrappers2.f90
gfortran -fPIC -shared fortranobject.o libsplinemodule.o libspline-f2pywrappers2.o  -fdefault-real-8 -O2 -fPIC -std=f2008 -L../../lib -lspline  -o libspline.so
python3 importTest.py libspline.so
Testing if module libspline can be imported...
Error: /home/ee331/Dev/pyspline/src/f2py/libspline.so: undefined symbol: Npy__PyLong_AsInt
Error: library libspline.so was not imported correctly
make[2]: *** [Makefile:37: all] Error 1
make[2]: Leaving directory '/home/ee331/Dev/pyspline/src/f2py'
make[1]: *** [Makefile:36: module] Error 2
make[1]: Leaving directory '/home/ee331/Dev/pyspline'
make: *** [Makefile:7: default] Error 2

I use python3.8 and my pip list is as follows;

Package                       Version   Editable project location
----------------------------- --------- -----------------------------
adios4dolfinx                 0.1.0     /home/ee331/Dev/adios4dolfinx
alabaster                     0.7.13
appdirs                       1.4.4
argon2-cffi                   21.3.0
argon2-cffi-bindings          21.2.0
asttokens                     2.2.1
attrs                         22.2.0
Babel                         2.11.0
backcall                      0.2.0
beautifulsoup4                4.11.2
bleach                        6.0.0
certifi                       2022.12.7
cffi                          1.15.1
charset-normalizer            3.0.1
colorcet                      3.0.1
comm                          0.1.2
contourpy                     1.0.7
coverage                      7.2.0
cppimport                     22.8.2
cycler                        0.11.0
debugpy                       1.6.6
decorator                     5.1.1
defusedxml                    0.7.1
docutils                      0.19
dolfinx-mpc                   0.6.1
entrypoints                   0.4
et-xmlfile                    1.1.0
exceptiongroup                1.1.0
execnet                       1.9.0
executing                     1.2.0
fastjsonschema                2.16.2
fenics-basix                  0.6.0
fenics-dolfinx                0.6.0
fenics-ffcx                   0.6.0
fenics-ufl                    2023.1.0
filelock                      3.9.0
flake8                        6.0.0
fonttools                     4.38.0
geomdl                        5.3.1
geomdl.shapes                 1.3.0
gmsh                          4.11.1
gmsh-x                        0.0       /home/ee331/Dev/gmsh-x
h5py                          3.8.0
helmholtz-x                   2.1       /home/ee331/Dev/Helmholtz-x
idna                          3.4
imageio                       2.25.1
imagesize                     1.4.1
importlib-metadata            6.0.0
importlib-resources           5.10.2
iniconfig                     2.0.0
ipydatawidgets                4.3.2
ipykernel                     6.21.2
ipympl                        0.9.3
ipyparallel                   8.4.1
ipython                       8.10.0
ipython-genutils              0.2.0
ipywidgets                    7.7.3
isort                         5.12.0
itk-core                      5.3.0
itk-filtering                 5.3.0
itk-meshtopolydata            0.10.0
itk-numerics                  5.3.0
itkwidgets                    0.32.5
jedi                          0.18.2
Jinja2                        3.1.2
joblib                        1.2.0
jsonschema                    4.17.3
jupyter_client                8.0.2
jupyter_core                  5.2.0
jupyterlab-pygments           0.2.2
jupyterlab-widgets            1.1.2
jupytext                      1.14.4
kiwisolver                    1.4.4
llvmlite                      0.39.1
Mako                          1.2.4
markdown-it-py                2.1.0
MarkupSafe                    2.1.2
matplotlib                    3.6.3
matplotlib-inline             0.1.6
mccabe                        0.7.0
mdit-py-plugins               0.3.3
mdurl                         0.1.2
meshio                        5.3.4
mistune                       2.0.5
mpi4py                        3.1.4
mpmath                        1.2.1
multiphenicsx                 0.2.dev1
mypy                          0.991
mypy-extensions               0.4.3
myst-parser                   0.18.1
nbclient                      0.7.2
nbconvert                     7.2.9
nbformat                      5.7.3
nbval                         0.10.0
nbvalx                        0.0.dev1
nest-asyncio                  1.5.6
networkx                      3.1
notebook                      6.4.12
numba                         0.56.4
numpy                         1.24.4
odfpy                         1.4.1
openpyxl                      3.1.2
packaging                     23.0
pandas                        1.5.3
pandocfilters                 1.5.0
param                         1.12.3
parso                         0.8.3
petsc4py                      3.17.2
pexpect                       4.8.0
pickleshare                   0.7.5
Pillow                        9.4.0
pip                           23.0
pkg_resources                 0.0.0
pkgutil_resolve_name          1.3.10
platformdirs                  2.6.2
plotly                        5.13.0
pluggy                        1.0.0
pooch                         1.6.0
prometheus-client             0.16.0
prompt-toolkit                3.0.36
psutil                        5.9.4
ptyprocess                    0.7.0
pure-eval                     0.2.2
pybind11                      2.10.1
pycodestyle                   2.10.0
pycparser                     2.21
pyct                          0.5.0
pyflakes                      3.0.1
Pygments                      2.14.0
pyparsing                     3.0.9
PyQt5                         5.15.9
PyQt5-Qt5                     5.15.2
PyQt5-sip                     12.11.1
pyrsistent                    0.19.3
pytest                        7.2.1
pytest-xdist                  3.1.0
python-dateutil               2.8.2
pythreejs                     2.4.1
pytz                          2022.7.1
pyvista                       0.37.0
PyYAML                        6.0
pyzmq                         25.0.0
requests                      2.28.2
rich                          13.3.1
scikit-learn                  1.2.2
scipy                         1.10.0
scooby                        0.7.1
Send2Trash                    1.8.0
setuptools                    44.0.0
six                           1.16.0
sklearn                       0.0.post5
slepc4py                      3.17.1
snowballstemmer               2.2.0
soupsieve                     2.4
Sphinx                        6.1.3
sphinx-rtd-theme              1.1.1
sphinxcontrib-applehelp       1.0.4
sphinxcontrib-devhelp         1.0.2
sphinxcontrib-htmlhelp        2.0.1
sphinxcontrib-jsmath          1.0.1
sphinxcontrib-qthelp          1.0.3
sphinxcontrib-serializinghtml 1.1.5
stack-data                    0.6.2
sympy                         1.11.1
tenacity                      8.2.1
terminado                     0.17.1
threadpoolctl                 3.1.0
tinycss2                      1.2.1
toml                          0.10.2
tomli                         2.0.1
tornado                       6.2
tqdm                          4.64.1
traitlets                     5.6.0
traittypes                    0.2.1
typing_extensions             4.4.0
urllib3                       1.26.14
vtk                           9.2.6
wcwidth                       0.2.6
webencodings                  0.5.1
widgetsnbextension            3.6.2
zipp                          3.12.0
zstandard                     0.20.0

And my config file is;

# Config File for LINUX and GFORTRAN Compiler
AR       = ar
AR_FLAGS = -rvs
RM       = /bin/rm -rf

# Fortran compiler and flags
FF90        = gfortran
FF90_FLAGS  = -fdefault-real-8 -O2 -fPIC -std=f2008

# C compiler and flags
CC       = gcc
CC_FLAGS   = -O2 -fPIC

# Define potentially different python, python-config and f2py executables:
PYTHON = python3
PYTHON-CONFIG = python3-config # use python-config for python 2
F2PY = f2py

# Define additional flags for linking
LINKER_FLAGS = 
SO_LINKER_FLAGS =-fPIC -shared

I appreciate any help to solve this installation problem.

Best regards

marcomangano commented 1 year ago

Hello Ekrem, We don't test the combination of python 3.8 and numpy 1.24.4 you are using here, and I suspect the numpy error you are getting is due to some backwards incompatibility. I would suggest to roll back to numpy 1.21.x and recompile the code from scratch with make clean && make.

kensukenk commented 1 year ago

Hi I have the exact same issue. I tried rolling back to numpy 1.21.x and 1.20.x but the issue remained.

kensukenk commented 1 year ago

When I tried compiling in a new conda environment it worked!

ekremekc commented 1 year ago

I rolled back to numpy 1.18.0 and scipy 1.8.0 and it worked.