Error while installing a python code

[Marco Sulla]

Little errata: you have only to install or update Cython, remove the
.c files as I wrote before and run again

python setup.py build_ext -b PoissonSolver/

No intermediate steps are required. The generated ELF files are three.
You have also to rename them with the names in the README file.


On Mon, 9 Mar 2020 at 22:36, Marco Sulla <elbarbun at gmail.com> wrote:
>
> I suppose you tried to use this setup.py:
> https://github.com/breathe/coffee_conda_package/blob/master/0001-Add-alternative-setup.py-script.patch
>
> It's not well written IMHO... anyway this is not the problem.
>
> I suppose you also downloaded the required sources from here:
> https://data.mendeley.com/datasets/s2x4d542dc/1
>
> It seems the problem is that the above sources are generated by an old
> version of Cython:
>
> https://github.com/mcfletch/pyopengl/issues/11
>
> You have "simply" to enter any subdir of PoissonSolver that ends with
> "_cy", remove the .c file inside and do:
> python setup.py build_ext --inplace
>
> After that, you'll be able to compile. The result is an ELF file. On
> my PC, the generated file is
> PoissonSolver/PoissonSolver/ps3d.cpython-38-x86_64-linux-gnu.so
>
> On Mon, 9 Mar 2020 at 15:27, Tim Ko <thardaway1 at gmail.com> wrote:
> >
> > Hello,
> >
> > I am trying to install a custom Python code but ran into an error. The error presumably associated with cython. I tried a different compiler since Intel compiler often crashes when using cython, but couldn't get it working.
> >
> > Attached is the installation error log. I have installed and updated all essential packages such as numpy and scipy. Could someone please give me advice to resolve this issue? Many thanks in advance.
> >
> > Sincerely,
> > TK
> >
> >
> > ===================
> > $ python setup.py build_ext -b PoissonSolver/
> > running build_ext
> > skipping 'PoissonSolver/MV_2D_cy/matvec2D.c' Cython extension (up-to-date)
> > skipping 'PoissonSolver/MV_1D_cy/matvec1D.c' Cython extension (up-to-date)
> > skipping 'PoissonSolver/PS_3D_cy/ps3d.c' Cython extension (up-to-date)
> > building 'matvec2D' extension
> > icc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home01/r782a03/.conda/envs/hko_env/lib/python3.7/site-packages/numpy/core/include -I/home01/r782a03/.conda/envs/hko_env/include/python3.7m -c PoissonSolver/MV_2D_cy/matvec2D.c -o build/temp.linux-x86_64-3.7/PoissonSolver/MV_2D_cy/matvec2D.o -ffast-math
> > icc: command line warning #10006: ignoring unknown option '-ffast-math'
> > In file included from /home01/r782a03/.conda/envs/hko_env/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h(1830),
> >                  from /home01/r782a03/.conda/envs/hko_env/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h(12),
> >                  from /home01/r782a03/.conda/envs/hko_env/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h(4),
> >                  from PoissonSolver/MV_2D_cy/matvec2D.c(232):
> > /home01/r782a03/.conda/envs/hko_env/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h(17): warning #1224: #warning directive: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
> >   #warning "Using deprecated NumPy API, disable it with " \
> >    ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17500): error: struct "_ts" has no field "exc_type"
> >       *type = tstate->exc_type;
> >                       ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17501): error: struct "_ts" has no field "exc_value"
> >       *value = tstate->exc_value;
> >                        ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17502): error: struct "_ts" has no field "exc_traceback"
> >       *tb = tstate->exc_traceback;
> >                     ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17514): error: struct "_ts" has no field "exc_type"
> >       tmp_type = tstate->exc_type;
> >                          ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17515): error: struct "_ts" has no field "exc_value"
> >       tmp_value = tstate->exc_value;
> >                           ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17516): error: struct "_ts" has no field "exc_traceback"
> >       tmp_tb = tstate->exc_traceback;
> >                        ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17517): error: struct "_ts" has no field "exc_type"
> >       tstate->exc_type = type;
> >               ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17518): error: struct "_ts" has no field "exc_value"
> >       tstate->exc_value = value;
> >               ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17519): error: struct "_ts" has no field "exc_traceback"
> >       tstate->exc_traceback = tb;
> >               ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17562): error: struct "_ts" has no field "exc_type"
> >       tmp_type = tstate->exc_type;
> >                          ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17563): error: struct "_ts" has no field "exc_value"
> >       tmp_value = tstate->exc_value;
> >                           ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17564): error: struct "_ts" has no field "exc_traceback"
> >       tmp_tb = tstate->exc_traceback;
> >                        ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17565): error: struct "_ts" has no field "exc_type"
> >       tstate->exc_type = local_type;
> >               ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17566): error: struct "_ts" has no field "exc_value"
> >       tstate->exc_value = local_value;
> >               ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17567): error: struct "_ts" has no field "exc_traceback"
> >       tstate->exc_traceback = local_tb;
> >               ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17589): error: struct "_ts" has no field "exc_type"
> >       tmp_type = tstate->exc_type;
> >                          ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17590): error: struct "_ts" has no field "exc_value"
> >       tmp_value = tstate->exc_value;
> >                           ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17591): error: struct "_ts" has no field "exc_traceback"
> >       tmp_tb = tstate->exc_traceback;
> >                        ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17592): error: struct "_ts" has no field "exc_type"
> >       tstate->exc_type = *type;
> >               ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17593): error: struct "_ts" has no field "exc_value"
> >       tstate->exc_value = *value;
> >               ^
> >
> > PoissonSolver/MV_2D_cy/matvec2D.c(17594): error: struct "_ts" has no field "exc_traceback"
> >       tstate->exc_traceback = *tb;
> >               ^
> >
> > compilation aborted for PoissonSolver/MV_2D_cy/matvec2D.c (code 2)
> > error: command 'icc' failed with exit status 2
> > ===================
> > --
> > https://mail.python.org/mailman/listinfo/python-list