simpeg
BUG: cannot import scipy.interpolate.quadrature for SciPy >= 1.5.0
Hello,
I'm trying to install SimPEGEM1D, but I'm getting an error with the fortran compiler. I have standard SimPEG 14.0 running. I already had in my PC the fortran 95 from Silverfrost and I also have installed through conda : conda install -c conda-forge fortran-compiler . I also installed MinGW64 I add everything to my Path but still not working.
Would you please help me?
@jc-barreto we are currently updating the simpegEM1D repository so that we can add it directly to the SimPEG framework. The master branch of this repository is actually not compatible with the latest version of SimPEG. If you need to use this code right away, I suggest working on the branch "update_to_simulation" within the simpegEM1D repository. Please note this branch is being actively worked on.
The Fortran addon will speed up the runtime for any simulation or inversion but it is not actually necessary for running the code. If the Fortran is not compiled, the same operations will instead be performed purely in Python.
Hi @jc-barreto,
The fortran compiler should be handled now by scipy anyway.
What I would recommend doing is to install SimPEG from conda-forge
conda install -c conda-forge simpeg=0.13.1
Once that's done, just path the simpegEM1D folder to your system environments under a PYTHONPATH variable.
On Windows, it should look like this.
This should do the trick... no need to run the setup.py
Hi @jc-barreto,
I am sorry to hear that you are having problem for installing. Below is the copy and paste from #28:
1- Install tdm64-gcc-5.1.0
2- Download and unzip the fortran compiler (overwrite) in the C:\TDM-GCC-64 directory
3- Add the C:\TDM-GCC-64\bin to your PATH environment
(Since you have other compilers installed, you might also need to temporarily remove them from your path.)
4- In a command terminal run conda uninstall mingw, this makes sure that the install goes through the TDM-GCC-64 compiler.
5- Re-run the pip install simpegEM1D
Try this, and let us know if you still have problem. Also, try pip install SimPEG==0.13.1 because simpegEM1D is not up-to-date for the latest SimPEG version.
Hello @dccowan , @sgkang and @domfournier thank you for the answers. I have first tried the solution proposed by @domfournier but unfortunately didn't work.
1- So I created a new env, and I installed SimPEG = 0.13.1
2- I tried the one @sgkang, and for that one, I had to modify a little, because with the step 2 didn't work. After installing TDM-GCC-64 and doing all the steps I tried to install SimPEGEM1D, didn't work. So I uninstall everything and install it again without doing the step 2, and this worked for installing SimPEGEM1D.
My problem now is that when I try to run the example from the notebook folder in simpegEM1d it gives an error with scipy.
ModuleNotFoundError: No module named 'scipy.integrate.quadrature'
But I have scipy installed, it was installed when I installed SimPEG 0.13.1
Do you know why is not working? is it because the Scipy version? The one I have is 1.5.0
No, it is not the SciPy version. This is potentially a bug, as quadrature has first to be imported.
Try running this before the other commands:
from scipy.integrate import quadrature
That should hopefully work.
Actually it might be the SciPy version @jc-barreto . If above doesn't work try installing older SciPy versions, e.g. 1.3 or so.
Yeah, that is it. It is probably broken since SciPy 1.5.0, as quadrature was moved to a private namespace _quadrature. So installing SciPy < 1.5.0 should be fine.
Maybe we should open a separate issue with this.
Here the change in SciPy https://github.com/scipy/scipy/commit/d1c119150d1c11eb9025b21afc5505ff3ee42911#diff-44389779461bd39a8cfbcac8e69e470eL89
@prisae It was a problem with SciPy version, I installed the 1.3 and worked. thank you
Hi @jc-barreto - Great it worked! I reopen and rename the issue, as it is actually a bug and we should fix it. Thanks for reporting.