Re: FiPy on Linux
Am 20.07.18 um 03:20 schrieb Carsten Langrock: > Hi, > > Since the macOS install didn’t result in much, I tried it under Linux. No > luck, > it’s actually even worse. I cannot import fipy without generating errors. It > appears to hang on > > ‘Could not import any solver package’ > > I saw that some reported the same problem but I didn’t see a solution. SciPy > is > installed, of course. This is following the recommended installation modality > using miniconda. The conda-based approach works for me with Python 3.6 on MacOS and Windows. I have not tried on Linux yet. I created a new conda-environment for Python 3.6 first, activated it, and installed the required packages. BTW, NumPy will get new Python 2 releases only for about 5 months: """ Until December 31, 2018, all NumPy releases will fully support both Python2 and Python3. Starting on January 1, 2019, any new feature releases will support only Python3. """ https://docs.scipy.org/doc/numpy/neps/dropping-python2.7-proposal.html Seems like a good reason to fully support Python 3. Mike > > Carsten > > _ > *Dipl.-Phys. Carsten Langrock, Ph.D.* > > Senior Research Scientist > Edward L. Ginzton Laboratory, Rm. 202 > Stanford University > > 348 Via Pueblo Mall > 94305 Stanford, CA > > Tel. (650) 723-0464 > Fax (650) 723-2666 > > Ginzton Lab Shipping Address: > James and Anna Marie Spilker Engineering and Applied Sciences Building > 04-040 > 348 Via Pueblo Mall > 94305 Stanford, CA > _ > > > ___ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
Re: FiPy on Linux
Augh. This much I can explain: I copied the installation from .travis.yml without thinking about it. `conda create` does not explicitly install fipy because the whole point of that file is to test the current git commit, which is done later in the recipe. Adding `fipy` to the `conda create` line should be sufficient. I believe the gmsh issue is that the [gmsh-feedstock](https://github.com/guyer/gmsh-feedstock) recipe I wrote has a runtime dependency on gcc that isn't satisfied on Debian, but is on the Ubuntu image that TravisCI sets up. I'll not be able to look into this for at least three weeks. Ideally, the gcc dependency should not be necessary, but reckless usage of apt-get could probably resolve the issue. As I recall, attempting to run gmsh from the command line is more instructive than letting fipy do it. > On Jul 20, 2018, at 1:28 PM, Keller, Trevor (Fed) > wrote: > > Hi Carsten, > > Unfortunately, I can confirm that the Conda-based process does not currently > work on > Debian 9. > > $ ./Miniconda3-latest-Linux-x86_64.sh > $ cat /absolute/path/to/miniconda/etc/profile.d/conda.sh >> ~/.bashrc > $ . ~/.bashrc > $ conda update conda > $ conda create --name fipy --channel guyer --channel conda-forge python=2.7 > numpy scipy gmsh pysparse mpi4py matplotlib mayavi fipytrilinos weave > $ conda activate fipy > $ python > Python 2.7.15 | packaged by conda-forge | (default, May 8 2018, 14:46:53) > [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>> import fipy > Traceback (most recent call last): > File "", line 1, in > ImportError: No module named fipy > >>> > > I can partially work around this problem by hybridizing the Conda and GitHub > installation methods, > i.e. let Conda install the prereqs, then install FiPy from source. > $ conda activate fipy > $ conda install -n fipy gmsh > $ git clone https://github.com/usnistgov/fipy > $ cd fipy > $ python setup.py install > $ python > Python 2.7.15 | packaged by conda-forge | (default, May 8 2018, 14:46:53) > [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>> from fipy import test > >>> test() > ... > -- > Ran 347 tests in 4.113s > > OK > !!! > Skipped 105 doctest examples because `gmsh` cannot be found on the $PATH > Skipped 83 doctest examples because the `tvtk` package cannot be imported > !!! > >>> > > The failure to recognize gmsh -- which is most definitely present on $PATH -- > is vexing. > Thanks for bringing this to our attention. > > Trevor > From: fipy-boun...@nist.gov on behalf of Carsten > Langrock > Sent: Thursday, July 19, 2018 9:20:54 PM > To: FIPY > Subject: FiPy on Linux > > Hi, > > Since the macOS install didn’t result in much, I tried it under Linux. No > luck, it’s actually even worse. I cannot import fipy without generating > errors. It appears to hang on > > ‘Could not import any solver package’ > > I saw that some reported the same problem but I didn’t see a solution. SciPy > is installed, of course. This is following the recommended installation > modality using miniconda. > > Carsten > > _ > Dipl.-Phys. Carsten Langrock, Ph.D. > > Senior Research Scientist > Edward L. Ginzton Laboratory, Rm. 202 > Stanford University > > 348 Via Pueblo Mall > 94305 Stanford, CA > > Tel. (650) 723-0464 > Fax (650) 723-2666 > > Ginzton Lab Shipping Address: > James and Anna Marie Spilker Engineering and Applied Sciences Building > 04-040 > 348 Via Pueblo Mall > 94305 Stanford, CA > _ > ___ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
Re: FiPy on Linux
Hi Carsten, Unfortunately, I can confirm that the Conda-based process does not currently work on Debian 9. $ ./Miniconda3-latest-Linux-x86_64.sh $ cat /absolute/path/to/miniconda/etc/profile.d/conda.sh >> ~/.bashrc $ . ~/.bashrc $ conda update conda $ conda create --name fipy --channel guyer --channel conda-forge python=2.7 numpy scipy gmsh pysparse mpi4py matplotlib mayavi fipytrilinos weave $ conda activate fipy $ python Python 2.7.15 | packaged by conda-forge | (default, May 8 2018, 14:46:53) [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import fipy Traceback (most recent call last): File "", line 1, in ImportError: No module named fipy >>> I can partially work around this problem by hybridizing the Conda and GitHub installation methods, i.e. let Conda install the prereqs, then install FiPy from source. $ conda activate fipy $ conda install -n fipy gmsh $ git clone https://github.com/usnistgov/fipy $ cd fipy $ python setup.py install $ python Python 2.7.15 | packaged by conda-forge | (default, May 8 2018, 14:46:53) [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from fipy import test >>> test() ... -- Ran 347 tests in 4.113s OK !!! Skipped 105 doctest examples because `gmsh` cannot be found on the $PATH Skipped 83 doctest examples because the `tvtk` package cannot be imported !!! >>> The failure to recognize gmsh -- which is most definitely present on $PATH -- is vexing. Thanks for bringing this to our attention. Trevor ____ From: fipy-boun...@nist.gov on behalf of Carsten Langrock Sent: Thursday, July 19, 2018 9:20:54 PM To: FIPY Subject: FiPy on Linux Hi, Since the macOS install didn’t result in much, I tried it under Linux. No luck, it’s actually even worse. I cannot import fipy without generating errors. It appears to hang on ‘Could not import any solver package’ I saw that some reported the same problem but I didn’t see a solution. SciPy is installed, of course. This is following the recommended installation modality using miniconda. Carsten _ Dipl.-Phys. Carsten Langrock, Ph.D. Senior Research Scientist Edward L. Ginzton Laboratory, Rm. 202 Stanford University 348 Via Pueblo Mall 94305 Stanford, CA Tel. (650) 723-0464 Fax (650) 723-2666 Ginzton Lab Shipping Address: James and Anna Marie Spilker Engineering and Applied Sciences Building 04-040 348 Via Pueblo Mall 94305 Stanford, CA _ ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
FiPy on Linux
Hi, Since the macOS install didn’t result in much, I tried it under Linux. No luck, it’s actually even worse. I cannot import fipy without generating errors. It appears to hang on ‘Could not import any solver package’ I saw that some reported the same problem but I didn’t see a solution. SciPy is installed, of course. This is following the recommended installation modality using miniconda. Carsten _Dipl.-Phys. Carsten Langrock, Ph.D. Senior Research Scientist Edward L. Ginzton Laboratory, Rm. 202 Stanford University 348 Via Pueblo Mall 94305 Stanford, CA Tel. (650) 723-0464 Fax (650) 723-2666 Ginzton Lab Shipping Address: James and Anna Marie Spilker Engineering and Applied Sciences Building 04-040 348 Via Pueblo Mall 94305 Stanford, CA _ ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
