conda-forge / pytrilinos-feedstock

A conda-smithy repository for pytrilinos.

About pytrilinos

Home: https://trilinos.github.io

Package license: BSD-3-Clause

Feedstock license: BSD-3-Clause

Summary: Python interfaces to Sandia's suite of HPC solvers and enabling technologies

Development: https://github.com/trilinos/Trilinos

Python interfaces to fast, compiled object-oriented algorithms and enabling technologies that support the solution of large-scale, complex multi-physics engineering and scientific problems.

Current build status

Azure

Variant Status linux_64_mpimpichpython3.6.____cpython linux_64_mpimpichpython3.7.____cpython linux_64_mpimpichpython3.8.____cpython linux_64_mpiopenmpipython3.6.____cpython linux_64_mpiopenmpipython3.7.____cpython linux_64_mpiopenmpipython3.8.____cpython osx_64_mpimpichpython3.6.____cpython osx_64_mpimpichpython3.7.____cpython osx_64_mpimpichpython3.8.____cpython osx_64_mpiopenmpipython3.6.____cpython osx_64_mpiopenmpipython3.7.____cpython osx_64_mpiopenmpipython3.8.____cpython

Current release info

Name	Downloads	Version	Platforms

Installing pytrilinos

Installing pytrilinos from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge

Once the conda-forge channel has been enabled, pytrilinos can be installed with:

conda install pytrilinos

It is possible to list all of the versions of pytrilinos available on your platform with:

conda search pytrilinos --channel conda-forge

About conda-forge

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by CircleCI, AppVeyor and TravisCI it is possible to build and upload installable packages to the conda-forge Anaconda-Cloud channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating pytrilinos-feedstock

If you would like to improve the pytrilinos recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/pytrilinos-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

• If the version of a package is not being increased, please add or increase the build/number.
• If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

• @pyt-viper

pytrilinos-feedstock's Issues

Can't import modules on Mac OS X

$ conda create -n trilinos --channel conda-forge "mpich=3.2.*" mpi4py python "numpy>=1.7" pytrilinos
Fetching package metadata .............
Solving package specifications: .

Package plan for installation in environment /Users/guyer/anaconda/envs/trilinos:

The following NEW packages will be INSTALLED:

    blas:            1.1-openblas                  conda-forge
    ca-certificates: 2018.1.18-0                   conda-forge
    certifi:         2018.1.18-py27_0              conda-forge
    libgfortran:     3.0.0-0                       conda-forge
    mpi4py:          3.0.0-py27_0                  conda-forge
    mpich:           3.2-5                         conda-forge
    ncurses:         5.9-10                        conda-forge
    numpy:           1.14.1-py27_blas_openblas_200 conda-forge [blas_openblas]
    openblas:        0.2.20-7                      conda-forge
    openmpi:         3.0.0-0                       conda-forge
    openssl:         1.0.2n-0                      conda-forge
    pip:             9.0.1-py27_1                  conda-forge
    python:          2.7.14-4                      conda-forge
    pytrilinos:      12.10.1-py27_1                conda-forge
    readline:        7.0-0                         conda-forge
    scipy:           1.0.0-py27_blas_openblas_201  conda-forge [blas_openblas]
    setuptools:      38.5.1-py27_0                 conda-forge
    sqlite:          3.20.1-2                      conda-forge
    tk:              8.6.7-0                       conda-forge
    wheel:           0.30.0-py27_2                 conda-forge
    zlib:            1.2.11-0                      conda-forge

Proceed ([y]/n)? 

certifi-2018.1 100% |###########################################################################################################| Time: 0:00:00   3.81 MB/s
setuptools-38. 100% |###########################################################################################################| Time: 0:00:00   3.40 MB/s
#
# To activate this environment, use:
# > source activate trilinos
#
# To deactivate an active environment, use:
# > source deactivate
#

$ source activate trilinos
(trilinos) $ python exAztecOO.py 
Traceback (most recent call last):
  File "exAztecOO.py", line 71, in <module>
    from PyTrilinos import Epetra
  File "/Users/guyer/anaconda/envs/trilinos/lib/python2.7/site-packages/PyTrilinos/Epetra.py", line 73, in <module>
    _Epetra = swig_import_helper()
  File "/Users/guyer/anaconda/envs/trilinos/lib/python2.7/site-packages/PyTrilinos/Epetra.py", line 72, in swig_import_helper
    return importlib.import_module('_Epetra')
  File "/Users/guyer/anaconda/envs/trilinos/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
ImportError: No module named _Epetra

Libopenblas not found

Issue:

While trying to import the Epetra package, I get the following error.

python -c 'from PyTrilinos import Epetra'

Traceback (most recent call last):
File "", line 1, in
File "/home/jc.giret/.conda/envs/trilinos/lib/python2.7/site-packages/PyTrilinos/Epetra.py", line 73, in
_Epetra = swig_import_helper()
File "/home/jc.giret/.conda/envs/trilinos/lib/python2.7/site-packages/PyTrilinos/Epetra.py", line 72, in swig_import_helper
return importlib.import_module('_Epetra')
File "/home/jc.giret/.conda/envs/trilinos/lib/python2.7/importlib/init.py", line 37, in import_module
import(name)
ImportError: libopenblas.so.0: cannot open shared object file: No such file or directory

Then, I install manually openblas by typing the following command under the right conda env:

conda install -c conda-forge openblas

When I try again the same python command as before:

python -c 'from PyTrilinos import Epetra'

I get the following error:

Traceback (most recent call last):
File "", line 1, in
File "/home/jc.giret/.conda/envs/trilinos/lib/python2.7/site-packages/PyTrilinos/Epetra.py", line 73, in
_Epetra = swig_import_helper()
File "/home/jc.giret/.conda/envs/trilinos/lib/python2.7/site-packages/PyTrilinos/Epetra.py", line 70, in swig_import_helper
return importlib.import_module(mname)
File "/home/jc.giret/.conda/envs/trilinos/lib/python2.7/importlib/init.py", line 37, in import_module
import(name)
ValueError: mpi4py.MPI.Message has the wrong size, try recompiling. Expected 40, got 32

This is strange as both MPICH and MPI4Py have been installed by conda.

Environment (conda list):

blas 1.0 mkl anaconda

ca-certificates 2019.1.23 0 anaconda

certifi 2019.3.9 py27_0 anaconda

intel-openmp 2019.3 199 anaconda

libedit 3.1.20181209 hc058e9b_0 anaconda

libffi 3.2.1 h4deb6c0_3 anaconda

libgcc-ng 8.2.0 hdf63c60_1 anaconda

libgfortran 3.0.0 1 anaconda

libgfortran-ng 7.3.0 hdf63c60_0 anaconda

libstdcxx-ng 8.2.0 hdf63c60_1 anaconda

mkl 2019.3 199 anaconda

mkl_fft 1.0.10 py27ha843d7b_0 anaconda

mkl_random 1.0.2 py27hd81dba3_0 anaconda

mpi 1.0 mpich anaconda

mpi4py 2.0.0 py27_2 anaconda

mpich 3.2.1 hf39692e_8 anaconda

mpich2 1.4.1p1 0 anaconda

ncurses 6.1 he6710b0_1 anaconda

numpy 1.16.2 py27h7e9f1db_0 anaconda

numpy-base 1.16.2 py27hde5b4d6_0 anaconda

openssl 1.1.1 h7b6447c_0 anaconda

pip 19.0.3 py27_0 anaconda

python 2.7.16 h9bab390_0 anaconda

pytrilinos 12.10.1 py27h7127e17_2 conda-forge

readline 7.0 h7b6447c_5 anaconda

setuptools 41.0.0 py27_0 anaconda

sqlite 3.27.2 h7b6447c_0 anaconda

tk 8.6.8 hbc83047_0 anaconda

wheel 0.33.1 py27_0 anaconda

zlib 1.2.11 h7b6447c_3 anaconda

Details about conda and system ( conda info ):

active environment : trilinos
active env location : /home/jc.giret/.conda/envs/trilinos
shell level : 2
user config file : /home/jc.giret/.condarc
populated config files :
conda version : 4.5.4
conda-build version : 3.10.9
python version : 2.7.15.final.0
base environment : /opt/anaconda/envs/python27_2 (read only)
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/linux-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/pro/linux-64
https://repo.anaconda.com/pkgs/pro/noarch
package cache : /opt/anaconda/envs/python27_2/pkgs
/home/jc.giret/.conda/pkgs
envs directories : /home/jc.giret/.conda/envs
/opt/anaconda/envs/python27_2/envs
platform : linux-64
user-agent : conda/4.5.4 requests/2.14.2 CPython/2.7.15 Linux/2.6.32-696.3.1.el6.x86_64 centos/6.9 glibc/2.12
UID:GID : 20719:10513
netrc file : None
offline mode : False

@conda-forge-admin please rerender

Additional comment:

No response

Post-processing script

I would like to add a post-processing script that runs after PyTrilinos gets built that alters the export files for cmake and make. it will remove the pytrilinos library from these files so that users trying to link against Trilinos will not link against any of the Python wrappers.

I think I know how to do this, so this issue report is just tracking purposes.

Can't import modules on macOS (again)

As previously reported (#10), imports on macOS fail with

ImportError: Unable to load solver trilinos: No module named _ML

or similar.

This was previously remedied by the upload of 12.10.1 build 2.

Can you please remove or hide the osx-64/pytrilinos-12.10.1-py27_0.tar.bz2 and osx-64/pytrilinos-12.10.1-py27_1.tar.bz2 builds? They are broken and conda seems to keep changing its precedence semantics, such that build 2 is not reliably found first.

Linux Circle-CI failing

The Linux Circle-CI is flagged as failing. Checking the report, everything appears to build and test properly, but the report ends with

TEST END: /feedstock_root/build_artefacts/linux-64/pytrilinos-12.10.1-py27_0.tar.bz2
INFO:conda_build.config:--dirty flag and --keep-old-work not specified.Removing build/test folder after successful build/test.

# Automatic uploading is disabled
# If you want to upload package(s) to anaconda.org later, type:

anaconda upload /feedstock_root/build_artefacts/linux-64/pytrilinos-12.10.1-py27_0.tar.bz2

# To have conda build upload to anaconda.org automatically, use
# $ conda config --set anaconda_upload yes

anaconda_upload is not set.  Not uploading wheels: []
+ test -f /home/circleci/test/build_artefacts/conda-forge-build-done
+ exit 1
Exited with code 1

I don't know where to proceed from here.

Split trilinos into separate package from pytrilinos

Add a trilinos feedstock, with an identical build recipe as pytrilinos, except that the Python wrappers are not enabled. Make this a requirement for pytrilinos.

Task list:

• Create trilinos feedstocks
  • 12.10.1, Linux, mpich
  • 12.10.1, Linux, openmpi
  • 12.10.1, Mac OS X, mpich
  • 12.10.1, Mac OS X, openmpi
  • 12.12.1, Linux, mpich
  • 12.12.1, Linux, openmpi
  • 12.12.1, Mac OS X, mpich
  • 12.12.1, Mac OS X, openmpi
• Develop new pytrilinos feedstocks that depend on trilinos
  • 12.10.1, Linux, mpich
  • 12.10.1, Linux, openmpi
  • 12.10.1, Mac OS X, mpich
  • 12.10.1, Mac OS X, openmpi
  • 12.12.1, Linux, mpich, python 2
  • 12.12.1, Linux, openmpi, python 2
  • 12.12.1, Mac OS X, mpich, python 2
  • 12.12.1, Mac OS X, openmpi, python 2
  • 12.12.1, Linux, mpich, python 3
  • 12.12.1, Linux, openmpi, python 3
  • 12.12.1, Mac OS X, mpich, python 3
  • 12.12.1, Mac OS X, openmpi, python 3

PyTrilinos for Windows

I would like to expand the pytrilinos recipe to include Windows, but I do not have a Windows machine set up for scientific computing to test on. How should I proceed?