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A conda-smithy repository for adios.

License: BSD 3-Clause "New" or "Revised" License

Shell 50.55% Python 49.45%

adios-feedstock's Introduction

About adios-feedstock

Feedstock license: BSD-3-Clause

Home: https://www.olcf.ornl.gov/center-projects/adios/

Package license: BSD-3-Clause

Summary: The Adaptable IO System (ADIOS) for flexible and fast scientific data processing.

Development: https://github.com/ornladios/ADIOS

Documentation: https://users.nccs.gov/~pnorbert/ADIOS-UsersManual-1.13.1.pdf

The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation. By providing an external to the code XML file describing the various elements, their types, and how you wish to process them this run, the routines in the host code (either Fortran or C) can transparently change how they process the data.

Current build status

Travis

Azure

Variant	Status
linux_64_mpimpich
linux_64_mpinompi
linux_64_mpiopenmpi
linux_aarch64_mpimpich
linux_aarch64_mpinompi
linux_aarch64_mpiopenmpi
linux_ppc64le_mpimpich
linux_ppc64le_mpinompi
linux_ppc64le_mpiopenmpi
osx_64_mpimpich
osx_64_mpinompi
osx_64_mpiopenmpi
osx_arm64_mpimpich
osx_arm64_mpinompi
osx_arm64_mpiopenmpi

Current release info

Name	Downloads	Version	Platforms

Installing adios

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

conda config --add channels conda-forge
conda config --set channel_priority strict

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

conda install adios

or with mamba:

mamba install adios

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

conda search adios --channel conda-forge

or with mamba:

mamba search adios --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search adios --channel conda-forge

# List packages depending on `adios`:
mamba repoquery whoneeds adios --channel conda-forge

# List dependencies of `adios`:
mamba repoquery depends adios --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 Azure, GitHub, CircleCI, AppVeyor, Drone, 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 adios-feedstock

If you would like to improve the adios 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/adios-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

@ax3l

adios-feedstock's People

Contributors

Stargazers

Watchers

Forkers

ax3l regro-cf-autotick-bot chrisburr

adios-feedstock's Issues

HDF5 Support

ADIOS has a transport to HDF5.

The build hdf5 tools such as bp2h5 and h52bp are useful.

Adding HDF5 to configure fails with a compile check error in autotools.

IIRC, the parallel HDF5 transport (not super performant) and the serial HDF5 tools don't build at the same time.

Fortran Support

Issue: For some reason, adding Fortran bindings does not work yet and fails in a libtool error.

Update: libtool works, now it's a compile error because somehow the scripts forget the - when passing -DHAVE_CONFIG_H to make...

Bug identified, only in no-MPI mode:
https://github.com/ornladios/ADIOS/blob/v1.13.1/tests/test_src/Makefile.am#L121

Let's add support for it!

Add MPI Variant

Add new MPI variants with (No-MPI as now, OpenMPI and MPICH).

Apple M1 Builds Broken

The apple aarch64/arm64 builds are actually building x86 binaries and are thus broken.

Seen in conda-forge/warpx-feedstock#51

~~We need to~~

~~purge them~~
~~disable them~~

conda install does not provide python module

Issue:
After installing adios via conda, I cam use the exectuables bpls etc. but i can not load adios as python module:

>>> import adios
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'adios'

I used the python from the newly created adios environment. Executing which bpls returns ~/.conda/envs/adios/bin/bpls. I can use other via conda freshly installed modules like h5py (pointing to the adios environment).

Environment:
Python 3.6.8 from Anaconda, Inc. - via the local cluster module
created a clean environment via conda conda create --name adios
installed numpy, matplotlib, scipy, h5py, jupyter via conda
installed adios via conda via: conda install -c conda-forge adios

$ conda list

adios                     1.13.1          nompi_h7bdf1ca_1112    conda-forge
backcall                  0.1.0                    py36_0  
blas                      1.0                         mkl  
bleach                    3.1.0                    py36_0  
blosc                     1.15.1            hf484d3e_1002    conda-forge
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2018.12.5                     0  
certifi                   2018.11.29               py36_0  
cycler                    0.10.0                   py36_0  
dbus                      1.13.6               h746ee38_0  
decorator                 4.3.0                    py36_0  
entrypoints               0.3                      py36_0  
expat                     2.2.6                he6710b0_0  
fontconfig                2.13.0               h9420a91_0  
freetype                  2.9.1                h8a8886c_1  
glib                      2.56.2               hd408876_0  
gmp                       6.1.2                h6c8ec71_1  
gst-plugins-base          1.14.0               hbbd80ab_1  
gstreamer                 1.14.0               hb453b48_1  
h5py                      2.9.0            py36h7918eee_0  
hdf5                      1.10.4               hb1b8bf9_0  
icu                       58.2                 h9c2bf20_1  
intel-openmp              2019.1                      144  
ipykernel                 5.1.0            py36h39e3cac_0  
ipython                   7.2.0            py36h39e3cac_0  
ipython_genutils          0.2.0                    py36_0  
ipywidgets                7.4.2                    py36_0  
jedi                      0.13.2                   py36_0  
jinja2                    2.10                     py36_0  
jpeg                      9b                   h024ee3a_2  
jsonschema                2.6.0                    py36_0  
jupyter                   1.0.0                    py36_7  
jupyter_client            5.2.4                    py36_0  
jupyter_console           6.0.0                    py36_0  
jupyter_core              4.4.0                    py36_0  
kiwisolver                1.0.1            py36hf484d3e_0  
libedit                   3.1.20181209         hc058e9b_0  
libffi                    3.2.1                hd88cf55_4  
libgcc-ng                 8.2.0                hdf63c60_1  
libgfortran-ng            7.3.0                hdf63c60_0  
libpng                    1.6.36               hbc83047_0  
libsodium                 1.0.16               h1bed415_0  
libstdcxx-ng              8.2.0                hdf63c60_1  
libuuid                   1.0.3                h1bed415_2  
libxcb                    1.13                 h1bed415_1  
libxml2                   2.9.9                he19cac6_0  
markupsafe                1.1.0            py36h7b6447c_0  
matplotlib                3.0.2            py36h5429711_0  
mistune                   0.8.4            py36h7b6447c_0  
mkl                       2019.1                      144  
mkl_fft                   1.0.10           py36ha843d7b_0  
mkl_random                1.0.2            py36hd81dba3_0  
mpi4py                    2.0.0                    py36_2  
mpich2                    1.4.1p1                       0  
nbconvert                 5.3.1                    py36_0  
nbformat                  4.4.0                    py36_0  
ncurses                   6.1                  he6710b0_1  
notebook                  5.7.4                    py36_0  
numpy                     1.15.4           py36h7e9f1db_0  
numpy-base                1.15.4           py36hde5b4d6_0  
openssl                   1.1.1a               h7b6447c_0  
pandoc                    2.2.3.2                       0  
pandocfilters             1.4.2                    py36_1  
parso                     0.3.1                    py36_0  
pcre                      8.42                 h439df22_0  
pexpect                   4.6.0                    py36_0  
pickleshare               0.7.5                    py36_0  
pip                       18.1                     py36_0  
prometheus_client         0.5.0                    py36_0  
prompt_toolkit            2.0.7                    py36_0  
ptyprocess                0.6.0                    py36_0  
pygments                  2.3.1                    py36_0  
pyparsing                 2.3.1                    py36_0  
pyqt                      5.9.2            py36h05f1152_2  
python                    3.6.8                h0371630_0  
python-dateutil           2.7.5                    py36_0  
pytz                      2018.9                   py36_0  
pyzmq                     17.1.2           py36he6710b0_2  
qt                        5.9.7                h5867ecd_1  
qtconsole                 4.4.3                    py36_0  
readline                  7.0                  h7b6447c_5  
scipy                     1.2.0            py36h7c811a0_0  
send2trash                1.5.0                    py36_0  
setuptools                40.6.3                   py36_0  
sip                       4.19.8           py36hf484d3e_0  
six                       1.12.0                   py36_0  
sqlite                    3.26.0               h7b6447c_0  
terminado                 0.8.1                    py36_1  
testpath                  0.4.2                    py36_0  
tk                        8.6.8                hbc83047_0  
tornado                   5.1.1            py36h7b6447c_0  
traitlets                 4.3.2                    py36_0  
wcwidth                   0.1.7                    py36_0  
webencodings              0.5.1                    py36_1  
wheel                     0.32.3                   py36_0  
widgetsnbextension        3.4.2                    py36_0  
xz                        5.2.4                h14c3975_4  
zeromq                    4.3.1                he6710b0_3  
zlib                      1.2.11               h7b6447c_3

Details about conda and system ( conda info ):

$ conda info

     active environment : adios
    active env location : /home/.../.conda/envs/adios
            shell level : 1
       user config file : /home/.../.condarc
 populated config files : 
          conda version : 4.4.7
    conda-build version : not installed
         python version : 3.6.4.final.0
       base environment : /sw/taurus/libraries/python/3.6-anaconda4.4.0  (read only)
           channel URLs : https://repo.continuum.io/pkgs/main/linux-64
                          https://repo.continuum.io/pkgs/main/noarch
                          https://repo.continuum.io/pkgs/free/linux-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/linux-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/linux-64
                          https://repo.continuum.io/pkgs/pro/noarch
          package cache : /sw/taurus/libraries/python/3.6-anaconda4.4.0/pkgs
                          /home/.../.conda/pkgs
       envs directories : /home/.../.conda/envs
                          /sw/taurus/libraries/python/3.6-anaconda4.4.0/envs
               platform : linux-64
             user-agent : conda/4.4.7 requests/2.18.4 CPython/3.6.4 Linux/3.10.0-693.21.1.el7.x86_64 rhel/7.4 glibc/2.17
                UID:GID : 66053:200046
             netrc file : None
           offline mode : False