conda-forge / hoomd-feedstock

A conda-smithy repository for hoomd.

About hoomd-feedstock

Feedstock license: BSD-3-Clause

Home: https://glotzerlab.engin.umich.edu/hoomd-blue/

Package license: BSD-3-Clause

Summary: HOOMD-blue is a general-purpose particle simulation toolkit.

Development: https://github.com/glotzerlab/hoomd-blue/

Documentation: https://hoomd-blue.readthedocs.io

HOOMD-blue is a general-purpose particle simulation toolkit, implementing molecular dynamics and hard particle Monte Carlo optimized for fast execution on both GPUs and CPUs. As a Python package, HOOMD-blue gives you the flexibility to create custom initialization routines, control simulation parameters, perform in situ analysis, use interactive notebooks, and more.

Current build status

Azure

Variant Status linux_64_cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.22python3.10.____cpythonpython_implcpython linux_64_cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.22python3.8.____cpythonpython_implcpython linux_64_cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.22python3.9.____cpythonpython_implcpython linux_64_cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.23python3.11.____cpythonpython_implcpython linux_64_cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.26python3.12.____cpythonpython_implcpython linux_64_cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.10.____cpythonpython_implcpython linux_64_cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.8.____cpythonpython_implcpython linux_64_cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.9.____cpythonpython_implcpython linux_64_cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.23python3.11.____cpythonpython_implcpython linux_64_cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.26python3.12.____cpythonpython_implcpython linux_64_cuda_compilernvcccuda_compiler_version11.2cxx_compiler_version10numpy1.22python3.10.____cpythonpython_implcpython linux_64_cuda_compilernvcccuda_compiler_version11.2cxx_compiler_version10numpy1.22python3.8.____cpythonpython_implcpython linux_64_cuda_compilernvcccuda_compiler_version11.2cxx_compiler_version10numpy1.22python3.9.____cpythonpython_implcpython linux_64_cuda_compilernvcccuda_compiler_version11.2cxx_compiler_version10numpy1.23python3.11.____cpythonpython_implcpython linux_64_cuda_compilernvcccuda_compiler_version11.2cxx_compiler_version10numpy1.26python3.12.____cpythonpython_implcpython linux_64_cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.10.____cpythonpython_implcpython linux_64_cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.8.____cpythonpython_implcpython linux_64_cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.9.____cpythonpython_implcpython linux_64_cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.23python3.11.____cpythonpython_implcpython linux_64_cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.26python3.12.____cpythonpython_implcpython osx_64_numpy1.22python3.10.____cpythonpython_implcpython osx_64_numpy1.22python3.8.____cpythonpython_implcpython osx_64_numpy1.22python3.9.____cpythonpython_implcpython osx_64_numpy1.23python3.11.____cpythonpython_implcpython osx_64_numpy1.26python3.12.____cpythonpython_implcpython osx_arm64_numpy1.22python3.10.____cpython osx_arm64_numpy1.22python3.8.____cpython osx_arm64_numpy1.22python3.9.____cpython osx_arm64_numpy1.23python3.11.____cpython osx_arm64_numpy1.26python3.12.____cpython

Current release info

Name	Downloads	Version	Platforms

Installing hoomd

Installing hoomd 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, hoomd can be installed with conda:

conda install hoomd

or with mamba:

mamba install hoomd

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

conda search hoomd --channel conda-forge

or with mamba:

mamba search hoomd --channel conda-forge

Alternatively, mamba repoquery may provide more information:

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

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

# List dependencies of `hoomd`:
mamba repoquery depends hoomd --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.org 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 hoomd-feedstock

If you would like to improve the hoomd 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/hoomd-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

• @b-butler
• @bdice
• @joaander

hoomd-feedstock's Issues

CMake config files installed to incorrect location.

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

The hoomd-config.cmake file as well as the rest of the files usually found in $CONDA_PREFIX/lib/cmake/hoomd when compiling HOOMD-blue oneself are not copied to a conda environment when installing hoomd.

This would be useful for external hoomd plugins to be build and distributed via conda-forge.

Installed packages

Name                      Version       Build                Channel    
────────────────────────────────────────────────────────────────────────────
  _libgcc_mutex             0.1           conda_forge          conda-forge
  _openmp_mutex             4.5           2_gnu                conda-forge
  attrs                     22.2.0        pyh71513ae_0         conda-forge
  binutils_impl_linux-64    2.39          he00db2b_1           conda-forge
  brotlipy                  0.7.0         py310h5764c6d_1005   conda-forge
  bzip2                     1.0.8         h7f98852_4           conda-forge
  c-ares                    1.18.1        h7f98852_0           conda-forge
  ca-certificates           2022.12.7     ha878542_0           conda-forge
  cachecontrol              0.12.11       pyhd8ed1ab_0         conda-forge
  certifi                   2022.12.7     pyhd8ed1ab_0         conda-forge
  cffi                      1.15.1        py310h255011f_3      conda-forge
  charset-normalizer        2.1.1         pyhd8ed1ab_0         conda-forge
  clang                     14.0.6        ha770c72_0           conda-forge
  clang-14                  14.0.6        default_h2e3cab8_0   conda-forge
  clangxx                   14.0.6        default_ha074a59_0   conda-forge
  cleo                      2.0.1         pyhd8ed1ab_0         conda-forge
  cmake                     3.25.2        h077f3f9_0           conda-forge
  crashtest                 0.4.1         pyhd8ed1ab_0         conda-forge
  cryptography              39.0.0        py310h34c0648_0      conda-forge
  cudatoolkit               11.8.0        h37601d7_11          conda-forge
  dbus                      1.13.6        h5008d03_3           conda-forge
  distlib                   0.3.6         pyhd8ed1ab_0         conda-forge
  dulwich                   0.20.50       py310h1fa729e_0      conda-forge
  expat                     2.5.0         h27087fc_0           conda-forge
  filelock                  3.9.0         pyhd8ed1ab_0         conda-forge
  gcc                       12.2.0        h26027b1_11          conda-forge
  gcc_impl_linux-64         12.2.0        hcc96c02_19          conda-forge
  gettext                   0.21.1        h27087fc_0           conda-forge
  hoomd                     3.8.0         gpu_py310h1ad6b7a_0  conda-forge
  html5lib                  1.1           pyh9f0ad1d_0         conda-forge
  icu                       70.1          h27087fc_0           conda-forge
  idna                      3.4           pyhd8ed1ab_0         conda-forge
  importlib-metadata        4.11.4        py310hff52083_0      conda-forge
  importlib_metadata        4.11.4        hd8ed1ab_0           conda-forge
  importlib_resources       5.10.2        pyhd8ed1ab_0         conda-forge
  jaraco.classes            3.2.3         pyhd8ed1ab_0         conda-forge
  jeepney                   0.8.0         pyhd8ed1ab_0         conda-forge
  jsonschema                4.17.3        pyhd8ed1ab_0         conda-forge
  kernel-headers_linux-64   2.6.32        he073ed8_15          conda-forge
  keyring                   23.13.1       py310hff52083_0      conda-forge
  keyutils                  1.6.1         h166bdaf_0           conda-forge
  krb5                      1.20.1        h81ceb04_0           conda-forge
  ld_impl_linux-64          2.39          hcc3a1bd_1           conda-forge
  libblas                   3.9.0         16_linux64_openblas  conda-forge
  libcblas                  3.9.0         16_linux64_openblas  conda-forge
  libclang-cpp              14.0.6        default_h2e3cab8_0   conda-forge
  libclang-cpp14            14.0.6        default_h2e3cab8_0   conda-forge
  libcurl                   7.87.0        hdc1c0ab_0           conda-forge
  libcxx                    14.0.6        hf52228f_0           conda-forge
  libcxxabi                 14.0.6        ha770c72_0           conda-forge
  libedit                   3.1.20191231  he28a2e2_2           conda-forge
  libev                     4.33          h516909a_1           conda-forge
  libffi                    3.4.2         h7f98852_5           conda-forge
  libgcc-devel_linux-64     12.2.0        h3b97bd3_19          conda-forge
  libgcc-ng                 12.2.0        h65d4601_19          conda-forge
  libgfortran-ng            12.2.0        h69a702a_19          conda-forge
  libgfortran5              12.2.0        h337968e_19          conda-forge
  libglib                   2.74.1        h606061b_1           conda-forge
  libgomp                   12.2.0        h65d4601_19          conda-forge
  libhwloc                  2.8.0         h32351e8_1           conda-forge
  libiconv                  1.17          h166bdaf_0           conda-forge
  liblapack                 3.9.0         16_linux64_openblas  conda-forge
  libllvm14                 14.0.6        he0ac6c6_1           conda-forge
  libnghttp2                1.51.0        hff17c54_0           conda-forge
  libnsl                    2.0.0         h7f98852_0           conda-forge
  libopenblas               0.3.21        pthreads_h78a6416_3  conda-forge
  libsanitizer              12.2.0        h46fd767_19          conda-forge
  libsqlite                 3.40.0        h753d276_0           conda-forge
  libssh2                   1.10.0        hf14f497_3           conda-forge
  libstdcxx-devel_linux-64  12.2.0        h3b97bd3_19          conda-forge
  libstdcxx-ng              12.2.0        h46fd767_19          conda-forge
  libuuid                   2.32.1        h7f98852_1000        conda-forge
  libuv                     1.44.2        h166bdaf_0           conda-forge
  libxml2                   2.10.3        h7463322_0           conda-forge
  libzlib                   1.2.13        h166bdaf_4           conda-forge
  lockfile                  0.12.2        py_1                 conda-forge
  micromamba                1.2.0         1                    conda-forge
  more-itertools            9.0.0         pyhd8ed1ab_0         conda-forge
  msgpack-python            1.0.4         py310hbf28c38_1      conda-forge
  ncurses                   6.3           h27087fc_1           conda-forge
  numpy                     1.24.1        py310h08bbf29_0      conda-forge
  openssl                   3.0.7         h0b41bf4_1           conda-forge
  packaging                 23.0          pyhd8ed1ab_0         conda-forge
  pcre2                     10.40         hc3806b6_0           conda-forge
  pexpect                   4.8.0         pyh1a96a4e_2         conda-forge
  pip                       22.3.1        pyhd8ed1ab_0         conda-forge
  pkginfo                   1.9.6         pyhd8ed1ab_0         conda-forge
  pkgutil-resolve-name      1.3.10        pyhd8ed1ab_0         conda-forge
  platformdirs              2.6.2         pyhd8ed1ab_0         conda-forge
  poetry                    1.3.2         linux_pyhd8ed1ab_0   conda-forge
  poetry-core               1.4.0         pyhd8ed1ab_0         conda-forge
  poetry-plugin-export      1.2.0         pyhd8ed1ab_1         conda-forge
  ptyprocess                0.7.0         pyhd3deb0d_0         conda-forge
  pybind11-abi              4             hd8ed1ab_3           conda-forge
  pycparser                 2.21          pyhd8ed1ab_0         conda-forge
  pyopenssl                 23.0.0        pyhd8ed1ab_0         conda-forge
  pyrsistent                0.19.3        py310h1fa729e_0      conda-forge
  pysocks                   1.7.1         pyha2e5f31_6         conda-forge
  python                    3.10.8        h4a9ceb5_0_cpython   conda-forge
  python_abi                3.10          3_cp310              conda-forge
  rapidfuzz                 2.13.7        py310heca2aa9_0      conda-forge
  readline                  8.1.2         h0f457ee_0           conda-forge
  requests                  2.28.2        pyhd8ed1ab_0         conda-forge
  requests-toolbelt         0.10.1        pyhd8ed1ab_0         conda-forge
  rhash                     1.4.3         h166bdaf_0           conda-forge
  secretstorage             3.3.3         py310hff52083_1      conda-forge
  setuptools                66.1.1        pyhd8ed1ab_0         conda-forge
  shellingham               1.5.0.post1   pyhd8ed1ab_0         conda-forge
  six                       1.16.0        pyh6c4a22f_0         conda-forge
  sysroot_linux-64          2.12          he073ed8_15          conda-forge
  tbb                       2021.7.0      h924138e_1           conda-forge
  tk                        8.6.12        h27826a3_0           conda-forge
  tomli                     2.0.1         pyhd8ed1ab_0         conda-forge
  tomlkit                   0.11.6        pyha770c72_0         conda-forge
  trove-classifiers         2023.1.20     pyhd8ed1ab_0         conda-forge
  typing                    3.10.0.0      pyhd8ed1ab_0         conda-forge
  typing-extensions         4.4.0         hd8ed1ab_0           conda-forge
  typing_extensions         4.4.0         pyha770c72_0         conda-forge
  tzdata                    2022g         h191b570_0           conda-forge
  urllib3                   1.26.14       pyhd8ed1ab_0         conda-forge
  virtualenv                20.17.1       py310hff52083_0      conda-forge
  webencodings              0.5.1         py_1                 conda-forge
  wheel                     0.38.4        pyhd8ed1ab_0         conda-forge
  xz                        5.2.6         h166bdaf_0           conda-forge
  zipp                      3.11.0        pyhd8ed1ab_0         conda-forge
  zlib                      1.2.13        h166bdaf_4           conda-forge
  zstd                      1.5.2         h3eb15da_6           conda-forge

Environment info

environment : hoomd-pysages (active)
           env location : ~/.mamba/envs/hoomd-pysages
      user config files : ~/.mambarc
 populated config files : ~/.condarc
       libmamba version : 1.2.0
     micromamba version : 1.2.0
           curl version : libcurl/7.87.0 OpenSSL/1.1.1s zlib/1.2.13 libssh2/1.10.0 nghttp2/1.47.0
     libarchive version : libarchive 3.6.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.2
       virtual packages : __unix=0=0
                          __linux=6.0.12=0
                          __glibc=2.35=0
                          __archspec=1=x86_64
                          __cuda=11.7=0
               channels : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
       base environment : ~/.mamba
               platform : linux-64

[warning] failed package validation and/or copy for commit 59a3623561166fb78842c5790b3eacda1175e377

Hi @conda-forge/hoomd! This is the friendly automated conda-forge-webservice!

It appears that one or more of your feedstock's outputs did not copy from the
staging channel (cf-staging) to the production channel (conda-forge). :(

This failure can happen for a lot of reasons, including an outdated feedstock
token. Below we have put some information about the failure to help you debug it.

Rerendering the feedstock will usually fix these problems.

If you have any issues or questions, you can find us on Element in the
community channel or you can bump us right here.

output validation (is this output allowed for your feedstock?):

• linux-64/hoomd-4.0.1-gpu_py311h2171c2e_2.conda: True

copied (did this output get copied to the production channel?):

• linux-64/hoomd-4.0.1-gpu_py311h2171c2e_2.conda: False

LLVM install bring in mismatched libraries and headers

Installing HOOMD in a fresh mambaforge environment pulls in:

  + clang                13.0.1  hce30654_0            conda-forge/osx-arm64     128kB
  + clang-13             13.0.1  default_h2cfa9b4_0    conda-forge/osx-arm64       1MB
  + clangxx              13.0.1  default_hf584372_0    conda-forge/osx-arm64     128kB
  + hoomd                 3.3.0  cpu_py39hb778b30_0    conda-forge/osx-arm64       7MB
  + libblas               3.9.0  15_osxarm64_openblas  conda-forge/osx-arm64      13kB
  + libcblas              3.9.0  15_osxarm64_openblas  conda-forge/osx-arm64      13kB
  + libclang-cpp         14.0.6  default_h81a5282_0    conda-forge/osx-arm64     130kB
  + libclang-cpp13       13.0.1  default_h2cfa9b4_0    conda-forge/osx-arm64      13MB
  + libclang-cpp14       14.0.6  default_h81a5282_0    conda-forge/osx-arm64      14MB
  + libgfortran      5.0.0.dev0  11_0_1_hf114ba7_23    conda-forge/osx-arm64      20kB
  + libgfortran5    11.0.1.dev0  hf114ba7_23           conda-forge/osx-arm64     923kB
  + liblapack             3.9.0  15_osxarm64_openblas  conda-forge/osx-arm64      13kB
  + libllvm14            14.0.6  h37c5ba8_0            conda-forge/osx-arm64      26MB
  + libopenblas          0.3.20  openmp_h130de29_1     conda-forge/osx-arm64       4MB
  + llvm-openmp          14.0.4  hd125106_0            conda-forge/osx-arm64     304kB
  + numpy                1.23.1  py39h7df2422_0        conda-forge/osx-arm64       6MB
  + tbb                2021.5.0  h3e96240_1            conda-forge/osx-arm64     129kB

libclang-cpp14=14.0.6 apparently causes HOOMD to search for includes in mambaforge/lib/clang/14.0.6 which doesn't exist in this installation.

• llvm-openmp=14.0.4 created mambaforge/lib/clang/14.0.4/include/omp.h
• clang=13.0.1 created mambaforge/lib/clang/13.0.1/include with the needed files.

Proposed fix:

Pin llvmdev, clangdev, libclang-cpp, libcxx, clang, and clangxx all to the same version (14.0.6 is the latest at the moment). @tcmoore3 please make this change in a new pull request from your fork.