Problem running HOOMD with AZPLUGINS

[tpaul-softmat]

Hello!

I am new to Hoomd-Blue. I am using HOOMD 4.8.2 on CPU. Recently, I tried to install 'azplugins' (https://github.com/mphowardlab/azplugins) which is supposedly compatible with this version. After a successful installation, I tried to test the installation by the following command, as suggested on the doc page:
python -m pytest --pyargs hoomd.azplugins

However, it returns one error. Please look at the attached screenshot of the error message.

I have tried changing the HOOMD version but with no help. Could you please suggest a possible solution to this?

Many thanks for considering my request.
Tanay.

[tcmoore3]

Hi Tanay, It looks like your azplugins install cannot find your HOOMD libraries. Without more information, it is impossible to know why. I recommend reaching out to the azplugins developers (with the CMake output from building and installing azplugins) for help. Tim

…

On Thu, Nov 7, 2024 at 6:00 PM tpaul-softmat ***@***.***> wrote: Hello! I am new to Hoomd-Blue. I am using HOOMD 4.8.2 on CPU. Recently, I tried to install 'azplugins' (https://github.com/mphowardlab/azplugins) which is supposedly compatible with this version. After a successful installation, I tried to test the installation by the following command, as suggested on the doc page: *python -m pytest --pyargs hoomd.azplugins* However, it returns one error. Please look at the attached screenshot of the error message. azplugins-test-error.png (view on web) <https://github.com/user-attachments/assets/42bf6b73-abe3-4823-a983-ef10bfb2bc23> I have tried changing the HOOMD version but with no help. Could you please suggest a possible solution to this? Many thanks for considering my request. Tanay. — Reply to this email directly, view it on GitHub <#1930>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABMLTGFZJQVXTXASHWRT42TZ7PWJPAVCNFSM6AAAAABRMISXKSVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZXGQ2DEMRYGE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[mphoward]

Are you able to run any of the regular HOOMD unit tests, or do you get the same error?

https://hoomd-blue.readthedocs.io/en/v4.9.1/testing.html#running-tests

[tpaul-softmat]

Thank you all for your responses!

As @mphoward asked, I tried running some regular HOOMD unit tests. I was unsure about the build directory, though. So, I am giving all the details and uploading the corresponding snapshots below. For your information, I installed HOOMD using conda.

1. I used Python to find where HOOMD is installed by doing the following:

   import hoomd
print(hoomd.__file__)

   The output was anaconda3/lib/python3.11/site-packages/hoomd. Then I ran python3 -m pytest in that directory. It returned the same errors I got while testing for azplugins. Below I attach the snapshot of the error messages.

   

2. Next, I checked if HOOMD initializes properly using the following script:

   import hoomd
device = hoomd.device.auto_select()
sim = hoomd.Simulation(device=device)

   It ran without error.

3. Next, I navigated to the subdirectory pytest in anaconda3/lib/python3.11/site-packages/hoomd and ran pytest. Among 2868 items, 2846 passed, and 22 were skipped. Please have a look at the snapshot attached below.

   

Please let me know whether I have successfully tested the HOOMD installation. If not, then could you let me know how to do that? If HOOMD is correctly installed, please let me know where the problem is and how to rectify it.

Thanks again for your time and assistance. Best regards,
Tanay.

[joaander]

For future reference, python3 -m pytest --pyargs hoomd (as mentioned in the documentation) will test the HOOMD-blue installation in your current python environment. There is no need to switch directories.

[tpaul-softmat]

Many thanks, for the clarification. I tried with --pyargs flag. The same errors I got.

[joaander]

You posted images of text, not actual text. This makes it frustrating to try to reply as I cannot copy and paste relevant portions of your output. My reply is therefore somewhat vague.

That being said: I have seen this type of error before when an extension module is imported before the main _hoomd.so which defines the base classes. @mphoward, or one of the other azplugins developers, should check their code and tests to ensure that import hoomd appears before any import of an azplugins .so file.

[tpaul-softmat]

@mphoward Thanks for your response.

I installed HOOMD using conda:
$ conda install -c conda-forge hoomd=4.8.2
For the installation of azplugins, I followed the instructions given in the azplugins GitHub page:

$ git clone https://github.com/mphowardlab/azplugins
$ cmake -B build/azplugins -S azplugins
$ cmake --build build/azplugins
$ cmake --install build/azplugins

[mphoward]

Thanks! Are you then also running the pytest command from the same location as the last step?

[tpaul-softmat]

Yes, at the same location, with the --pyargs flag.
To test HOOMD: $ python3 -m pytest --pyargs hoomd
To test azplugins: $ python3 -m pytest --pyargs hoomd.azplugins
Both are returning the same error.

[joaander]

It is possible that there are ABI incompatibilities if your compilation environment does not match what conda-forge uses to build hoomd-blue.

Try uninstalling hoomd-blue and building it from source as well. You will then need to clear the azplugins build/ directory and rebuild it as well.

[tpaul-softmat]

Many thanks for the suggestion.

I tried uninstalling hoomd-blue and building it from the source. After the installation, tests for hoomd were completed successfully. Next, I tried to reinstall azplugins, which gave me the following errors in the cmake --build build/azplugins step:

Consolidate compiler generated dependencies of target _azplugins
[  4%] Building CXX object src/CMakeFiles/_azplugins.dir/export_AnisoPotentialPairTwoPatchMorse.cc.o
In file included from /home/tanay/build/azplugins/src/export_AnisoPotentialPairTwoPatchMorse.cc:9:
/home/tanay/anaconda3/lib/python3.11/site-packages/hoomd/include/hoomd/md/AnisoPotentialPair.h: In instantiation of ‘void hoomd::md::detail::export_AnisoPotentialPair(pybind11::module&, const string&) [with T = hoomd::azplugins::detail::AnisoPairEvaluatorTwoPatchMorse; pybind11::module = pybind11::module_; std::string = std::__cxx11::basic_string<char>]’:
/home/tanay/build/azplugins/src/export_AnisoPotentialPairTwoPatchMorse.cc:24:66:   required from here
/home/tanay/anaconda3/lib/python3.11/site-packages/hoomd/include/hoomd/md/AnisoPotentialPair.h:708:43: error: ‘getShapeParamName’ is not a member of ‘hoomd::azplugins::detail::AnisoPairEvaluatorTwoPatchMorse’
  708 |         .def(("set" + T::getShapeParamName()).c_str(), &AnisoPotentialPair<T>::setShapePython)
      |                       ~~~~~~~~~~~~~~~~~~~~^~
/home/tanay/anaconda3/lib/python3.11/site-packages/hoomd/include/hoomd/md/AnisoPotentialPair.h:709:43: error: ‘getShapeParamName’ is not a member of ‘hoomd::azplugins::detail::AnisoPairEvaluatorTwoPatchMorse’
  709 |         .def(("get" + T::getShapeParamName()).c_str(), &AnisoPotentialPair<T>::getShapePython)
      |                       ~~~~~~~~~~~~~~~~~~~~^~
gmake[2]: *** [src/CMakeFiles/_azplugins.dir/build.make:216: src/CMakeFiles/_azplugins.dir/export_AnisoPotentialPairTwoPatchMorse.cc.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:117: src/CMakeFiles/_azplugins.dir/all] Error 2
gmake: *** [Makefile:136: all] Error 2

I think this happened because of a version mismatch between hoomd and azplugins. When I built hoomd by cloning that from the GitHub repository with the command $ git clone --recursive https://github.com/glotzerlab/hoomd-blue, automatically the latest version, which I believe is 4.9.1, is downloaded. However, azplugins works with as latest as hoomd-4.8.2. If my guess is correct, please let me know how to install hoomd-4.8.2 or older versions by building it from the source. Also, please let me know how to uninstall the already installed versions of hoomd before reinstalling an older version if needed.

Thank you very much for your constant support.

[mphoward]

You can checkout the right tag after you clone

cd hoomd-blue
git checkout v4.8.2

We haven't bumped azplugins to test against 4.9.1, so we will have a look at that.

[tpaul-softmat]

Many thanks for the help.

This worked. Tests for both hoomd and azplugins are completed successfully. So, the solution is to build hoomd first from the source by checking out the right version compatible with azplugins after cloning from GitHub and then to add azplugins to hoomd.

Thank you, @mphoward, @joaander, and @tcmoore3, for all of your valuable suggestions and help.

[joaander]

@mphoward have you considered releasing azplugins on conda-forge? That way, users could install binaries directly.