Building AZ Plugins with HOOMD Blue 2.9.6

[gauravmitra1995]

Hi everyone,

I am having an issue with building AZ plugins with HOOMD 2.9.6. I have HOOMD 2.9.6 installed using conda. I have git cloned the repository for azplugins (https://github.com/mphowardlab/azplugins.git)
and when I try to do:

cmake -B build/azplugins -S azplugins

it gives me the following error:

dyld[47127]: Library not loaded: @rpath/librhash.0.dylib
Referenced from: <276AFB20-1FE1-3459-BFD7-8ABFEE0D7EED> /Users/gauravmitra/anaconda3/envs/hoomdtest/bin/cmake
Reason: tried: '/Users/gauravmitra/anaconda3/envs/hoomdtest/bin/../lib/librhash.0.dylib' (no such file), '/Users/gauravmitra/anaconda3/envs/hoomdtest/bin/../lib/librhash.0.dylib' (no such file), '/usr/local/lib/librhash.0.dylib' (no such file), '/usr/lib/librhash.0.dylib' (no such file, not in dyld cache)
zsh: abort cmake -B build/azplugins -S azplugins

I am not sure where I am going wrong. My Python version is 3.8.5

(hoomdtest) (.venv) gauravmitra@Gauravs-MacBook-Pro Condensates_softwares % python --version
Python 3.8.5

Please help.

Best,
Gaurav

[mphoward]

The most recent release of azplugins (1.1.0) requires HOOMD 5, so it should not build with HOOMD 2.9.6. I do not provide backsupport for older releases of azplugins, so I recommend upgrading your HOOMD installation and trying again.

If the problem persists, it may be an incompatibility between the conda installation and your own compilers (see #1930). In that case, I suggest compiling HOOMD from source.

[mphoward]

zsh: command not found: cmake

Install cmake...

[mphoward]

Did you install HOOMD's build dependencies?

https://hoomd-blue.readthedocs.io/en/v5.1.0/building.html

[gauravmitra1995]

I did now....using micromamba

(hoomdtest_5.0.0) gauravmitra@Gauravs-MacBook-Pro Condensates_softwares % cmake -B build/azplugins -S azplugins
-- Performing Test HAS_FLTO_THIN
-- Performing Test HAS_FLTO_THIN - Success
-- Found pybind11: /Users/gauravmitra/anaconda3/envs/hoomdtest_5.0.0/include (found version "2.13.6")
-- Found pybind11: /Users/gauravmitra/anaconda3/envs/hoomdtest_5.0.0/share/cmake/pybind11 /Users/gauravmitra/anaconda3/envs/hoomdtest_5.0.0/include (version 2.13.6)
-- Found eigen: /Users/gauravmitra/anaconda3/envs/hoomdtest_5.0.0/share/eigen3/cmake /Users/gauravmitra/anaconda3/envs/hoomdtest_5.0.0/include/eigen3 (version 3.4.0)
-- Found HOOMD 5.0.0: /Users/gauravmitra/anaconda3/envs/hoomdtest_5.0.0/lib/python3.9/site-packages/hoomd
-- Configuring done (1.0s)
-- Generating done (0.0s)
-- Build files have been written to: /Users/gauravmitra/Condensates_softwares/build/azplugins

(hoomdtest_5.0.0) gauravmitra@Gauravs-MacBook-Pro Condensates_softwares % cmake --build build/azplugins
[ 3%] Building CXX object src/CMakeFiles/_azplugins.dir/ConstantFlow.cc.o
In file included from /Users/gauravmitra/Condensates_softwares/azplugins/src/ConstantFlow.cc:5:
In file included from /Users/gauravmitra/Condensates_softwares/azplugins/src/ConstantFlow.h:9:
In file included from /Users/gauravmitra/anaconda3/envs/hoomdtest_5.0.0/include/pybind11/pybind11.h:12:
In file included from /Users/gauravmitra/anaconda3/envs/hoomdtest_5.0.0/include/pybind11/detail/class.h:12:
In file included from /Users/gauravmitra/anaconda3/envs/hoomdtest_5.0.0/include/pybind11/attr.h:13:
/Users/gauravmitra/anaconda3/envs/hoomdtest_5.0.0/include/pybind11/detail/common.h:314:10: fatal error: 'cstddef' file not found
314 | #include
| ^~~~~~~~~
1 error generated.
make[2]: *** [src/CMakeFiles/_azplugins.dir/ConstantFlow.cc.o] Error 1
make[1]: *** [src/CMakeFiles/_azplugins.dir/all] Error 2
make: *** [all] Error 2

Got an error in this step.

[mphoward]

cstddef is part of the standard library, so you have something setup incorrectly in your build environment.

I can't help you learn how to compile software on your computer. Please consult with your research advisor or HPC admins to get with setting up the appropriate compilers and dependencies.

[gauravmitra1995]

Okay, thanks a lot!