Hey @chenzhao,
You can get around this by installing pycuda manually, then editing the config file to have the new path.
cd cryosparc2_worker
eval $(bin/cryosparcw env)
pip install "deps_bundle/python/python_packages/pip_packages/pycuda-2018.1.1.tar.gz" --no-cache-dir
nano cryosparc2_worker/config.sh
//edit the line CRYOSPARC_CUDA_PATH to have the new path
//save and exit