Hi,
When i try to install cryosparc master, everything is going well until i got pycuda issue. Please check the attached. Does anyone know what is going on?
Preparing transaction: done
Executing transaction: done
installation finished.
Done.
anaconda python installation successful.
Extracting all conda packages…
…
Done.
conda packages installation successful.
Preparing to install all pip packages…
Processing ./deps_bundle/python/python_packages/pip_packages/pycuda-2020.1.tar.gz
Preparing metadata (setup.py) … done
Building wheels for collected packages: pycuda
Building wheel for pycuda (setup.py) … error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [13157 lines of output]
*************************************************************
*** I have detected that you have not run configure.py.
*************************************************************
*** Additionally, no global config files were found.
*** I will go ahead with the default configuration.
pe) [with ExceptionType = pycuda::error; Translate = void ()(const pycuda::error&)]’
src/wrapper/wrap_cudadrv.cpp:691:74: required from here
bpl-subset/bpl_subset/boost/function/function_base.hpp:318:54: warning: placement new constructing an object of type ‘pycudaboost::detail::function::functor_manager_common<pycudaboost::_bi::bind_t<bool, pycudaboost::python::detail::translate_exception<pycuda::error, void ()(const pycuda::error&)>, pycudaboost::_bi::list3<pycudaboost::arg<1>, pycudaboost::arg<2>, pycudaboost::_bi::value<void ()(const pycuda::error&)> > > >::functor_type’ {aka ‘pycudaboost::_bi::bind_t<bool, pycudaboost::python::detail::translate_exception<pycuda::error, void ()(const pycuda::error&)>, pycudaboost::_bi::list3<pycudaboost::arg<1>, pycudaboost::arg<2>, pycudaboost::_bi::value<void ()(const pycuda::error&)> > >’} and size ‘16’ in a region of type ‘char’ and size ‘1’ [-Wplacement-new=]
new (reinterpret_cast<void*>(&out_buffer.data)) functor_type(*in_functor);
~~~~~~~~~^~
error: command ‘/usr/bin/gcc’ failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure
× Encountered error while trying to install package.
╰─> pycuda
note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
check_install_deps.sh: 66: ERROR: installing python failed.
the command that you ran to get this error. Please conceal any email address, license id, password that may have been included in the command
the outputs of these commands
gcc --version
nvidia-smi --query-gpu=index,name,driver_version --format=csv
# based on what you provided for --cudapath
/path/to/cuda/bin/nvcc --version
export | grep PATH
In case /usr/local/cuda points to a toolkit version 12 or newer, please be aware that 11.8 is the latest version of the toolkit currently supported by CryoSPARC, and that you may have better luck re-trying the installation with --cudapath usr/local/cuda-11.6, if that directory inside your $LD_LIBRARY_PATH does indeed contain a viable toolkit.
Thank you for troubleshooting. I re-run these commonds, it gave output below
1: gcc --version
output: gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-18)
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
2: readlink -e $(which gcc)
output: /usr/bin/gcc
3: /usr/local/bin/nvcc --version
output: -bash: /usr/local/bin/nvcc: No such file or directory
I tried as you said, but when i got another issue below when i run cryosparcm restart,
CryoSPARC is not already running.
If you would like to restart, use cryosparcm restart
Starting cryoSPARC System master process…
CryoSPARC is not already running.
configuring database
configuration complete
database: started
checkdb success
command_core: ERROR (spawn error)