Installing 3DFlex Dependencies
3DFlex jobs will not work without first installing the dependencies required to run the jobs.
Please ensure your system meets the following requirements:
- CryoSPARC v4.1 or higher
- Internet connection for downloading additional packages
- Nvidia driver version is 460.32.03 or newer on all GPU machines. Run
nvidia-smi
to verify - No CUDA directories are in your
PATH
orLD_LIBRARY_PATH
environment variables before running this command. To display the variables set in your environment, runexport
. Also ensure that the commandwhich nvcc
does not return a path tonvcc
.
Log onto each machine where
cryosparc_worker
is installed, and run the command cryosparcw install-3dflex
inside the cryosparc_worker
folder. For example:
cd cryosparc_worker
./bin/cryosparcw install-3dflex
Aside from the Nvidia driver, dependencies for 3DFlex jobs are downloaded during the
install-3dflex
commands. There is no need to supply any external dependencies.The
install-3dflex
command does the following:- Download and install CUDA Toolkit
- Download and install PyTorch with CUDA Toolkit
- Reinstall PyCUDA with CUDA Toolkit
- Verify PyTorch can use CUDA (Requires an NVIDIA GPU)
If you run this command on a machine without GPUs, you may see the message
PyTorch not installed correctly, or NVIDIA GPU not detected.
You may safely ignore this if there are no other error messages and the remaining verification tests pass.To further verify that your CryoSPARC instance is ready to run 3DFlex jobs, use the Installation Tests to check that PyTorch is working on every worker node connected to your CryoSPARC instance. For example:
cryosparcm test workers P1 --test gpu --test-pytorch
To uninstall the 3DFlex dependencies and return the worker to its original state, run
cryosparcw forcedeps
. For example:cd cryosparc_worker
./bin/cryosparcw forcedeps
After updating CryoSPARC to a new full or point release, 3DFlex dependencies can be updated by this sequence of two
cryosparcw
commands:cd cryosparc_worker
./bin/cryosparcw forcedeps
./bin/cryosparcw install-3dflex