Installing 3DFlex Dependencies (v4.1–v4.3)

All 3D Flex requirements are installed with CryoSPARC v4.4+. Skip this section unless you are running v4.1–v4.3.

In CryoSPARC v4.1–v4.3, 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 newer

  • 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 or LD_LIBRARY_PATH environment variables before running this command. To display the variables set in your environment, run export. Also ensure that the command which nvcc does not return a path to nvcc.

Installation of Dependencies

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

Update of Dependencies

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

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