Setting up cryo-EM conda instance 

  • Log in to S3DF and then remote into an interactive pool node:
ssh iana
  • Start an interactive session on a GPU batch node:
    • Note that the topaz install is only tested on a turing host, so be sure to use that one. 
srun --partition turing --account cryoem:<proposal_number> -n 1 --time=01:00:00 --pty /bin/bash
  • Permanently add cryo-EM’s conda instance to your PATH environment variable 
echo "export PATH=/sdf/group/cryoem/sw/conda/bin:${PATH}" >> ~/.bashrc
  • Create a personal .condarc file at the top of your home directory and set the envs_dirs and pkg_dirs fields to make them point at somewhere in your /sdf/group/cryoem/g/<proposal_number>/... directory
$ cat ~/.condarc
channels:
  - defaults
  - anaconda
  - conda-forge
  - pytorch
envs_dirs:
  - /sdf/group/cryoem/g/<proposal_number>/conda/envs
pkgs_dirs:
  - /sdf/group/cryoem/g/<proposal_number>/conda/pkgs
auto_activate_base: false

Topaz Install 

  • Create the conda environment for topaz
conda create -n topaz python=3.6
source activate topaz
  • Install precompiled topaz package and its dependencies, including pytorch (note that as of Dec 2024, cryoSPARC is only compatible with topaz v0.2.5, so we must force the install to this version):
conda install topaz=0.2.5 mkl=2024.0.0 -c tbepler -c pytorch -c conda-forge
  • To test your install, run:
topaz --version
  • Deactivate your conda environment and leave the interactive batch node 
conda deactivate
exit

Connecting Topaz to CryoSPARC

  • When you run cryosparc, for the path to topaz executable, try the following path: 
/sdf/group/cryoem/g/<proposal_number>/conda/envs/topaz/bin/topaz


ALTERNATIVELY

  • Create a wrapper script in your home directory to connect topaz to cryosparc by using the command: nano ~/topaz.sh
  • Copy+paste the following into your file:
#!/usr/bin/env bash
if command -v conda > /dev/null 2>&1; then
    conda deactivate > /dev/null 2>&1 || true  # ignore any errors
    conda deactivate > /dev/null 2>&1 || true  # ignore any errors
fi

unset _CE_CONDA
unset CONDA_DEFAULT_ENV
unset CONDA_EXE
unset CONDA_PREFIX
unset CONDA_PROMPT_MODIFIER
unset CONDA_PYTHON_EXE
unset CONDA_SHLVL
unset PYTHONPATH
unset LD_PRELOAD
unset LD_LIBRARY_PATH

source /sdf/group/cryoem/sw/conda/etc/profile.d/conda.sh
conda activate topaz
topaz $@
  • Make this file executable by running
chmod +x ~/topaz.sh
  • When you run cryosparc, for the path to topaz executable, connect the file you just created (should be in a directory that looks like /sdf/home/<first letter of your username>/<your username>/topaz.sh )


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