Relion operation testing

1.1. Launch ParallelCluster

Create ParallelCluster by referring to step3.1 here.

1.2. Create Project directory

Connect Head node of ParallelCluster via NiceDCV (refer to step 3.3 here)

Open the terminal of Head node and run following commands.

See here and download relion tutorial data and prepare project didrectory.

$ cd /fsx 

$ wget ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/relion30_tutorial_data.tar

$ wget ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/relion50_tutorial_precalculated_results.tar.gz

$ tar -xf relion30_tutorial_data.tar

$ tar -zxf relion50_tutorial_precalculated_results.tar.gz

$ mv /fsx/relion30_tutorial /fsx/relion50_tutorial

$ rm -r /fsx/Tutorial5.0/Movies

$ mv /fsx/Tutorial5.0/* /fsx/relion50_tutorial

$ rm -r /fsx/Tutorial5.0

Copy test schemes for relion tutorial

$ cd relion50_tutorial

$ cp -r /efs/em/test_schemes/Schemes_relion5_tutorial_slurm_gpu ./     

Note: If testing relion for cpu-acceleration compilation, copy Schemes_relion5_tutorial_slurm_cpu

$ mv Schemes_relion5_tutorial_slurm_gpu Schemes/

1.3. Run Schemes for relion tutorial data.

Open the new terminal of Head node. Run following commands in relion project directory.

$ cd /fsx/relion50_tutorial

$ module unload relion

$ module load relion/5.0-beta-pc3.7.0/intel_amd-gcc-intelmpi-gpu     

Note: Switch to relion module to test 

$ module list

Currently Loaded Modulefiles:

 1) chimera/1.15(default)   2) relion/5.0-beta-pc3.7.0/intel_amd-gcc-intelmpi-gpu(default)

$ relion_schemegui.py relion5_tutorial_aws_pcluster &

When Schemes GUI starts, click dolop down list in "Set Scheme variable" and make sure that the following, executable file paths for each software is correct.

• ctffined_exe

• cryolo_repo

• cryolo_exe

The executable file paths are correct, you don't have to do anything.

If the executable file path is incorrect, input correct path in text box of new value and click [set] to updata the value in Scheme with the correct path.

After confirming the executable file path, click the [Restart] button to start Scheme.