Running and Verification

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the test directory.

   cd /path/to/CASE

3. Decompress the test case file.

   tar xvf relion_benchmark.tar.gz

4. Go to the directory generated after the decompression.

   cd relion_benchmark

5. Perform the RELION test.

   mkdir class3d
   yum -y install time
   time -p mpirun --allow-run-as-root -n 4 relion_refine_mpi --j 24 --gpu 0 --pool 100 --dont_combine_weights_via_disc --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --maxsig 500 --fast_subsets --o class3d/test01