Relion Cryoem for Satorians

Prerequisites

A local installation of an X11 server is required to use the Relion GUI.

On a Mac computer the XQuartz ( https://www.xquartz.org ) software is a good option.

On a Window computer Cygwin/X ( http://x.cygwin.com ) software provides a free X server.

Quick start

• Transfer data

Data should be transferred to: /nobackup/users/your_kerbos_id . Use satori-login-002.mit.edu

• To access the Relion GUI

  1. Login:

     ssh -Y username@satori-login-002.mit.edu
     

  2. Submit a fake job to access a node:

     bsub -q normal sleep 7200
     

  3. Use bjobs to determine the node of the job ie:

     JOBID   USER    STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
     45954   seyvos  RUN   normal     service0002 node0028.in sleep 7200 Mar 10 13:50
     

  4. Login into the node:

     ssh -X node0028
     

  5. Add paths to access relion libraries:

     export PATH=/nobackup/users/ruzhu/RELION/bin:/nobackup/users/ruzhu/CTFfind4/bin:/opt/ibm/spectrum_mpi/bin:$PATH
     export LD_LIBRARY_PATH=/opt/ibm/spectrum_mpi/profilesupport/lib:/nobackup/users/ruzhu/CTFfind4/lib:$LD_LIBRARY_PATH
     

  6. Open Relion by typing:

     relion
     

  7. Use GUI to configure your job.

  8. Use “Print” command to print job commands to terminal.

  9. Adjust the relion submission script to incorporate the commands specific to your job. Note: If you have a job that requires a lot of memory, you should alter the --n and --j values. Save submission script. Make sure paths for --o already exist.

  10. Execute job

      bsub< run
      

  11. Check job is running with bjobs. Submission script generates a log file.

• Example job

Below is an example of a job file that Relion should generate. The file you generate should look something like this.

#BSUB -L /bin/bash
#BSUB -J "Relion"
#BSUB -o "Relion.%J"
#BSUB -n 40
#BSUB -R "span[ptile=40]"
#BSUB -gpu "num=4"
#BSUB -q "normal"

export PATH=/nobackup/users/ruzhu/RELION/bin:/nobackup/users/ruzhu/CTFfind4/bin:/opt/ibm/spectrum_mpi/bin:$PATH
export LD_LIBRARY_PATH=/nobackup/users/ruzhu/CTFfind4/lib:$LD_LIBRARY_PATH

#source ~/anaconda3/bin/activate
#conda activate CryoEM

unset CUDA_VISIBLE_DEVICES
export CUDA_VISIBLE_DEVICES="0,1,2,3"
(time -p mpirun -bind-to none -n 9 relion_refine_mpi --j 4 --gpu --pool 50 --dont_combine_weights_via_disc --scratch_dir /dev/shm  --o Refine3D/job005 --auto_refine --split_random_halves --i squirrel2.star --ref Import/job004/postprocess_refine850_resampled_775.mrc --firstiter_cc --ini_high 40  --ctf --ctf_corrected_ref --particle_diameter 340 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --sym C1 --low_resol_join_halves 40 --norm --scale) >run_21x8.log 2>&1

Other notes