Difference between revisions of "EMBO workshop 2020"

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* For the  Day 2 session: complete the  [[advanced starters guide]] (~2 hours)  
+
* Complete the  [[advanced starters guide]] (~2 hours)  
 
The data can be found in
 
The data can be found in
 
  <tt>/g/cryocourse/data/dynamo/crop.rec</tt>  
 
  <tt>/g/cryocourse/data/dynamo/crop.rec</tt>  
 
the chimera path you need in the tutorial is  
 
the chimera path you need in the tutorial is  
 
  <tt>/g/easybuild/x86_64/CentOS/7/haswell/software/Chimera/1.13-foss-2017b-Python-2.7.14/bin/chimera</tt>
 
  <tt>/g/easybuild/x86_64/CentOS/7/haswell/software/Chimera/1.13-foss-2017b-Python-2.7.14/bin/chimera</tt>
 
 
 
 
 
  
 
== Day 2 ==
 
== Day 2 ==

Revision as of 16:22, 7 August 2020

Materials

Day 1

Basic principles

Guided presentation:

Working on your own:

  • Basic walkthrough: creating a catalogue, picking particles, launching a project.
  • Further work:
    • tutorial on the use command line operations for general purposes.
    • tutorial on the use of the command line to manage projects.


The data can be found in

/g/cryocourse/data/dynamo/crop.rec 

the chimera path you need in the tutorial is

/g/easybuild/x86_64/CentOS/7/haswell/software/Chimera/1.13-foss-2017b-Python-2.7.14/bin/chimera

Day 2

Geometric modeling

Short guided presentation:

The data is available at

/g/cryocourse/data/dynamo/v17.rec


Day 3

Fiducial based alignment and reconstruction

These new features in Dynamo are at the testing stage.

GUI based alignment of tilt series

Walkthrough on GUI based tilt series alignment

Command line based alignment of tilt series

Walkthrough on command line based tilt series alignment

Manual clicking on gold beads

Walkthrough on manual marker clicking

Creation of 3D scenes

Working on your own:

Further support material.

  • Walkthrough on depiction and manipulation of triangulations (synthetic data).

Template matching

  • walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)

The data can be found in

/g/cryocourse/data/dynamo/t20s.mrc


Submitting jobs For GPU computing

The following is applicable for subtomogram averaging projects setup to be run in the "gpu_standalone" mode under computing environment.

Once your project is unfolded, you should have an executable file

wizardTestProject.exe

The EMBL-HD cluster uses slurm for job submission and resource allocation.

To run this project as a job on their computing resources, we should first set up a submission script, here is an example

#!/bin/bash
#SBATCH -N 1                        # number of nodes
#SBATCH -n 1                        # number of cores
#SBATCH -o slurm.%N.%j.out          # STDOUT
#SBATCH -e slurm.%N.%j.err          # STDERR
#SBATCH --mail-type=END,FAIL        # notifications for job done & fail
#SBATCH --mail-user=alisterburt@gmail.com # send-to address
#SBATCH -p gpu						# select gpu usage
#SBATCH --gres=gpu:1				# number of gpus (if using gpus)


module load dynamo
./wizardTestProject.exe

Save this text file in the same directory as the executable file, then submit the job using sbatch

sbatch dynamo_test_gpu.sl 

This should then confirm that the job has been submitted

Submitted batch job 65146729 

Submitting jobs for CPU computing

The following is applicable for subtomogram averaging projects setup to be run in the "standalone" mode under computing environment.

Once your project is unfolded, you should have an executable file

wizardTestProject.exe

The EMBL-HD cluster uses slurm for job submission and resource allocation.

To run this project as a job on their computing resources, we should first set up a submission script, here is an example using 6 cores on 1 node

#!/bin/bash
#SBATCH -N 1                        # number of nodes
#SBATCH -n 6                        # number of cores
#SBATCH -o slurm.%N.%j.out          # STDOUT
#SBATCH -e slurm.%N.%j.err          # STDERR
#SBATCH --mail-type=END,FAIL        # notifications for job done & fail
#SBATCH --mail-user=alisterburt@gmail.com # send-to address


module load dynamo
./wizardTestProject.exe

Save this text file in the same directory as the executable file, then submit the job using sbatch

sbatch dynamo_test_cpu.sl 

This should then confirm that the job has been submitted

Submitted batch job 65146755