Dynamo is a software environment for subtomogram averaging of cryo-EM data.

Usage on the IGBMC cluster

Running the Dynamo UI

Connect to Open OnDemand : https://ondemand.igbmc.fr

If you need help to get started with Open OnDemand, please visit Open OnDemand page.

Start a Desktop session

To know more about using the Desktop go to our Desktop documentation.

Once connected to the Desktop, open the Terminal application

Load the dynamo module:

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module load dynamo/1.1.532

Dynamo has been deployed on the IGBMC cluster using Singularity. That is why module will automatically load singularity when you load dynamo

You can now start Matlab by typing:

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matlab

If you see the message INFO: Could not find any nv files on this host ! it means that there is no GPU available in your current session. You can ignore this message if you don’t need GPU at this time.

Once Matlab is started, load dynamo using the following command inside the Matlab window:

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run /opt/DYNAMO/dynamo_activate.m

Dynamo is now activated and the Matlab shell will recognize any Dynamo command. You can type for instance:

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dynamo;

Running the dynamo from the command line

Dynamo is shipped with a headless Matlab runtime. This means that you can use the Dynamo commands outside of Matlab as well.

Connect to the cluster using SSH or the Open OnDemand Cluster shell access

ssh hpc.igbmc.fr

Load the dynamo module

module load dynamo/1.1.532

You can now use the following dynamo commands directly :

• dynamo
• dynamo_ccmatrix_assemble
• dynamo_ccmatrix_compute
• dynamo_execute_project
• dynamo_iteration_assemble
• dynamo_iteration_check
• dynamo_iteration_compute
• dynamo_iteration_compute_mpi_gpu_node
• dynamo_iteration_setup
• dynamo_MCR_testing
• dynamo_plugin_post_multireference_tutorial
• dynamo_plugin_xmipp_assemble
• dynamo_plugin_xmipp_compute
• dynamo_plugin_xmipp_setup
• dynamos