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

References:

• Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. Castaño-Díez D, Kudryashev M, Arheit M, Stahlberg H., J Struct Biol. 2012.

• Dynamo Main Site

• Module Name: dynamo (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres=gpu:k80:2,lscratch:10 --mem=20g -c14
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load dynamo
[+] Loading dynamo  1.4.01  on cn3144 

[user@cn3144 ~]$ source dynamo_activate_linux_shipped_MCR.sh /usr/local/apps/dynamo/1.4.01/
MCR for linux has been  found in location: /dynamo/1.4.01/MCRLinux/v94
Activating Dynamo as standalone
-------------------------------------------------------------
 
              Dynamo Setup for standalone Linux 
 
-------------------------------------------------------------
 
       
1- Adding execution paths
   ----------------------
       
    Identifying directories of Dynamo distribution hanging from the specified Dynamo root directory: 
     /dynamo/1.4.01
 
    [OK] Done updating Linux paths.
       
2- Testing OpenMP
   --------------
       
    checking functionality of OpenMP wrappers....

    [OK] OpenMP tools seem functional
       
3- Testing MCR libraries
   ---------------------
       
    [OK] MCR library seems active
  
  
------------------------------------
Dynamo is ready for standalone use in your Linux system
 
[user@cn3144 ~]$ export MCR_CACHE_ROOT=/lscratch/$SLURM_JOBID

[user@cn3144 ~]$ dynamo
Initializing MATLAB Runtime version 9.4
"MCR libraries starting dynamo. Starting the Dynamo console can take some time. A good choice of MCR_CACHE_ROOT might speed this up."
Launching the console....
 (use "dynamo x" for a Dynamo graphics terminal  on a independent window)
 
     Dynamo console for standalone modus
     -----------------------------------
       
       
     * Commands starting with the symbol "!" will be passed to the system
     * Commands starting with the symbol "\" will be executed as Matlab expressions
     * Strings including the symbol ":" are treated as database queries
     * Graphic output: enabled
     * Type "help" for a list of console control commands
       
       
Dynamo > exit
ok, bye!
 

Exiting Dynamo console.
Returning control to system.
 

 
 Note after exiting the Dynamo console:
   
       if you experience difficulties with the text display you might need to type: 
       stty echo 
       in your system shell to fix them.
 
[delete:pmodelpool.Manager] Deletion of model pool manager from memory.

[user@cn3144 ~]dynamo x &
[1] 5233
[user@cn3144 ~]$ Initializing MATLAB Runtime version 9.4
"MCR libraries starting dynamo. Starting the Dynamo console can take some time. A good choice of MCR_CACHE_ROOT might speed this up."
Launching a Dynamo graphics terminal in a separate window....