Biowulf High Performance Computing at the NIH
DYNAMO on Biowulf

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

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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....

The above should display dynamo's graphical interface.