Difference between revisions of "Analysis AWS"

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${PATH} is the path to the PEM key provided to you
 
${PATH} is the path to the PEM key provided to you
 
ssh -X -i ${PATH}/AWS.pem ubuntu@IP_ADDRESS_PROVIDED
 
ssh -X -i ${PATH}/AWS.pem ubuntu@IP_ADDRESS_PROVIDED
  +
  +
**FOR WINDOWS LAPTOPS TO WORK - YOU MUST DOWNLOAD AN Xterm software
  +
MobaXterm has been tested to work: https://mobaxterm.mobatek.net/download.html
   
 
== Jupyter Notebook Over a Remote Connection ==
 
== Jupyter Notebook Over a Remote Connection ==

Revision as of 15:28, 1 November 2019

For Workshop members without access to computing resources - Preconfigured Amazon Web Services servers can be used

Accessing compute resources on AWS:

Speak with Jeff Stout to get the current IP address and PEM key
${PATH} is the path to the PEM key provided to you

 ssh -X -i ${PATH}/AWS.pem ubuntu@IP_ADDRESS_PROVIDED
    • FOR WINDOWS LAPTOPS TO WORK - YOU MUST DOWNLOAD AN Xterm software

MobaXterm has been tested to work: https://mobaxterm.mobatek.net/download.html

Jupyter Notebook Over a Remote Connection

1) Run one terminal to start the notebook and forward the outputs to local web browser:

 ssh -i AWS.pem -L 8887:localhost:8887  ubuntu@IP_ADDRESS
 conda activate workshop  
 jupyter notebook --no-browser --port=8887

2) Copy the output of the jupyter notebook command (see example below) and enter into your laptop web browser (Firefox, Chrome, etc.). Do not click on the link - it will try to launch on the AWS computer

 JupyterAws2.png

3) Use the jupyter notebook to analyze MEG data with python tools

 TestJupyter.png


Installed software

Human Neocortical Neurosolver

 hnn
 #hnn is installed in the system level python >> may need to conda deactivate first

MNE python, Eelbrain, PyCTF

 conda activate workshop  (This environment has MNE, Eelbrain, and PyCtf installed)

CTF software

 singularity shell /opt/ctf/ctf.img
 $ctf_command
 singularity exec /opt/ctf/ctf.img $ctf_command

SAM version 5

 sam_cov ...
 sam_3d ...

Afni

 afni -dset $MRI_file


Done

SAM v5 singularity ? >> CTF Afni Jupyter HNN


TODO

Freesurfer Reinstall MNE python Pyctf FSL Brainstorm Fieldtrip Spyder