Analysis AWS: Difference between revisions

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jupyter notebook --no-browser --port=8887
jupyter notebook --no-browser --port=8887


2) Copy the output of the notebook (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
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


[[file:JupyterAws2.png]]
[[file:JupyterAws2.png]]

Revision as of 11:10, 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

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

 
 


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