Difference between revisions of "Analysis AWS"

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==Done==
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SAM v5
  +
singularity ? >> CTF
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Afni
 
Jupyter
  +
HNN
   
   
  +
==TODO==
 
 
Freesurfer
# Server Config
 
 
Reinstall MNE python
## google > fedora aws > select the AMI number for N.Virginia
 
  +
Pyctf
## In AWS > launch instance > search for AMI number > (Under community) > Launch
 
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FSL
### https://alt.fedoraproject.org/cloud/
 
 
Brainstorm
#Determine an image (search for fedora in community)
 
 
Fieldtrip
#Create a keypair and download the key
 
  +
Spyder
##The download will be in the form of a .pem file
 
## We will need to distribute this key to the users
 
#Launch the instance
 
#Log into the instance using ssh
 
 
 
 
# Freesurfer
 
# MNE python
 
# pyctf
 
Done # SAM v5
 
# Afni ###INSTALL ME neurodebian
 
# singularity ? >> CTF (need to use workstation version of fedora) << may need to compile for ubuntu or use 2.6
 
# Eelbrain (conda forge)
 
# Jupyter
 
Done# Forward sim HNN software
 
# FSL ###Install outside of neurodebian
 
# Brainstorm (compiled)
 
<br>
 
'''Matlab Based'''
 
# Brainstorm
 
# Fieldtrip
 

Revision as of 11:07, 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 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

 JupyterAws2.png
 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