Difference between revisions of "Analysis AWS"

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


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''' For Workshop members without access to computing resources - Preconfigured Amazon Web Services servers can be used'''
To access the compute system:
ssh -X -i ~/Downloads/AWS.pem ubuntu@IP_ADDRESS_PROVIDED


== Accessing compute resources on AWS: ==
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''' Installed software ''' <br>
Speak with Jeff Stout to get the current IP address and PEM key <br>
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Human Neocortical Neurosolver
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<br>
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hnn
chmod 400 AWS.pem
#hnn is installed in the system level python >> may need to conda deactivate first
${PATH} is the path to the PEM key provided to you
ssh -X -i AWS.pem user1@ec2-3-230-155-59.compute-1.amazonaws.com


'''Windows Laptops''' do not have X11 installed natively. Download an Xterm software for visualization. <br>
⚫
MNE python or Eelbrain
MobaXterm has been tested to work: https://mobaxterm.mobatek.net/download.html
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conda activate workshop (This environment has MNE and Eelbrain installed)


== Jupyter Notebook Over a Remote Connection ==
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CTF software
1) Run one terminal to start the notebook and forward the outputs to local web browser:
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singularity shell /opt/ctf/ctf.img
ssh -i AWS.pem -L 8887:localhost:8887 ubuntu@IP_ADDRESS
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$ctf_command
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
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singularity exec /opt/ctf/ctf.img $ctf_command


[[file:JupyterAws2.png]]
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SAM version 5
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sam_cov ...
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sam_3d ...


3) Use the jupyter notebook to analyze MEG data with python tools
Afni
[[File:TestJupyter.png]]
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afni -dset $MRI_file


<br>


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== Installed software ==
⚫
'''Human Neocortical Neurosolver ''' <br>
HNN website: https://hnn.brown.edu/
conda deactivate
⚫
hnn


⚫
'''MNE python, Eelbrain, PyCTF''' <br>
MNE website: https://mne.tools/stable/index.html <br>
Eelbrain website: https://eelbrain.readthedocs.io/en/stable/ <br>
PyCTF website: https://megcore.nih.gov/index.php/MEG_Software_and_Analysis#MEG_Core_pyctf_tools_ported_to_Python_3 <br>
⚫
conda activate workshop # This conda environment has the MNE, Eelbrain, and PyCtf toolboxes installed
ipython
import eelbrain, mne, pyctf


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'''CTF software'''
# Server Config
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singularity shell /opt/ctf/ctf.img
## google > fedora aws > select the AMI number for N.Virginia
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$ctf_command
## In AWS > launch instance > search for AMI number > (Under community) > Launch
### https://alt.fedoraproject.org/cloud/
#Determine an image (search for fedora in community)
#Create a keypair and download the key
##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


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


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'''SAM version 5'''
Conda installed
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sam_cov ...
Conda deactivate >> hnn
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sam_3d ...
Conda activate nih >> mne or eelbrain.....


'''Afni'''

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afni -dset $MRI_file
# 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)
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<br>
'''Matlab Based'''
# Brainstorm
# Fieldtrip

Latest revision as of 12:15, 7 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 

 chmod 400 AWS.pem

${PATH} is the path to the PEM key provided to you 

 ssh -X -i AWS.pem user1@ec2-3-230-155-59.compute-1.amazonaws.com

Windows Laptops do not have X11 installed natively. Download an Xterm software for visualization.
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 website: https://hnn.brown.edu/ 

 conda deactivate
 hnn

MNE python, Eelbrain, PyCTF
MNE website: https://mne.tools/stable/index.html
Eelbrain website: https://eelbrain.readthedocs.io/en/stable/
PyCTF website: https://megcore.nih.gov/index.php/MEG_Software_and_Analysis#MEG_Core_pyctf_tools_ported_to_Python_3 

 conda activate workshop  # This conda environment has the MNE, Eelbrain, and PyCtf toolboxes installed
 ipython
 import eelbrain, mne, pyctf

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
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