Analysis AWS: Difference between revisions
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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 |
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ssh -X -i ${PATH}/AWS.pem ubuntu@IP_ADDRESS_PROVIDED |
ssh -X -i ${PATH}/AWS.pem ubuntu@IP_ADDRESS_PROVIDED |
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**FOR WINDOWS LAPTOPS TO WORK - YOU MUST DOWNLOAD AN Xterm software |
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MobaXterm has been tested to work: https://mobaxterm.mobatek.net/download.html |
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== 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
3) Use the jupyter notebook to analyze MEG data with python tools
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