Analysis AWS: Difference between revisions
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==Done== |
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SAM v5 |
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singularity ? >> CTF |
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Afni |
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HNN |
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==TODO== |
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# Server Config |
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## google > fedora aws > select the AMI number for N.Virginia |
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Pyctf |
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## In AWS > launch instance > search for AMI number > (Under community) > Launch |
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FSL |
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### https://alt.fedoraproject.org/cloud/ |
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#Determine an image (search for fedora in community) |
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#Create a keypair and download the key |
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Spyder |
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##The download will be in the form of a .pem file |
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## We will need to distribute this key to the users |
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#Launch the instance |
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#Log into the instance using ssh |
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# pyctf |
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Done # SAM v5 |
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# Afni ###INSTALL ME neurodebian |
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# singularity ? >> CTF (need to use workstation version of fedora) << may need to compile for ubuntu or use 2.6 |
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# Eelbrain (conda forge) |
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Done# Forward sim HNN software |
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# FSL ###Install outside of neurodebian |
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# Brainstorm (compiled) |
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<br> |
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'''Matlab Based''' |
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Revision as of 10:07, 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
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