Analysis AWS: Difference between revisions
Jump to navigation
Jump to search
Content added Content deleted
No edit summary |
No edit summary |
||
| Line 43: | Line 43: | ||
==Done== |
|||
SAM v5 |
|||
singularity ? >> CTF |
|||
Afni |
|||
| ⚫ | |||
HNN |
|||
==TODO== |
|||
| ⚫ | |||
# Server Config |
|||
| ⚫ | |||
## google > fedora aws > select the AMI number for N.Virginia |
|||
Pyctf |
|||
## In AWS > launch instance > search for AMI number > (Under community) > Launch |
|||
FSL |
|||
### https://alt.fedoraproject.org/cloud/ |
|||
| ⚫ | |||
#Determine an image (search for fedora in community) |
|||
| ⚫ | |||
#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 |
|||
| ⚫ | |||
| ⚫ | |||
# 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) |
|||
| ⚫ | |||
Done# Forward sim HNN software |
|||
# FSL ###Install outside of neurodebian |
|||
# Brainstorm (compiled) |
|||
<br> |
|||
'''Matlab Based''' |
|||
| ⚫ | |||
| ⚫ | |||
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
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