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RAVE

RAVE Logo

Reproducible Analysis and Visualization of intracranial EEG Data (RAVE) is a powerful software tool for the analysis of intracranial electroencephalogram (iEEG) data, including data collected using strips and grids (ECoG) and depth electrodes (stereo EEG). Funding provided by NIH 1R24MH117529-01.

Using RAVE on the BCM Cluster

The first step is to request a login ID and password from the BCM Cluster administer. The username will be your BCM username but the password will be different and must be reset. Login to the cluster from a terminal window on your iMac

ssh beaucham@chemo.dldcc.bcm.edu

Load the required modules for RAVE

module load R
module load hdf5
module load fftw

Check what the IP address will be

ifconfig

e.g.

eth3     inet addr:10.22.223.200  Bcast:10.22.223.255  Mask:255.255.252.0

tells you that IP address will start with 10.22.223.200

Start R and launch RAVE

R -e "rave::init_app(host='10.22.223.200')"

this should tell you what IP and port to use, e.g.

 Now listening on X:Y

On your local machine, point your browser to this address

 http:\\10.22.223.200:XXXX

If needed, copy data to the cluster

cd /Volumes/Data/data/rave_data/raw 
sftp beaucham@chemo.dldcc.bcm.edu
cd /projects/camri
put YAB.zup

Before starting R, you can request more resources

qsub -I  -l vmem=200GB

To kill a job, use

qdel <jobid>

Use ps to determine the jobid.

For initial setup, must make the raw directory

mkdir /project/camri/raw
chmod -R 777 /project/camri/raw
mkdir /project/camri/data
chmod -R 777 /project/camri/data

And tell RAVE where they are

rave::rave_options(raw_data_dir = '/project/camri/raw')
rave::rave_options(data_dir = '/project/camri/data')

Launching RAVE on BCM Cluster from OSX

First install XQuartz if not installed

https://www.xquartz.org/

Next, on the local machine, open terminal, type

echo $DISPLAY

If nothing returns, run

dispdir=`dirname $DISPLAY`
dispfile=`basename $DISPLAY`
dispnew="$dispdir/:0"
if [ -e $DISPLAY -a "$dispfile" = "org.x:0" ]; then
  mv $DISPLAY $dispnew
fi
export DISPLAY=$dispnew

Then open or create a new file at

~/.ssh/config

Insert/edit the following lines:

Host *
    ForwardAgent yes
    ForwardX11 yes
    XAuthLocation /opt/X11/bin/xauth

Save and exit. Also exit terminal.

Open another terminal, test again

echo $DISPLAY

It should print out result similar to

/private/tmp/com.apple.launchd.q16FRU1JYw/org.macosforge.xquartz:0

Connect to server

ssh -Y beaucham@chemo.dldcc.bcm.edu

Test firefox

firefox

(TODO write sh script to launch rave in qsub and port forward), including data collected using strips and grids (ECoG) and depth electrodes (stereo EEG). Funding provided by NIH 1R24MH117529-01. Using RAVE on the BCM Cluster The first step is to request a login ID and password from the BCM Cluster administer. The username will be your BCM username but the password will be different and must be reset. Login to the cluster from a terminal window on your iMac ssh beaucham@chemo.dldcc.bcm.edu Load the required modules for RAVE module load R module load hdf5 module load fftw Check what the IP address will be ifconfig e.g. eth3 inet addr:10.22.223.200 Bcast:10.22.223.255 Mask:255.255.252.0 tells you that IP address will start with 10.22.223.200 Start R and launch RAVE R -e "rave::init_app(host='10.22.223.200')" this should tell you what IP and port to use, e.g. Now listening on X:Y On your local machine, point your browser to this address http:\\10.22.223.200:XXXX If needed, copy data to the cluster cd /Volumes/Data/data/rave_data/raw sftp beaucham@chemo.dldcc.bcm.edu cd /projects/camri put YAB.zup Before starting R, you can request more resources qsub -I -l vmem=200GB To kill a job, use qdel <jobid> Use ps to determine the jobid. For initial setup, must make the raw directory mkdir /project/camri/raw chmod -R 777 /project/camri/raw mkdir /project/camri/data chmod -R 777 /project/camri/data And tell RAVE where they are rave::rave_options(raw_data_dir = '/project/camri/raw') rave::rave_options(data_dir = '/project/camri/data') Launching RAVE on BCM Cluster from OSX First install XQuartz if not installed https://www.xquartz.org/ Next, on the local machine, open terminal, type echo $DISPLAY If nothing returns, run dispdir=`dirname $DISPLAY` dispfile=`basename $DISPLAY` dispnew="$dispdir/:0" if [ -e $DISPLAY -a "$dispfile" = "org.x:0" ]; then mv $DISPLAY $dispnew fi export DISPLAY=$dispnew Then open or create a new file at ~/.ssh/config Insert/edit the following lines: Host * ForwardAgent yes ForwardX11 yes XAuthLocation /opt/X11/bin/xauth Save and exit. Also exit terminal. Open another terminal, test again echo $DISPLAY It should print out result similar to /private/tmp/com.apple.launchd.q16FRU1JYw/org.macosforge.xquartz:0 Connect to server ssh -Y beaucham@chemo.dldcc.bcm.edu Test firefox firefox (TODO write sh script to launch rave in qsub and port forward)