Beauchamp:RAVE:Cluster

Beauchamp Lab

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RAVE RAVE Logo R 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)