Grid Wizard Enterprise Advanced Tutorial

General Considerations This tutorial assumes that you already completed the Basic Features tutorial: You already installed GWE in your machine. GWE Daemon has been already auto-deployed and it is running in the local machine (local cluster). You are familiar with GWE Terminal usage. If you have the GWE Terminal client application running, you must exit it before proceeding (input command exit). The detailed configuration guide can be found at:

Configuration: Grid Descriptor This configuration file provides GWE with the description of each of the GWE daemons GWE can access (and install if required). For each GWE daemon to access, a cluster entry must be found. Additionally, each cluster entry accepts a list of default P2EL variables. Each of these variables which will be brought into the scope of any P2EL statement queued into the particular daemon. Edit your $GWE_HOME/conf/gwe-grid.xml to look like this: Replace the SLICER_LOCATION placeholder for the real path where Slicer is installed on your local system.

Configuration: Key Store This configuration file provides GWE with the authentication information that will allow it to access SECURED networked resources, such as remote host where to install GWE daemons and secured file systems to download/upload files. Edit your $GWE_HOME/conf/gwe-auth.xml to look like this: Replace the placeholders (values between brackets) with your particular authentication information when accessing the BIRN cluster.

Study Case Slicers BSpline Deformable Registration of Online Brain Scans (OASIS Database)

Study Case: Creating Orders P2EL Statement Our target is to read a set of brain scans from the online OASIS database, extract their contents, process each one of them with Slicers Bspline Deformable Registration using different parameters (parameter exploration) and upload the generated output files to a specific directory in the remote host. The P2EL statement to express this will look like this: ${URI}= brains.org/app/action/DownloadImages/template/ClosePage.vm?download_type=zip&searc h_element=xnat%3AmrSessionData&search_field=xnat%3AmrSessionData.ID&scanmpr1=true& scanmpr2=true&scanmpr3=true&scanmpr4=true&search_value= ${FIX_NAME}=OAS1_0101_MR1 ${FIX}=$in(${URI}${FIX_NAME},${FIX_NAME}.zip,Y) ${MOV_NAME}=OAS1_00${MOV_NUM}_MR1 ${MOV_NUM}=$range(1,51,10) ${MOV}=$in(${URI}${MOV_NAME},${MOV_NAME}.zip,Y) ${SCAN}=$range(1,4) ${OUT}=sftp://birn-cluster0.nbirn.net/${SYSTEM.USER_HOME}/oasis/out-${SYSTEM.JOB_NUM}. ${OUT_HDR}=$out(${OUT}hdr) ${OUT_IMG}=$out(${OUT}img) ${ITER}=$const(10,20) ${HIST}=$range(20,100,060) ${SAM}=$range(500,5000,3000) ${SLICER_HOME}/Slicer3 –launch ${SLICER_HOME}/lib/Slicer3/Plugins/BSplineDeformableRegistration --iterations ${ITER} --gridSize 5 --histogrambins ${HIST} --spatialsamples ${SAM} -- maximumDeformation 1 --default 0 --resampledmovingfilename ${OUT_HDR} ${FIX}-contents/${FIX_NAME}/RAW/${FIX_NAME}_mpr-${SCAN}_anon.hdr ${MOV}-contents/${MOV_NAME}/RAW/${MOV_NAME}_mpr-${SCAN}_anon.hdr Iteration Variables Process Invocation Template

Study Case: Local Cluster Execution Launch GWE terminal application (gwe-terminal.sh). By default it will connect to the first daemon described in the gwe-grid.xml configuration file; which is the local one according to the configuration we are using. Queue the P2EL statement just created using the queue-order command. Gather the images (resulting of GWE processing these jobs in your local machine) by SSH-ing into the remote host birn-cluster0.nbirn.net and inspecting the path: ${SYSTEM.USER_HOME}/oasis/out-${SYSTEM.JOB_NUM}.

Study Case: BIRN Cluster Execution Launch GWE terminal application by invoking the gwe-terminal.sh as follows: The additional argument instructs the GWE terminal application to connects to your GWE daemon running at the BIRN cluster (previously installing if necessary). Queue the P2EL statement just created using the queue-order command. Gather the images (resulting of GWE processing these jobs in your local machine) by SSH-ing into the remote host birn-cluster0.nbirn.net and inspecting the path: IMPORTANT: You need to shutdown any local GWE daemon running if you intend to connect to any remote one. This is a alpha restriction only! gwe-terminal.sh –conf=BIRN ${SYSTEM.USER_HOME}/oasis/out-${SYSTEM.JOB_NUM}.

Study Case: P2EL Statement Analysis This is the same P2EL statement used in the Study Case 2 of the Basic Tutorial with 2 minor differences: The ${SLICER_HOME} variable is no longer explicitly defined (although still referenced in the process invocation template). This variable will be automatically injected by the GWE daemon into the statement with the value previously configured in the gwe-grid.xml file The out variable has been redefined to a remote file system location, specifically the birn-cluster0.nbirn.net file system, to truly test the uploading capabilites (in the Basic Tutorial we just saved the file in a different location on the same local file system: … ${OUT}=sftp://birn-cluster0.nbirn.net/${SYSTEM.USER_HOME}/oasis/out-${SYSTEM.JOB_NUM}. …