gate

gate is an advanced opensource software developed by the international opengate collaboration and dedicated to numerical simulations in medical imaging and radiotherapy. it currently supports simulations of emission tomography (positron emission tomography - pet and single photon emission computed tomography - spect), computed tomography (ct) and radiotherapy experiments.

see the gate homepage (http://www.opengatecollaboration.org) for further details.

availability on wesley

submitting gate jobs to the queue

as an example, assume your gate macro file is named mainmacro.mac

first create a torque/pbs qsub script as follows:

#!/bin/bash -l

# go to the same directory that we had submitted the job from
cd $pbs_o_workdir

# setup environment for running gate 6.1.0
source /shared/gate/6.1.0/gate6_1/env_gate.sh

# run gate specifying our macro.
gate mainmacro.mac

next, submit it to the queue with a qsub command similar to the following:

qsub -l walltime=2:30:00 mygatejob.qsub

note: the walltime=2:30:00 tells the queueing system that this job should only be allowed to run for a maximum of 2 hours and 30 minutes, after which it should be automatically killed. be sure to adjust your walltime appropriately.

running interactively with a visualization window

it is acceptable to run small interactive simulations with visualization on wesley's headnode. please limit yourself to one case at a time and to simulations that will not run for more than an hour. to allow the graphics display to open you will need to logon using either x11 forwarding, or vnc