• KIPS Transactions on Software and Data Engineering
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• v.2 no.2
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• pp.113-118
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• 2013

The current GPU virtualization techniques incur large overheads when executing application programs mainly due to the fine-grain time-sharing scheduling of the GPU among multiple Virtual Machines (VMs). Besides, the current techniques lack of portability, because they include the APIs for the GPU computations in the VM monitor. In this paper, we propose a low overhead and high performance GPU virtualization approach on a heterogeneous HPC system based on the open-source Xen. Our proposed techniques are tailored to the bio applications. In our virtualization framework, we allow a VM to solely occupy a GPU once the VM is assigned a GPU instead of relying on the time-sharing the GPU. This improves the performance of the applications and the utilization of the GPUs. Our techniques also allow a direct pass-through to the GPU by using the IOMMU virtualization features embedded in the hardware for the high portability. Experimental studies using microbiology genome analysis applications show that our proposed techniques based on the direct pass-through significantly reduce the overheads compared with the previous Domain0 based approaches. Furthermore, our approach closely matches the performance for the applications to the bare machine or rather improves the performance.

• Progress in Medical Physics
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• v.25 no.3
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• pp.139-142
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• 2014

The purpose of this study was to develop a system of clinical application of reconstructed dose that includes dose reconstruction, reconstructed dose registration between fractions of treatment, and dose-volume-histogram generation and to demonstrate the system on a deformable prostate phantom. To achieve this purpose, a deformable prostate phantom was embedded into a 20 cm-deep and 40 cm-wide water phantom. The phantom was CT scanned and the anatomical models of prostate, seminal vesicles, and rectum were contoured. A coplanar 4-field intensity modulated radiation therapy (IMRT) plan was used for this study. Organ deformation was simulated by inserting a "transrectal" balloon containing 20 ml of water. A new CT scan was obtained and the deformed structures were contoured. Dose responses in phantoms and electronic portal imaging device (EPID) were calculated by using the XVMC Monte Carlo code. The IMRT plan was delivered to the two phantoms and integrated EPID images were respectively acquired. Dose reconstruction was performed on these images using the calculated responses. The deformed phantom was registered to the original phantom using an in-house developed software based on the Demons algorithm. The transfer matrix for each voxel was obtained and used to correlate the two sets of the reconstructed dose to generate a cumulative reconstructed dose on the original phantom. Forwardly calculated planning dose in the original phantom was compared to the cumulative reconstructed dose from EPID in the original phantom. The prescribed 200 cGy isodose lines showed little difference with respect to the "prostate" and "seminal vesicles", but appreciable difference (3%) was observed at the dose level greater than 210 cGy. In the rectum, the reconstructed dose showed lower volume coverage by a few percent than the plan dose in the dose range of 150 to 200 cGy. Through this study, the system of clinical application of reconstructed dose was successfully developed and demonstrated. The organ deformation simulated in this study resulted in small but observable dose changes in the target and critical structure.