Scalable group-based checkpoint/restart for large-scale message-passing systems

The ever increasing number of processors used in parallel computers is making fault tolerance support in large-scale parallel systems more and more important. We discuss the inadequacies of existing system-level checkpointing solutions for message-passing applications as the system scales up. We analyze the coordination cost and blocking behavior of two current MPI implementations with checkpointing support. A group-based solution combining coordinated checkpointing and message logging is then proposed. Experiment results demonstrate its better performance and scalability than LAM/MPI and MPICH-VCL. To assist group formation, a method to analyze the communication behaviors of the application is proposed. ©2008 IEEE.published_or_final_versio

Lightweight process migration and memory prefetching in openMosix

We propose a lightweight process migration mechanism and an adaptive memory prefetching scheme called AMPoM (Adaptive Memory Prefetching in openMosix), whose goal is to reduce the migration freeze time in openMosix while ensuring the execution efficiency of migrants. To minimize the freeze time, our system transfers only a few pages to the destination node during process migration. After the migration, AMPoM analyzes the spatial locality of memory access and iteratively prefetches memory pages from remote to hide the latency of inter-node page faults. AMPoM adopts a unique algorithm to decide which and how many pages to prefetch. It tends to prefetch more aggressively when a sequential access pattern is developed, when the paging rate of the process is high or when the network is busy. This advanced strategy makes AMPoM highly adaptive to different application behaviors and system dynamics. The HPC Challenge benchmark results show that AMPoM can avoid 98% of migration freeze time while preventing 85-99% of page fault requests after the migration. Compared to openMosix which does not have remote page fault, AMPoM induces a modest overhead of 0-5% additional runtime. When the working set of a migrant is small, AMPoM outperforms openMosix considerably due to the reduced amount of data transfer. These results indicate that by exploiting memory access locality and prefetching, process migration can be a lightweight operation with little software overhead in remote paging. ©2008 IEEE.published_or_final_versionThe 2008 IEEE International Symposium on Parallel and Distributed Processing (IPDPS 2008), Miami, FL., 14-18 April 2008. In Proceedings of the 22nd IPDPS, 2008, p. 1-1

An update on hepatocarcinogenesis

Hepatocellular carcinoma is the most common cancer occurring in males in the world and has an annual incidence worldwide of 1 million. There are variations in its geographical distribution. It is the second most common cancer in Southeast Asia, including Hong Kong and ranks third among males in China.published_or_final_versio

Object co-location and memory reuse for Java programs

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A grid middleware for distributed Java computing with MPI binding and process migration supports

"Grid" computing has emerged as an important new research field. With years of efforts, grid researchers have successfully developed grid technologies including security solutions, resource management protocols, information query protocols, and data management services. However, as the ultimate goal of grid computing is to design an infrastructure which supports dynamic, cross-organizational resource sharing, there is a need of solutions for efficient and transparent task re-scheduling in the grid. In this research, a new grid middleware is proposed, called G-JavaMPI. This middleware adds the parallel computing capability of Java to the grid with the support of a Grid-enabled message passing interface (MPI) for inter-process communication between Java processes executed at different grid points. A special feature of the proposed G-JavaMPI is the support of Java process migration with post-migration message redirection. With these supports, it is possible to migrate executing Java process from site to site for continuous computation, if some site is scheduled to be turned down for system reconfiguration. Moreover, the proposed G-JavaMPI middleware is very portable since it requires no modification of underlying OS, Java virtual machine, and MPI package. Preliminary performance tests have been conducted. The proposed mechanisms have shown good migration efficiency in a simulated grid environment.postprin

The natural history of chronic hepatitis B infection

Chronic hepatitis B infection is a global health problem that affects about 300 million people. Of these, 75% are Chinese. Most Chinese who become chronic carriers, contract the virus during the perinatal period. The natural history of these chronic hepatitis B carriers includes an initial immune tolerance phase, followed by immune clearance and an inactive hepatitis B non-replicative phase with the development of cirrhosis that may be complicated by hepatocellular carcinoma. The classification of hepato-cellular carcinoma has recently been revised. Based on immunohistochemical studies, it has been found that patients with hepatocellular carcinoma and biliary markers have a poorer survival than patients with hepatocellular carcinoma but who have negative biliary markers. Sometimes, a fourth phase, a hepatitis B envelope-negative hepatitis B virus replicative phase, reflecting the emergence of a pre-core mutant strain, may follow. Our improved understanding of the natural history of chronic hepatitis B infection has led to more effective approaches towards the control of this viral infection and its sequelae. Most importantly, immunisation against hepatitis B virus in the perinatal setting has been shown to prevent chronic infection.published_or_final_versio

PZT/P(VDF-TrFE) nanocomposite hydrophones for ultrasonic measurements

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Cluster Computing with Single Thread Space

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Living donor liver transplantation in adults

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Liver transplantation for hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the third commonest cancer in Hong Kong. Up to 80% of patients have inoperable tumour at presentation, either because of underlying cirrhosis or advanced stage of the disease. The present report described a case of orthotopic liver transplantation (OLT) for HCC. Prognostic factors for survival and selection criteria for liver transplantation are discussed. Early referral of selected patients with HCC to a transplant centre can offer a hope of cure. The best candidate for OLT is a young patient with an asymptomatic small HCC in a cirrhotic liver.published_or_final_versio