A taxonomy of application scheduling tools for high performance cluster computing

Application scheduling plays an important role in high-performance cluster computing. Application scheduling can be classified as job scheduling and task scheduling. This paper presents a survey on the software tools for the graph-based scheduling on cluster systems with the focus on task scheduling. The tasks of a parallel or distributed application can be properly scheduled onto multi-processors in order to optimize the performance of the program (e.g., execution time or resource utilization). In general, scheduling algorithms are designed based on the notion of task graph that represents the relationship of parallel tasks. The scheduling algorithms map the nodes of a graph to the processors in order to minimize overall execution time. Although many scheduling algorithms have been proposed in the literature, surprisingly not many practical tools can be found in practical use. After discussing the fundamental scheduling techniques, we propose a framework and taxonomy for the scheduling tools on clusters. Using this framework, the features of existing scheduling tools are analyzed and compared. We also discuss the important issues in improving the usability of the scheduling tools. This work is supported by the Hong Kong Polytechnic University under grant H-ZJ80 and by NASA Ames Research Center by a cooperative grant agreement with the University of Texas at Arlington. Jiannong Cao received the BSc degree in computer science from Nanjing University, Nanjing, China in 1982, and the MSc and the Ph.D degrees in computer science from Washington State University, Pullman, WA, USA, in 1986 and 1990 respectively. He is currently an associate professor in Department of Computing at the Hong Kong Polytechnic University, Hong Kong. He is also the director of the Internet and Mobile Computing Lab in the department. He was on the faculty of computer science at James Cook University and University of Adelaide in Australia, and City University of Hong Kong. His research interests include parallel and distributed computing, networking, mobile computing, fault tolerance, and distributed software architecture and tools. He has published over 120 technical papers in the above areas. He has served as a member of editorial boards of several international journals, a reviewer for international journals/conference proceedings, and also as an organizing/programme committee member for many international conferences. Dr. Cao is a member of the IEEE Computer Society, the IEEE Communication Society, IEEE, and ACM. He is also a member of the IEEE Technical Committee on Distributed Processing, IEEE Technical Committee on Parallel Processing, IEEE Technical Committee on Fault Tolerant Computing, and Computer Architecture Professional Committee of the China Computer Federation. Alvin Chan is currently an assistant professor at the Hong Kong Polytechnic University. He graduated from the University of New South Wales with a Ph.D. degree in 1995 and was subsequently employed as a Research Scientist by the CSIRO, Australia. From 1997 to 1998, he was employed by the Centre for Wireless Communications, National University of Singapore as a Program Manager. Dr. Chan is one of the founding members and director of a university spin-off company, Information Access Technology Limited. He is an active consultant and has been providing consultancy services to both local and overseas companies. His research interests include mobile computing, context-aware computing and smart card applications. Yudong Sun received the B.S. and M.S. degrees from Shanghai Jiao Tong University, China. He received Ph.D. degree from the University of Hong Kong in 2002, all in computer science. From 1988 to 1996, he was among the teaching staff in Department of Computer Science and Engineering at Shanghai Jiao Tong University. From 2002 to 2003, he held a research position at the Hong Kong Polytechnic University. At present, he is a Research Associate in School of Computing Science at University of Newcastle upon Tyne, UK. His research interests include parallel and distributed computing, Web services, Grid computing, and bioinformatics. Sajal K. Das is currently a Professor of Computer Science and Engineering and the Founding Director of the Center for Research in Wireless Mobility and Networking (CReWMaN) at the University of Texas at Arlington. His current research interests include resource and mobility management in wireless networks, mobile and pervasive computing, sensor networks, mobile internet, parallel processing, and grid computing. He has published over 250 research papers, and holds four US patents in wireless mobile networks. He received the Best Paper Awards in ACM MobiCom’99, ICOIN-16, ACM, MSWiM’00 and ACM/IEEE PADS’97. Dr. Das serves on the Editorial Boards of IEEE Transactions on Mobile Computing, ACM/Kluwer Wireless Networks, Parallel Processing Letters, Journal of Parallel Algorithms and Applications. He served as General Chair of IEEE PerCom’04, IWDC’04, MASCOTS’02 ACM WoWMoM’00-02; General Vice Chair of IEEE PerCom’03, ACM MobiCom’00 and IEEE HiPC’00-01; Program Chair of IWDC’02, WoWMoM’98-99; TPC Vice Chair of ICPADS’02; and as TPC member of numerous IEEE and ACM conferences. Minyi Guo received his Ph.D. degree in information science from University of Tsukuba, Japan in 1998. From 1998 to 2000, Dr. Guo had been a research scientist of NEC Soft, Ltd. Japan. He is currently a professor at the Department of Computer Software, The University of Aizu, Japan. From 2001 to 2003, he was a visiting professor of Georgia State University, USA, Hong Kong Polytechnic University, Hong Kong. Dr. Guo has served as general chair, program committee or organizing committee chair for many international conferences, and delivered more than 20 invited talks in USA, Australia, China, and Japan. He is the editor-in-chief of the Journal of Embedded Systems. He is also in editorial board of International Journal of High Performance Computing and Networking, Journal of Embedded Computing, Journal of Parallel and Distributed Scientific and Engineering Computing, and International Journal of Computer and Applications. Dr. Guo’s research interests include parallel and distributed processing, parallelizing compilers, data parallel languages, data mining, molecular computing and software engineering. He is a member of the ACM, IEEE, IEEE Computer Society, and IEICE. He is listed in Marquis Who’s Who in Science and Engineering.     

Up-regulation in expression of vesicular glutamate transporter 3 in substantia nigra but not in striatum of 6-hydroxydopamine-lesioned rats

Overactivity of the glutamatergic system is suggested to be closely related to the onset and pathogenesis of Parkinson's disease. Vesicular glutamate transporters (VGLUT1, T2 and T3) are a group of glutamate transporters in neurons that are responsible for transporting glutamate into synaptic vesicles and they are key elements for homeostasis of glutamate neurotransmission. The present study was aimed to investigate the expression of VGLUT1, T2 and T3 proteins after the onset of Parkinson's disease. A rat model of Parkinson's disease, the 6-hydroxydopamine-lesioned rat, was employed. Immunocytochemistry revealed that VGLUT1, T2 and T3 immunoreactivity was not modulated in the striatum of the lesioned rat. Western blotting analyses also showed that there was no change in the expression of T1, T2 and T3 proteins in the striatum. In contrast, no VGLUT1 protein was detected in the substantia nigra. After the lesion, levels of VGLUT2 immunoreactivity and protein were not modulated. Significant increase of VGLUT3 immunoreactivity was observed in the perikarya of GABAergic substantia nigra pars reticulata neurons (+14.7%) although VGLUT3 protein was not modulated in the nigral tissues. VGLUT3 in GABAergic neurons is suggested to play a role in GABA synthesis. The present results may therefore implicate that VGLUT1 and T2 are not modulated in the striatum and the substantia nigra of the 6-hydroxydopamine-lesioned rat and only VGLUT3 plays a role in pathogenesis of Parkinson's disease.     

Pulsatile flow and mass transport over an array of cylinders: gas transfer in a cardiac-driven artificial lung

The pulsatile flow and gas transport of a Newtonian passive fluid across an array of cylindrical microfibers are numerically investigated. It is related to an implantable, artificial lung where the blood flow is driven by the right heart. The fibers are modeled as either squared or staggered arrays. The pulsatile flow inputs considered in this study are a steady flow with a sinusoidal perturbation and a cardiac flow. The aims of this study are twofold: identifying favorable array geometry/spacing and system conditions that enhance gas transport; and providing pressure drop data that indicate the degree of flow resistance or the demand on the right heart in driving the flow through the fiber bundle. The results show that pulsatile flow improves the gas transfer to the fluid compared to steady flow. The degree of enhancement is found to be significant when the oscillation frequency is large, when the void fraction of the fiber bundle is decreased, and when the Reynolds number is increased; the use of a cardiac flow input can also improve gas transfer. In terms of array geometry, the staggered array gives both a better gas transfer per fiber (for relatively large void fraction) and a smaller pressure drop (for all cases). For most cases shown, an increase in gas transfer is accompanied by a higher pressure drop required to power the flow through the device.     

Induction of somatic embryos of celery by control of gaseous compositions and other physical conditions

The celery (Tall Utah, Apium graveolens var. dulce) was adopted as a model system to investigate effective methods for enhancing embryogenesis. The focus was placed on attaining the optimum gaseous composition and the mixing intensity and viscosity of culture systems. The mixing intensity was investigated by using creased flasks and evaluated by shear force index (SFI). By using different closures with different ventilation coefficients, K w, to adjust the gaseous composition in the flasks, it was found that embryo frequency (EF) increased with high or low ethylene concentration in the headspace of the culture flasks. Cultivating the embryogenic cells under controlled ethylene concentrations depressed EF at ethylene concentrations higher than 0.08 ppm. Moreover, 0.1 μM of CoCl₂ remarkably repressed the ethylene formation in the culture medium and enhanced EF. and around 3% and 30%, respectively, favored EF. For non-creased flasks, addition of CMC (carboxymethyl cellulose) decreased the EF and DO level of the medium, due to lowered mass transfer rate attributed to high viscosity. For creased flasks, supplementation of 0.4 g/ 100 ml CMC reduced the ill-effects of high shear stress and maximized EF (7.22%). Our results are potentially applicable to other species and large-scale embryo production systems.     

Carbon monoxide uptake kinetics in unamended and long-term nitrogen-amended temperate forest soils

The effect of nitrogen (N) additions on the dynamics of carbon monoxide consumption in temperate forest soils is poorly understood. We measured soil CO profiles, potential rates of CO consumption and uptake kinetics in temperate hardwood and pine control plots and plots amended with 50 and 150 kg N ha-1 year-1 for more than 15 years. Soil profiles of CO concentrations were above atmospheric levels in the high-N plots of both stands, suggesting that in these forest soils the balance between consumption and production may be shifted so that either production is increased or consumption decreased. Highest rates of CO consumption were measured in the organic horizon and decreased with soil depth. In the N-amended plots, CO consumption increased in all but one soil depth of the hardwood stand, but decreased in all soil depths of the pine stand. CO enzyme affinities increased with soil depth in the control plots. However, enzyme affinities in the most active soil depths (organic and 0-5 cm mineral) decreased in response to low levels of N in both stands. In the high-N plots, affinities dramatically-increased in the hardwood stand, but decreased in the organic horizon and increased slightly in the 0-5 cm mineral soil in the pine stand. These findings indicate that long-term N addition either by fertilization or deposition may alter the size, composition and/or physiology of the community of CO consumers so that their ability to act as a sink for atmospheric CO has changed. This change could have a substantial effect on the lifetime of greenhouse gases such as CH4 and therefore the future of Earth's climate.     

镉对小鼠精子和生精细胞超微结构及生精细胞bcl-2、bax基因表达的影响

研究镉暴露对小鼠附睾精子和睾丸生精细胞超微结构的变化以及镉对生精细胞凋亡相关基因bcl-2、bax表达水平的影响。采用24只雄性ICR小鼠随机分为4组,每组6只,分别以0.183、0.915、1.83mg/kg氯化镉腹腔注射,每天1次,连续5次,设阴性对照生理盐水组。于第6天透射电镜观察附睾精子超微结构、睾丸生精细胞核和线粒体超微结构的变化,免疫组化方法检测生精细胞Bcl-2、Bax表达水平。透射电镜观察显示,0.183mg/kg组精子超微结构无显著性变化,0.915mg/kg组精子头部两侧膜与头部胞质间隙轻微扩大,线粒体嵴间腔扩大且轻度空泡化,但与对照组相比无统计学意义(P>0.05)。1.83mg/kg组头部两侧膜与胞质间隙扩大,与对照组相比有显著性差异(P<0.05),尾部线粒体嵴间腔扩大且轻度空泡化,与对照组相比有显著性差异(P<0.05)。3种剂量处理组睾丸生精细胞核超微结构异常发生率显著高于对照组(P<0.05),且随着处理浓度的升高异常发生率升高;1.83mg/kg组线粒体肿胀空泡化发生率显著高于对照组(P<0.05)。3种剂量实验组生精细胞Bcl-2表达水平(吸光度)显著低于对照组(P<0.01),0.915mg/kg组Bax表达水平显著高于对照组和0.183、1.83mg/kg组(P<0.01)。3种剂量实验组Bcl-2/Bax吸光度比值显著低于对照组(P<0.01);0.915mg/kg组Bcl-2/Bax比值显著低于1.83mg/kg组(P<0.01)。上述结果提示:高浓度镉诱导附睾精子超微结构改变,高中低浓度镉致睾丸生精细胞超微结构的改变,生精细胞超微结构发生凋亡现象。镉对Bcl-2、Bax表达水平的改变可能是生精细胞凋亡的分子机制之一。     

体外诱导成年大鼠骨髓间充质干细胞分化为 5-羟色胺敏感性神经元

体外诱导成年大鼠骨髓间充质干细胞分化为具有神经元表型和部分功能的细胞。在对Woodbury化学诱导法作改良的基础上,加用全反式视黄酸对骨髓间充质干细胞作预诱导。诱导3h后,细胞开始表现神经元的形态特征,细胞折光性增强,形成收缩的双极或多极胞体和细长突起。细胞可以维持神经元样存活72h以上。诱导5h后,对免疫染色的细胞用DAPI进行复染,(92.4±6.9)%的细胞表达神经元特异性烯醇化酶。诱导24h后,(93.9±5.2)%的细胞表达成熟神经元的标志物神经丝M H。在给予5-羟色胺刺激时可以产生与神经元相似的胞内钙离子峰,且免疫组化证实5-羟色胺1A受体在干细胞上表达微弱,但在分化后的神经元中表达较强。实验不仅从形态、细胞标志物而且从功能上证实诱导后的细胞为5-羟色胺敏感性神经元。     

Protection against fatty liver but normal adipogenesis in mice lacking adipose differentiation-related protein

Adipose differentiation-related protein (ADFP; also known as ADRP or adipophilin), is a lipid droplet (LD) protein found in most cells and tissues. ADFP expression is strongly induced in cells with increased lipid load. We have inactivated the Adfp gene in mice to better understand its role in lipid accumulation. The Adfp-deficient mice have unaltered adipose differentiation or lipolysis in vitro or in vivo. Importantly, they display a 60% reduction in hepatic triglyceride (TG) and are resistant to diet-induced fatty liver. To determine the mechanism for the reduced hepatic TG content, we measured hepatic lipogenesis, very-low-density lipoprotein (VLDL) secretion, and lipid uptake and utilization, all of which parameters were shown to be similar between mutant and wild-type mice. The finding of similar VLDL output in the presence of a reduction in total TG in the Adfp-deficient liver is explained by the retention of TG in the microsomes where VLDL is assembled. Given that lipid droplets are thought to form from the outer leaflet of the microsomal membrane, the reduction of TG in the cytosol with concomitant accumulation of TG in the microsome of Adfp-/- cells suggests that ADFP may facilitate the formation of new LDs. In the absence of ADFP, impairment of LD formation is associated with the accumulation of microsomal TG but a reduction in TG in other subcellular compartments.     

Confirmation of linkage to chromosome 1q for spine bone mineral density in southern Chinese

Chromosome 1q has previously been linked to bone mineral density (BMD) variation in the general population in several genome-wide linkage studies in both humans and mouse model. The aim of present study is to replicate and fine map the QTL influencing BMD in chromosome 1q in southern Chinese. Twelve microsatellite markers were genotyped for a 57 cΜ region in the chromosome 1q in 306 southern Chinese families with 1,459 subjects. Each of these families was ascertained through a proband with BMD Z-scores less than −1.3 at the hip or spine. BMD (g/cm²) at the L1-4 lumbar spine, femoral neck (FN), trochanter and total hip was measured by dual-energy X-ray absortiometry. Linkage analyses were performed using the variance component linkage analysis method implemented in Merlin software. Four markers (D1S2878, D1S196, D1S452, and D1S218) achieved a LOD score greater than 1.0 with spine BMD, with the maximum multipoint LOD score of 2.36 at the marker D1S196. We did not detect a LOD score greater than 1.0 for BMD at the FN, trochanter, or total hip in multipoint linkage analyses. Our results present the first evidence for the presence of an osteoporosis susceptibility gene on chromosome 1q in non-Caucasian subjects. Further analyses of candidate genes are warranted to identify QTL genes and variants underlying the variations of BMD in this region.