The Resource Usage Aware Backfilling

Abstract. Job scheduling policies for HPC centers have been extensively stud-ied in the last few years, especially backfilling based policies. Almost all of these studies have been done using simulation tools. All the existent simulators use the runtime (either estimated or real) provided in the workload as a basis of their sim-ulations. In our previous work we analyzed the impact on system performance of considering the resource sharing (memory bandwidth) of running jobs including a new resource model in the Alvio simulator. Based on this studies we proposed the LessConsume and LessConsume Threshold resource selection policies. Both are oriented to reduce the saturation of the shared resources thus increasing the performance of the system. The results showed how both resource allocation poli-cies shown how the performance of the system can be improved by considering where the jobs are finally allocated. Using the LessConsume Threshold Resource Selection Policy, we propose a new backfilling strategy: the Resource Usage Aware Backfilling job scheduling policy. This is a backfilling based scheduling policy where the algorithms which decide which job has to be executed and how jobs have to be backfilled are based on a different Threshold configurations. This backfilling variant that considers how the shared resources are used by the scheduled jobs. Rather than backfilling the first job that can moved to the run queue based on the job arrival time or job size, it looks ahead to the next queued jobs, and tries to allocate jobs that would experience lower penalized runtime caused by the resource sharing saturation. In the paper we demostrate how the exchange of scheduling information between the local resource manager and the scheduler can improve substantially the per-formance of the system when the resource sharing is considered. We show how it can achieve a close response time performance that the shorest job first Back-filling with First Fit (oriented to improve the start time for the allocated jobs) providing a qualitative improvement in the number of killed jobs and in the per-centage of penalized runtime.

Benchmarks and Standards for the Evaluation of Parallel Job Schedulers

The evaluation of parallel job schedulers hinges on the workloads used. It is suggested that this be standardized, in terms of both format and content, so as to ease the evaluation and comparison of different systems. The question remains whether this can encompass both traditional parallel systems and metacomputing systems. This paper is based on a panel on this subject that was held at the workshop, and the ensuing discussion; its authors are both the panel members and participants from the audience. Naturally, not all of us agree with all the opinions expressed here..

Formal Reduction Potential of 3,5-Difluorotyrosine in a Structured Protein: Insight into Multistep Radical Transfer

The reversible Y–O•/Y–OH redox properties of the α[subscript 3]Y model protein allow access to the electrochemical and thermodynamic properties of 3,5-difluorotyrosine. The unnatural amino acid has been incorporated at position 32, the dedicated radical site in α[subscript 3]Y, by in vivo nonsense codon suppression. Incorporation of 3,5-difluorotyrosine gives rise to very minor structural changes in the protein scaffold at pH values below the apparent pK (8.0 ± 0.1) of the unnatural residue. Square-wave voltammetry on α[subscript 3](3,5)F[subscript 2]Y provides an E°′(Y–O•/Y–OH) of 1026 ± 4 mV versus the normal hydrogen electrode (pH 5.70 ± 0.02) and shows that the fluoro substitutions lower the E°′ by −30 ± 3 mV. These results illustrate the utility of combining the optimized α[subscript 3]Y tyrosine radical system with in vivo nonsense codon suppression to obtain the formal reduction potential of an unnatural aromatic residue residing within a well-structured protein. It is further observed that the protein E°′ values differ significantly from peak potentials derived from irreversible voltammograms of the corresponding aqueous species. This is notable because solution potentials have been the main thermodynamic data available for amino acid radicals. The findings in this paper are discussed relative to recent mechanistic studies of the multistep radical-transfer process in Escherichia coli ribonucleotide reductase site-specifically labeled with unnatural tyrosine residues.National Institutes of Health (U.S.) (Grant GM29595

Sustained proliferation in cancer: mechanisms and novel therapeutic targets

Proliferation is an important part of cancer development and progression. This is manifest by altered expression and/or activity of cell cycle related proteins. Constitutive activation of many signal transduction pathways also stimulates cell growth. Early steps in tumor development are associated with a fibrogenic response and the development of a hypoxic environment which favors the survival and proliferation of cancer stem cells. Part of the survival strategy of cancer stem cells may manifested by alterations in cell metabolism. Once tumors appear, growth and metastasis may be supported by overproduction of appropriate hormones (in hormonally dependent cancers), by promoting angiogenesis, by undergoing epithelial to mesenchymal transition, by triggering autophagy, and by taking cues from surrounding stromal cells. A number of natural compounds (e.g., curcumin, resveratrol, indole-3-carbinol, brassinin, sulforaphane, epigallocatechin-3-gallate, genistein, ellagitannins, lycopene and quercetin) have been found to inhibit one or more pathways that contribute to proliferation (e.g., hypoxia inducible factor 1, nuclear factor kappa B, phosphoinositide 3 kinase/Akt, insulin-like growth factor receptor 1, Wnt, cell cycle associated proteins, as well as androgen and estrogen receptor signaling). These data, in combination with bioinformatics analyses, will be very important for identifying signaling pathways and molecular targets that may provide early diagnostic markers and/or critical targets for the development of new drugs or drug combinations that block tumor formation and progression

Down-regulation of SFRP1 as a putative tumor suppressor gene can contribute to human hepatocellular carcinoma

<p>Abstract</p> <p>Background</p> <p>Hepatocellular carcinoma (HCC) is one of the most common cancers in the world. SFRP1 (the secreted frizzled-related protein 1), a putative tumor suppressor gene mapped onto chromosome 8p12-p11.1, the frequent loss of heterozygosity (LOH) region in human HCC, encodes a Wingless-type (Wnt) signaling antagonist and is frequently inactivated by promoter methylation in many human cancers. However, whether the down-regulation of SFRP1 can contribute to hepatocarcinogenesis still remains unclear.</p> <p>Methods</p> <p>We investigated the expression of SFRP1 through real time RT-PCR and immunohistochemistry staining. The cell growth and colony formation were observed as the overexpression and knockdown of SFRP1. The DNA methylation status within SFRP1 promoter was analyzed through methylation-specific PCR or bisulphate-treated DNA sequencing assays. Loss of heterozygosity was here detected with microsatellite markers.</p> <p>Results</p> <p>SFRP1 was significantly down-regulated in 76.1% (35/46) HCC specimens at mRNA level and in 30% (30/100) HCCs indicated by immunohistochemistry staining, as compared to adjacent non-cancerous livers. The overexpression of SFRP1 can significantly inhibit the cell growth and colony formation of YY-8103, SMMC7721, and Hep3B cells. The RNA interference against the constitutional SFRP1 in the offspring SMMC7721 cells, which were stably transfected by ectopic SFRP1, can markedly promote cell growth of these cells. LOH of both microsatellite markers D8S532 and D8SAC016868 flanking the gene locus was found in 13% (6 of 46 HCCs) and 6.5% (3 of 46 HCCs) of the informative cases, respectively, where 5 of 8 HCC specimens with LOH showed the down-regulation of SFRP1. DNA hypermethylation within SFRP1 promoter was identified in two of three HCC specimens without SFRP1 expression. Moreover, the DNA methylation of SFRP1 promoter was significantly reduced, along with the re-expression of the gene, in those HCC cell lines, Bel7404, QGY7701, and MHCC-H, as treated by DAC.</p> <p>Conclusion</p> <p>Our data suggested that the down-regulation of SFRP1 as a candidate tumor suppressor gene, triggered by the epigenetic and/or genetic events, could contribute to the oncogenesis of HCC.</p