Simultaneous input and output matrix partitioning for outer-product-parallel sparse matrix-matrix multiplication

Cataloged from PDF version of article.FFor outer-product-parallel sparse matrix-matrix multiplication (SpGEMM) of the form C=A×B, we propose three hypergraph models that achieve simultaneous partitioning of input and output matrices without any replication of input data. All three hypergraph models perform conformable one-dimensional (1D) columnwise and 1D rowwise partitioning of the input matrices A and B, respectively. The first hypergraph model performs two-dimensional (2D) nonzero-based partitioning of the output matrix, whereas the second and third models perform 1D rowwise and 1D columnwise partitioning of the output matrix, respectively. This partitioning scheme induces a two-phase parallel SpGEMM algorithm, where communication-free local SpGEMM computations constitute the first phase and the multiple single-node-accumulation operations on the local SpGEMM results constitute the second phase. In these models, the two partitioning constraints defined on weights of vertices encode balancing computational loads of processors during the two separate phases of the parallel SpGEMM algorithm. The partitioning objective of minimizing the cutsize defined over the cut nets encodes minimizing the total volume of communication that will occur during the second phase of the parallel SpGEMM algorithm. An MPI-based parallel SpGEMM library is developed to verify the validity of our models in practice. Parallel runs of the library for a wide range of realistic SpGEMM instances on two large-scale parallel systems JUQUEEN (an IBM BlueGene/Q system) and SuperMUC (an Intel-based cluster) show that the proposed hypergraph models attain high speedup values. © 2014 Society for Industrial and Applied Mathematics

Exploiting Locality in Sparse Matrix-Matrix Multiplication on Many-Core Architectures

Exploiting spatial and temporal localities is investigated for efficient row-by-row parallelization of general sparse matrix-matrix multiplication (SpGEMM) operation of the form C=A,B on many-core architectures. Hypergraph and bipartite graph models are proposed for 1D rowwise partitioning of matrix A to evenly partition the work across threads with the objective of reducing the number of B-matrix words to be transferred from the memory and between different caches. A hypergraph model is proposed for B-matrix column reordering to exploit spatial locality in accessing entries of thread-private temporary arrays, which are used to accumulate results for C-matrix rows. A similarity graph model is proposed for B-matrix row reordering to increase temporal reuse of these accumulation array entries. The proposed models and methods are tested on a wide range of sparse matrices from real applications and the experiments were carried on a 60-core Intel Xeon Phi processor, as well as a two-socket Xeon processor. Results show the validity of the models and methods proposed for enhancing the locality in parallel SpGEMM operations. © 1990-2012 IEEE

Locality-Aware Parallel Sparse Matrix-Vector and Matrix-Transpose-Vector Multiplication on Many-Core Processors

Sparse matrix-vector and matrix-transpose-vector multiplication (SpMMTV) repeatedly performed as z ← ATx and y ← A z (or y ← A w) for the same sparse matrix A is a kernel operation widely used in various iterative solvers. One important optimization for serial SpMMTV is reusing A-matrix nonzeros, which halves the memory bandwidth requirement. However, thread-level parallelization of SpMMTV that reuses A-matrix nonzeros necessitates concurrent writes to the same output-vector entries. These concurrent writes can be handled in two ways: via atomic updates or thread-local temporary output vectors that will undergo a reduction operation, both of which are not efficient or scalable on processors with many cores and complicated cache-coherency protocols. In this work, we identify five quality criteria for efficient and scalable thread-level parallelization of SpMMTV that utilizes one-dimensional (1D) matrix partitioning. We also propose two locality-aware 1D partitioning methods, which achieve reusing A-matrix nonzeros and intermediate z-vector entries; exploiting locality in accessing x -, y -, and -vector entries; and reducing the number of concurrent writes to the same output-vector entries. These two methods utilize rowwise and columnwise singly bordered block-diagonal (SB) forms of A. We evaluate the validity of our methods on a wide range of sparse matrices. Experiments on the 60-core cache-coherent Intel Xeon Phi processor show the validity of the identified quality criteria and the validity of the proposed methods in practice. The results also show that the performance improvement from reusing A-matrix nonzeros compensates for the overhead of concurrent writes through the proposed SB-based methods. © 2015 IEEE

Cisgenesis and intragenesis as new strategies for crop improvement

Cisgenesis and intragenesis are emerging plant breeding technologies which offer great promise for future acceptance of genetically engineered crops. The techniques employ traditional genetic engineering methods but are confined to transferring of genes and genetic elements between sexually compatible species that can breed naturally. One of the main requirements is the absence of selectable marker genes (such as antibiotic resistance genes) in the genome. Hence the sensitive issues with regard to transfer of foreign genes and antibiotic resistance are overcome. It is a targeted technique involving specific locus; therefore, linkage drag that prolongs the time for crop improvement in traditional breeding does not occur. It has great potential for crop improvement using superior alleles that exist in the untapped germplasm or wild species. Cisgenic and intragenic plants may not face the same stringent regulatory assessment for field release as transgenic plants which is a clear added advantage that would save time. In this chapter, the concepts of cis/intragenesis and the prerequisites for the development of cis/intragenesis plants are elaborated. Strategies for marker gene removal after selection of transformants are discussed based on the few recent reports from various plant species

First Brillouin zone-centre phonon frequencies and elastic stiffness of the Ln(2)Hf(2)O(7) (Ln = La, Nd, Sm and Eu) pyrochlore

WOS: 000490421300015First Brillouin zone-centre phonon frequencies, elastic stiffness and mechanical properties of the Ln2Hf20 7 [Ln: La, Nd, Sm and Eu] pyrochlore structure were predicted by using an eight parameter bond-bending force constant model. One of the preliminary results of our study is that all the examined compounds are mechanically stable, and the elastic stiffness constants, and bulk and shear moduli decrease in the following sequence: La2Hf2O7 -> Nd2Hf2O7 -> Sm2Hf2O7 -> Eu2Hf2O7. The Poisson's ratio reveals that the interatomic bonding of the studied compounds has an ionic character and their ionicity decreases when one moves from La to Eu. The elastic properties are anisotropic and the anisotropy increases from La to Eu. The Raman and infrared active and inactive modes of the studied materials were calculated. Our findings are in good accordance with the related available data. (C) 2019 Elsevier B.V. All rights reserved

Structural, elastic, electronic and vibrational properties of XAl2O4 (X = Ca, Sr and Cd) semiconductors with orthorhombic structure

WOS: 000483698900057Structural, elastic, electronic and vibrational properties of XAl2O4 (X = Ca, Sr and Cd) compounds with orthorhombic structure are studied by first principles method within generalized gradient approximation. The calculated negative formation enthalpy for each compounds indicates the thermodynamical stability of the studied phase. Band structure calculations reveal that CaAl2O4, SrAl2O4 and CdAl2O4 compounds have a direct band gap of 4.86, 4.54 and 2.46 eV, respectively. Besides, from the analysis of the band gap values, one can notice that the replacement of Ca atoms by Sr and Cd atoms in these compounds reduces the band gap energy values. It is also observed that the CaAl2O4, SrAl2O4 and CdAl2O4 compounds are less compressible along b-axis and their compressibility decreases in the sequence SrAl2O4 > CdAl2O4 > CaAl2O4. Similarly, it is also noticeable that the CaAl2O4 compound have more resisting power against the monoclinic shear distortion along {100} plane and along {110} direction compared to CdAl2O4 and SrAl2O4 compounds. Moreover, Cauchy pressures confirm that the CaAl2O4 and SrAl2O4 compounds are ductile while the CdAl2O4 compound is brittle in nature. This fit very well with the forecast from B/G relation. The calculated elastic constants and the phonon dispersion relations of the studied compounds show that these compounds are both mechanically and dynamically stable. Moreover the temperature dependence of the specific heat and entropy have been discussed in detail and calculated Debye temperature is in good agreement with the related study in literature. (C) 2019 Elsevier B.V. All rights reserved

First principles investigations of the structural, elastic, electronic, vibrational and thermodynamic properties of hexagonal XAl2O4 (X = Cd, Ca and Sr)

WOS: 000468342100004Developing functional semiconductors for electronics, catalysis and photo electrochemical cells (PECs) that will take place of conventional semiconductors is very important. Despite intensive studies conducted about semiconductors, it is still a challenging issue to find more stable, functional, nontoxic and cheap materials for future electronic applications. Spinel oxides are among the promising materials that can be used as semiconductors due to their suitable band gap values. Here we study the structural, elastic, electronic, vibrational and thermodynamic properties of hexagonal XAl2O4 (X = Cd, Ca and Sr) spinels with space group P6(3) using first principles methods. The electronic band structure of XAl2O4 (X = Cd, Ca and Sr) reveales that the examined materials are direct band gap semiconductors. The calculated elastic constants and the phonon spectrum along high symmetry directions show that these materials are mechanically stable since they satisfy the generalised stability condition. Contrary, due to negative phonons at some high symmetry points XAl2O4 (X = Cd, Ca and Sr) spinels are dynamically unstable. Results obtained in this study show that of XAl2O4 (X = Cd, Ca and Sr) spinels are very promising for future electronic, catalysis and PECs applications

Kritik zehirlenme olgularında mortalite belirteçleri: Tek merkez deneyimi

Objective: Poisoning is among the common health care problems which may be fatal and 3-5% of the acutely poisoned patients need intensive care admission. The aim of this study was to examine the acutely poisoned patients admitted to intensive care unit (ICU) in terms of individual, etiological and demographical characteristics and also to determine the factors affecting mortality. Material and Methods: This study was retrospectively conducted on the patients admitted to medical ICU of a university hospital due to acute poisoning over a six year period. The patients' age, gender, comorbid disease status, sociocultural characteristics, cause of the poisoning, transfer time to hospital and to the ICU, signs and symptoms, laboratory data, Glasgow coma score, Acute Physiology and Chronic Health Evaluation II (APACHE II) score, Sequential Organ Failure Assessment score, length of stay in ICU, the treatments employed and their results were analyzed. Results: The total number of the patients included in the study was 190. The median age of the patients was 28.5 (16-72) years and 97 (51%) patients were females. The mean length of stay in ICU was 4.2±3.6 days. The overall mortality rate was 8.4%. Independent risk factors for mortality were presence of concomitant physical disorders, time to ICU admission, and higher APACHE II scores. Conclusion: Individual characteristics, cause of poisoning and type of toxic agent should be clearly determined since they are predictors for mortality. Early intervention is life saving. ICU scoring systems in predicting mortality are very valuable and should be used. © 2013 by Türkiye Klinikleri