Supercomputer Emulation For Evaluating Scheduling Algorithms

Scheduling algorithms have a significant impact on the optimal utilization of HPC facilities, yet the vast majority of the research in this area is done using simulations. In working with simulations, a great deal of factors that affect a real scheduler, such as its scheduling processing time, communication latencies and the scheduler intrinsic implementation complexity are not considered. As a result, despite theoretical improvements reported in several articles, practically no new algorithms proposed have been implemented in real schedulers, with HPC facilities still using the basic first-come-first-served (FCFS) with Backfill policy scheduling algorithm. A better approach could be, therefore, the use of real schedulers in an emulation environment to evaluate new algorithms. This thesis investigates two related challenges in emulations: computational cost and faithfulness of the results to real scheduling environments. It finds that the sampling, shrinking and shuffling of a trace must be done carefully to keep the classical metrics invariant or linear variant in relation to size and times of the original workload. This is accomplished by the careful control of the submission period and the consideration of drifts in the submission period and trace duration. This methodology can help researchers to better evaluate their scheduling algorithms and help HPC administrators to optimize the parameters of production schedulers. In order to assess the proposed methodology, we evaluated both the FCFS with Backfill and Suspend/Resume scheduling algorithms. The results strongly suggest that Suspend/Resume leads to a better utilization of a supercomputer when high priorities are given to big jobs

New method for SAXS curves analysis and its application to an inhibitor of α-amylase, hexokinase and aspartate of transcarbamilase

Este trabalho teve por finalidade a implementação e desenvolvimento de novos métodos para a análise de curvas de espalhamento de raios X a baixo ângulo por sistemas monodispersos. O resultado básico final deste trabalho foi a confecção de três programas de computador e suas aplicações em proteínas de interesse biológico. ELLFIT é um programa de computador que encontra o elipsóide cuja curva de SAXS melhor se ajusta a uma dada curva experimental. Para casos favoráveis este programa é capaz de determinar a dimensão máxima e algumas características básicas do formato da partícula. CRYSOL é um programa para a avaliação de curvas de espalhamento em solução para proteínas com estrutura atômica conhecida. O programa usa a expansão de multipolos para o cálculo rápido da promediação espacial e simula uma camada de hidratação ao redor da proteína. CRYSOL pode predizer a curva de SAXS de uma determinada proteína e compará-la com dados experimentais. HOMDIM é um programa para a determinação da posição das sub-unidades de um homodímero no caso de ser conhecida somente a estrutura da sub-unidade sozinha. Dada a curva experimental e a amplitude da sub-unidade, HOMDIM procura os parâmetros posicionais que descrevem o homodímero. Estes e outros programas foram aplicados a várias proteínas. O método da expansão de multipolos foi usado na determinação do envelope molecular de uma inibidora de ALPHA-amilase. O programa CRYSOL foi utilizado para resolver uma ambiguidade na estrutura quatemária cristalina da hexocinase e o programa HOMDIM para a proposição de um novo modelo para a estrutura quatemária da aspartato transcarbamilase no estado R em soluçãoThis work was aimed at the implementation and development of new methods for solution scattering analysis of monodisperse systems. The basic final result of this work was the development of three programs and their applications to proteins of biological interest. ELLFIT is a computer program, which finds the elipsoid whose SAXS curve has the best fit to a given experimental curve. In favorable cases, this program is able to determine the maximum dimension and some basic characteristic of the particle shape. CRYSOL is a program for evaluating the solution scattering from, proteins of known structure. The program uses multipole expansion for fast calculation of the spherically averaged scattering pattern and takes into account the hydration shell. Given the atomic coordinates it can predict the solution scattering curve and compare it with the experimental scattering curve. HOMDIM is a program to determine the position of both subunits of a homodimer when only one sub-unit structure is known. Given the experimental curve of the homodimer and the subunit scattering amplitudes. HOMDIM searches for the positional parameters, which describe the homodimer. These and other programs were used to study several proteins. The multipole expansion method was used in the shape determination of an ALPHA-amylase inhibitor. The program CRYSOL was used to solve the ambiguity in the hexokinase quaternary crystal structures and the program HOMDIM was utilized for the quaternary structure modeling of the R-state of the aspartate transcarbamilase in solutio

Introduction to crystallographic symmetry and determination of small molecules structures by X-ray diffraction

Foram determinadas quatro estruturas de complexos de Lantanóides utilizando a difração de raios-X. As intensidades dos feixes difratados foram medidas com um difratômetro automático de 4 ciclos CAD-4. As estruturas foram resolvidas utilizando o método de Patterson, sínteses de Fourier e Fourier Diferença e refinadas por métodos de mínimos quadrados com matriz bloqueada. Os poliedros de coordenação foram obtidos considerando as distâncias quadráticas médias mínimas entre os coordenantes e poliedros ideais. Y(C6H2N3O)3(6H18N3OP)2 e Ho(C6H2N3O)3(C6H18N3OP)2 são complexos isomorfos pertencentes ao sistema monoclínico, P21/n, tendo como parâmetros de rede para o complexo de Y: a = 17.104(2), b = 16.328(1), c = 17.671(6) &#197, &#946 = 95.40(1)&#176, Z = 4, Dc = 1.53 gcm-3, V = 4913(4) ޵ e para o complexo de Ho: a = 17.097(2), b = 16.299(1), c = 17.685(3) &#197, &#946 = 95.41(1)&#176, V = 4907(2) &#1973, Dc = 1.63 gcm-3. O poliedro de coordenação para esses complexos é o dodecaedro, simetria D2d (42m). Ce(C6H2N3O)3(C5H12N2O)3, é uma estrutura pertencente ao sistema triclínico, P-1, a = 1.495(5), b = 11.815(5), c = 18.40(1)&#197, &#945 = 83.09(5)&#176, &#946 = 76.7995)&#176, &#947 = 77.00(3)&#176, Z = 2, V = 4800(2)&#1973, Dc = 1.63 gcm-3. Existem 8 coordenantes ao redor do átomo pesado formando um Prisma Trigonal Biencapuzado. Nd(C6H2N3O)3(C5H12N2O)3, pertence ao sistema monoclínico, P21/c, a = 18.913(5), b = 12.386(5), c = 22.134(5)&#197, &#946 = 120.20(5)&#176, V = 4800(2)&#1973, Dc = 1.63 gcm-3. O número de coordenação é igual a 9 e o poliedro de coordenação é uma forma intermediária entre o antiprisma quadrado monoencapuzado e o prisma trigonal Trigonal Triencapuzado.It were determinated four small molecules structures by X-Ray diffraction. The intensities of the reflections were measured with an automatic four-cicle difractometer CAD-4. The structures were solved by Patterson, Fourier Synthesis and refined by least squares methods. The coordination polyedras were obtained considering the minimal root mean distances between the polyedras founded and the ideal polyedras. Y(C6H2N3O)3(6H18N3OP)2 e Ho(C6H2N3O)3(C6H18N3OP)2 are isomorphos strutures belong to the monoclinic system, P21/n; Y: a = 17.104(2), b = 16.328(1), c = 17.671(6) &#197, &#946 = 95.40(1)&#176, Z = 4, Dc = 1.53 gcm-3, V = 4913(4) ޵ Ho: a = 17.097(2), b = 16.299(1), c = 17.685(3)&#197, &#946 = 95.41(1)&#176, V = 4907(2)&#1973, Dc = 1.63 gcm-3. The coordination number of these structures is 8 and the coordination polyedra is dodecahedro, with simetry D2d (42m). Ce(C6H2N3O)3(C5H12N2O)3, is a structure belongs to the triclinic system. P-1, a = 1.495(5), b = 11.815(5), c = 18.40(1)&#197, &#945 = 83.09(5)&#176, &#946 = 76.7995)&#176, &#947 = 77.00(3)&#176, Z = 2, V = 4800(2)&#1973, Dc = 1.63 gcm-3. There are 8 coordinates around the heavy metal forming a Two-couped Trigonal Prism. Nd(C6H2N3O)3(C5H12N2O)3, belongs to the monoclinic system, P21/c, a = 18.913(5), b = 12.386(5), c = 22.134(5)&#197, &#946 = 120.20(5)&#176, V = 4800(2)&#1973, Dc = 1.63 gcm-3. The coordination number is a 9 and the coordination polyedra is intermediate between mono-couped square antiprism and three-couped trigonal

New method for SAXS curves analysis and its application to an inhibitor of α-amylase, hexokinase and aspartate of transcarbamilase

Este trabalho teve por finalidade a implementação e desenvolvimento de novos métodos para a análise de curvas de espalhamento de raios X a baixo ângulo por sistemas monodispersos. O resultado básico final deste trabalho foi a confecção de três programas de computador e suas aplicações em proteínas de interesse biológico. ELLFIT é um programa de computador que encontra o elipsóide cuja curva de SAXS melhor se ajusta a uma dada curva experimental. Para casos favoráveis este programa é capaz de determinar a dimensão máxima e algumas características básicas do formato da partícula. CRYSOL é um programa para a avaliação de curvas de espalhamento em solução para proteínas com estrutura atômica conhecida. O programa usa a expansão de multipolos para o cálculo rápido da promediação espacial e simula uma camada de hidratação ao redor da proteína. CRYSOL pode predizer a curva de SAXS de uma determinada proteína e compará-la com dados experimentais. HOMDIM é um programa para a determinação da posição das sub-unidades de um homodímero no caso de ser conhecida somente a estrutura da sub-unidade sozinha. Dada a curva experimental e a amplitude da sub-unidade, HOMDIM procura os parâmetros posicionais que descrevem o homodímero. Estes e outros programas foram aplicados a várias proteínas. O método da expansão de multipolos foi usado na determinação do envelope molecular de uma inibidora de ALPHA-amilase. O programa CRYSOL foi utilizado para resolver uma ambiguidade na estrutura quatemária cristalina da hexocinase e o programa HOMDIM para a proposição de um novo modelo para a estrutura quatemária da aspartato transcarbamilase no estado R em soluçãoThis work was aimed at the implementation and development of new methods for solution scattering analysis of monodisperse systems. The basic final result of this work was the development of three programs and their applications to proteins of biological interest. ELLFIT is a computer program, which finds the elipsoid whose SAXS curve has the best fit to a given experimental curve. In favorable cases, this program is able to determine the maximum dimension and some basic characteristic of the particle shape. CRYSOL is a program for evaluating the solution scattering from, proteins of known structure. The program uses multipole expansion for fast calculation of the spherically averaged scattering pattern and takes into account the hydration shell. Given the atomic coordinates it can predict the solution scattering curve and compare it with the experimental scattering curve. HOMDIM is a program to determine the position of both subunits of a homodimer when only one sub-unit structure is known. Given the experimental curve of the homodimer and the subunit scattering amplitudes. HOMDIM searches for the positional parameters, which describe the homodimer. These and other programs were used to study several proteins. The multipole expansion method was used in the shape determination of an ALPHA-amylase inhibitor. The program CRYSOL was used to solve the ambiguity in the hexokinase quaternary crystal structures and the program HOMDIM was utilized for the quaternary structure modeling of the R-state of the aspartate transcarbamilase in solutio

Introduction to crystallographic symmetry and determination of small molecules structures by X-ray diffraction

Foram determinadas quatro estruturas de complexos de Lantanóides utilizando a difração de raios-X. As intensidades dos feixes difratados foram medidas com um difratômetro automático de 4 ciclos CAD-4. As estruturas foram resolvidas utilizando o método de Patterson, sínteses de Fourier e Fourier Diferença e refinadas por métodos de mínimos quadrados com matriz bloqueada. Os poliedros de coordenação foram obtidos considerando as distâncias quadráticas médias mínimas entre os coordenantes e poliedros ideais. Y(C6H2N3O)3(6H18N3OP)2 e Ho(C6H2N3O)3(C6H18N3OP)2 são complexos isomorfos pertencentes ao sistema monoclínico, P21/n, tendo como parâmetros de rede para o complexo de Y: a = 17.104(2), b = 16.328(1), c = 17.671(6) &#197, &#946 = 95.40(1)&#176, Z = 4, Dc = 1.53 gcm-3, V = 4913(4) ޵ e para o complexo de Ho: a = 17.097(2), b = 16.299(1), c = 17.685(3) &#197, &#946 = 95.41(1)&#176, V = 4907(2) &#1973, Dc = 1.63 gcm-3. O poliedro de coordenação para esses complexos é o dodecaedro, simetria D2d (42m). Ce(C6H2N3O)3(C5H12N2O)3, é uma estrutura pertencente ao sistema triclínico, P-1, a = 1.495(5), b = 11.815(5), c = 18.40(1)&#197, &#945 = 83.09(5)&#176, &#946 = 76.7995)&#176, &#947 = 77.00(3)&#176, Z = 2, V = 4800(2)&#1973, Dc = 1.63 gcm-3. Existem 8 coordenantes ao redor do átomo pesado formando um Prisma Trigonal Biencapuzado. Nd(C6H2N3O)3(C5H12N2O)3, pertence ao sistema monoclínico, P21/c, a = 18.913(5), b = 12.386(5), c = 22.134(5)&#197, &#946 = 120.20(5)&#176, V = 4800(2)&#1973, Dc = 1.63 gcm-3. O número de coordenação é igual a 9 e o poliedro de coordenação é uma forma intermediária entre o antiprisma quadrado monoencapuzado e o prisma trigonal Trigonal Triencapuzado.It were determinated four small molecules structures by X-Ray diffraction. The intensities of the reflections were measured with an automatic four-cicle difractometer CAD-4. The structures were solved by Patterson, Fourier Synthesis and refined by least squares methods. The coordination polyedras were obtained considering the minimal root mean distances between the polyedras founded and the ideal polyedras. Y(C6H2N3O)3(6H18N3OP)2 e Ho(C6H2N3O)3(C6H18N3OP)2 are isomorphos strutures belong to the monoclinic system, P21/n; Y: a = 17.104(2), b = 16.328(1), c = 17.671(6) &#197, &#946 = 95.40(1)&#176, Z = 4, Dc = 1.53 gcm-3, V = 4913(4) ޵ Ho: a = 17.097(2), b = 16.299(1), c = 17.685(3)&#197, &#946 = 95.41(1)&#176, V = 4907(2)&#1973, Dc = 1.63 gcm-3. The coordination number of these structures is 8 and the coordination polyedra is dodecahedro, with simetry D2d (42m). Ce(C6H2N3O)3(C5H12N2O)3, is a structure belongs to the triclinic system. P-1, a = 1.495(5), b = 11.815(5), c = 18.40(1)&#197, &#945 = 83.09(5)&#176, &#946 = 76.7995)&#176, &#947 = 77.00(3)&#176, Z = 2, V = 4800(2)&#1973, Dc = 1.63 gcm-3. There are 8 coordinates around the heavy metal forming a Two-couped Trigonal Prism. Nd(C6H2N3O)3(C5H12N2O)3, belongs to the monoclinic system, P21/c, a = 18.913(5), b = 12.386(5), c = 22.134(5)&#197, &#946 = 120.20(5)&#176, V = 4800(2)&#1973, Dc = 1.63 gcm-3. The coordination number is a 9 and the coordination polyedra is intermediate between mono-couped square antiprism and three-couped trigonal

Crystal structures and magnetic properties of CuX2(pdmp)2 complexes (X = Br, Cl)

We report the synthesis and the structural and magnetic characterization of two new compounds: dibromobis-(pdmp)copper(II), CuBr2C22H24N4 (1), and dichlorobis(pdmp)copper(II), CuCl2C22H24N4 (2), where pdmp = 1-phenyl-3,5-dimethylpyrazole. The structures were refined by full-matrix least-squares techniques to R1 = 0.0620 and 0.0777, respectively. Compound 1 belongs to the space group P21/n with a = 8.165(5) Å, b = 10.432(3) Å, c = 13.385(4) Å, β = 100.12(4)̊, and Z = 2. Compound 2 belongs to the space group P21/c with a = 8.379(2) Å, b = 22.630(2) Å, c = 12.256(2) Å, β= 98.43(3)°, and Z = 4. It has the same molecular formula as a compound reported previously but a different crystal structure. Detailed single-crystal EPR measurements were performed for single-crystal samples of 1 and 2 at 9 and 35 GHz and at room temperature. The positions and line widths of the EPR lines were measured as a function of the magnetic field orientation in three orthogonal planes. The data were used to study the electronic properties of the copper ions and to evaluate the exchange interactions between them. Our results are discussed in terms of the electronic pathways for superexchange between copper ions, which are provided by the stacking of pyrazole and phenyl rings of neighboring molecules and by hydrogen-halogen bonds. © 1999 American Chemical Society