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Papers by Guillermo Miranda
In this Project, the obtaining of ZnO varistors with the controlled precipitation technique from ... more In this Project, the obtaining of ZnO varistors with the controlled precipitation technique from the (C 2 H 3 O 2 ) 2 , Mn (C 2 H 3 O 2 ) 2 , and Bi (C 2 H 3 O 2 ) 3 organic salts dissolved in nitric acid is presented. The resulting precipitation was subjected to the washing processes and a crystalline phases and functional groups evolution following was made by DTIR, DRX and SEM. The temperaturetime for the thermic treatments programs were determined using TGA, DTA. Finally the obtained varistors were characterized electronically. The attained samples were compared to the varistors fabricated by the oxide’s mixture technique.
Introduction: Migraine is the primary headache with the highest impact in the general population.... more Introduction: Migraine is the primary headache with the highest impact in the general population. According to local information, about 3 million people in Colombia suffer from this neurological condition leading to high burden and disability. Objective: To provide uniform information regarding the acute and preventive treatment of patients with migraine. Information about chronic migraine, medication overuse was considered. Materials and methods: Expert consensus by using online Delphi methodology. Three rounds were carried out, the whole group participated in two of them and the developer group in the total number of rounds. A review of the literature was conducted to obtain academic support to design questions with clinical relevance. Neurologists from the main Colombian regions were included. Results: Preventive treatment should be offered to patients with more than 6 headache days for 6 to 12 months according to individual clinical features. Topiramate, Divalproex sodium/Valpro...
Lecture Notes in Computational Science and Engineering, 2017
Mimetic difference operators Div, Grad and Curl, have been constructed to provide a high order of... more Mimetic difference operators Div, Grad and Curl, have been constructed to provide a high order of accuracy in numerical schemes that mimic the properties of their corresponding continuum operators; hence they would be faithful to the physics. However, this faithfulness of the discrete basic operators might not be sufficient if the numerical difference scheme introduces some numerical energy increase, which would obviously result in a potentially unstable performance. We present a high order compact mimetic scheme for 2D wave motions and show that the energy of the system is also conserved in the discrete sense.
SEG Technical Program Expanded Abstracts 2020, 2020
ACM Transactions on Parallel Computing, 2016
Biological sequence alignment is a very popular application in Bioinformatics, used routinely wor... more Biological sequence alignment is a very popular application in Bioinformatics, used routinely worldwide. Many implementations of biological sequence alignment algorithms have been proposed for multicores, GPUs, FPGAs and CellBEs. These implementations are platform-specific; porting them to other systems requires considerable programming effort. This article proposes and evaluates MASA, a flexible and customizable software architecture that enables the execution of biological sequence alignment applications with three variants (local, global, and semiglobal) in multiple hardware/software platforms with block pruning, which is able to reduce significantly the amount of data processed. To attain our flexibility goals, we also propose a generic version of block pruning and developed multiple parallelization strategies as building blocks, including a new asynchronous dataflow-based parallelization, which may be combined to implement efficient aligners in different platforms. We provide f...
IEEE Transactions on Parallel and Distributed Systems, 2016
This paper proposes and evaluates CUDAlign 4.0, a parallel strategy to obtain the optimal alignme... more This paper proposes and evaluates CUDAlign 4.0, a parallel strategy to obtain the optimal alignment of huge DNA sequences in multi-GPU platforms, using the exact Smith-Waterman (SW) algorithm. In the first phase of CUDAlign 4.0, a huge Dynamic Programming (DP) matrix is computed by multiple GPUs, which asynchronously communicate border elements to the right neighbor in order to find the optimal score. After that, the traceback phase of SW is executed. The efficient parallelization of the traceback phase is very challenging because of the high amount of data dependency, which particularly impacts the performance and limits the application scalability. In order to obtain a multi-GPU highly parallel traceback phase, we propose and evaluate a new parallel traceback algorithm called Incremental Speculative Traceback (IST), which pipelines the traceback phase, speculating incrementally over the values calculated so far, producing results in advance. With CUDAlign 4.0, we were able to calculate SW matrices with up to 60 Peta cells, obtaining the optimal local alignments of all Human and Chimpanzee homologous chromosomes, whose sizes range from 26 Millions of Base Pairs (MBP) up to 249 MBP. As far as we know, this is the first time such comparison was made with the SW exact method. We also show that the IST algorithm is able to reduce the traceback time from 2.15⇥ up to 21.03⇥, when compared with the baseline traceback algorithm. The human⇥chimpanzee chromosome 5 comparison (180 MBP⇥183 MBP) attained 10,370.00 GCUPS (Billions of Cells Updated per Second) using 384 GPUs, with a speculation hit ratio of 98.2%.
Mimetic Discretization Methods, 2013
Mimetic Discretization Methods, 2013
Mimetic Discretization Methods, 2013
Mimetic Discretization Methods, 2013
Mimetic Discretization Methods, 2013
Mimetic Discretization Methods, 2013
Mimetic Discretization Methods, 2013
Lecture Notes in Mathematics, 1983
partially or totally submerged body of arbitrary shape moving with constant speed is analyzed usi... more partially or totally submerged body of arbitrary shape moving with constant speed is analyzed using Oseen's approximate equation for viscous incompressible fluids. This Analysis is based upon the derivation of integral identities of Green's type, and identification of surface hydrodynamic pote~ tlala completely analogous to the classical single and double-layer potentials already found for Laplace's equation, heat equation, Stokes flow
Mimetic Discretization Methods, 2013
ACM SIGPLAN Notices, 2014
This paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman (SW) al... more This paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman (SW) algorithm for megabase DNA sequences in heterogeneous multi-GPU platforms. In our strategy, the computation of a single huge SW matrix is spread over multiple GPUs, which communicate border elements to the neighbour, using a circular buffer mechanism that hides the communication overhead. We compared 4 pairs of human-chimpanzee homologous chromosomes using 2 different GPU environments, obtaining a performance of up to 140.36 GCUPS (Billion of cells processed per second) with 3 heterogeneous GPUS.
In this Project, the obtaining of ZnO varistors with the controlled precipitation technique from ... more In this Project, the obtaining of ZnO varistors with the controlled precipitation technique from the (C 2 H 3 O 2 ) 2 , Mn (C 2 H 3 O 2 ) 2 , and Bi (C 2 H 3 O 2 ) 3 organic salts dissolved in nitric acid is presented. The resulting precipitation was subjected to the washing processes and a crystalline phases and functional groups evolution following was made by DTIR, DRX and SEM. The temperaturetime for the thermic treatments programs were determined using TGA, DTA. Finally the obtained varistors were characterized electronically. The attained samples were compared to the varistors fabricated by the oxide’s mixture technique.
Introduction: Migraine is the primary headache with the highest impact in the general population.... more Introduction: Migraine is the primary headache with the highest impact in the general population. According to local information, about 3 million people in Colombia suffer from this neurological condition leading to high burden and disability. Objective: To provide uniform information regarding the acute and preventive treatment of patients with migraine. Information about chronic migraine, medication overuse was considered. Materials and methods: Expert consensus by using online Delphi methodology. Three rounds were carried out, the whole group participated in two of them and the developer group in the total number of rounds. A review of the literature was conducted to obtain academic support to design questions with clinical relevance. Neurologists from the main Colombian regions were included. Results: Preventive treatment should be offered to patients with more than 6 headache days for 6 to 12 months according to individual clinical features. Topiramate, Divalproex sodium/Valpro...
Lecture Notes in Computational Science and Engineering, 2017
Mimetic difference operators Div, Grad and Curl, have been constructed to provide a high order of... more Mimetic difference operators Div, Grad and Curl, have been constructed to provide a high order of accuracy in numerical schemes that mimic the properties of their corresponding continuum operators; hence they would be faithful to the physics. However, this faithfulness of the discrete basic operators might not be sufficient if the numerical difference scheme introduces some numerical energy increase, which would obviously result in a potentially unstable performance. We present a high order compact mimetic scheme for 2D wave motions and show that the energy of the system is also conserved in the discrete sense.
SEG Technical Program Expanded Abstracts 2020, 2020
ACM Transactions on Parallel Computing, 2016
Biological sequence alignment is a very popular application in Bioinformatics, used routinely wor... more Biological sequence alignment is a very popular application in Bioinformatics, used routinely worldwide. Many implementations of biological sequence alignment algorithms have been proposed for multicores, GPUs, FPGAs and CellBEs. These implementations are platform-specific; porting them to other systems requires considerable programming effort. This article proposes and evaluates MASA, a flexible and customizable software architecture that enables the execution of biological sequence alignment applications with three variants (local, global, and semiglobal) in multiple hardware/software platforms with block pruning, which is able to reduce significantly the amount of data processed. To attain our flexibility goals, we also propose a generic version of block pruning and developed multiple parallelization strategies as building blocks, including a new asynchronous dataflow-based parallelization, which may be combined to implement efficient aligners in different platforms. We provide f...
IEEE Transactions on Parallel and Distributed Systems, 2016
This paper proposes and evaluates CUDAlign 4.0, a parallel strategy to obtain the optimal alignme... more This paper proposes and evaluates CUDAlign 4.0, a parallel strategy to obtain the optimal alignment of huge DNA sequences in multi-GPU platforms, using the exact Smith-Waterman (SW) algorithm. In the first phase of CUDAlign 4.0, a huge Dynamic Programming (DP) matrix is computed by multiple GPUs, which asynchronously communicate border elements to the right neighbor in order to find the optimal score. After that, the traceback phase of SW is executed. The efficient parallelization of the traceback phase is very challenging because of the high amount of data dependency, which particularly impacts the performance and limits the application scalability. In order to obtain a multi-GPU highly parallel traceback phase, we propose and evaluate a new parallel traceback algorithm called Incremental Speculative Traceback (IST), which pipelines the traceback phase, speculating incrementally over the values calculated so far, producing results in advance. With CUDAlign 4.0, we were able to calculate SW matrices with up to 60 Peta cells, obtaining the optimal local alignments of all Human and Chimpanzee homologous chromosomes, whose sizes range from 26 Millions of Base Pairs (MBP) up to 249 MBP. As far as we know, this is the first time such comparison was made with the SW exact method. We also show that the IST algorithm is able to reduce the traceback time from 2.15⇥ up to 21.03⇥, when compared with the baseline traceback algorithm. The human⇥chimpanzee chromosome 5 comparison (180 MBP⇥183 MBP) attained 10,370.00 GCUPS (Billions of Cells Updated per Second) using 384 GPUs, with a speculation hit ratio of 98.2%.
Mimetic Discretization Methods, 2013
Mimetic Discretization Methods, 2013
Mimetic Discretization Methods, 2013
Mimetic Discretization Methods, 2013
Mimetic Discretization Methods, 2013
Mimetic Discretization Methods, 2013
Mimetic Discretization Methods, 2013
Lecture Notes in Mathematics, 1983
partially or totally submerged body of arbitrary shape moving with constant speed is analyzed usi... more partially or totally submerged body of arbitrary shape moving with constant speed is analyzed using Oseen's approximate equation for viscous incompressible fluids. This Analysis is based upon the derivation of integral identities of Green's type, and identification of surface hydrodynamic pote~ tlala completely analogous to the classical single and double-layer potentials already found for Laplace's equation, heat equation, Stokes flow
Mimetic Discretization Methods, 2013
ACM SIGPLAN Notices, 2014
This paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman (SW) al... more This paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman (SW) algorithm for megabase DNA sequences in heterogeneous multi-GPU platforms. In our strategy, the computation of a single huge SW matrix is spread over multiple GPUs, which communicate border elements to the neighbour, using a circular buffer mechanism that hides the communication overhead. We compared 4 pairs of human-chimpanzee homologous chromosomes using 2 different GPU environments, obtaining a performance of up to 140.36 GCUPS (Billion of cells processed per second) with 3 heterogeneous GPUS.