A user-friendly web portal for T-Coffee on supercomputers

Background: Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is to reduce the execution time of the large-scale sequence alignments. It can be run on distributed memory clusters allowing users to align data sets consisting of hundreds of proteins within a reasonable time. However, most of the potential users of this tool are not familiar with the use of grids or supercomputers. Results: In this paper we show how PTC can be easily deployed and controlled on a super computer architecture using a web portal developed using Rapid. Rapid is a tool for efficiently generating standardized portlets for a wide range of applications and the approach described here is generic enough to be applied to other applications, or to deploy PTC on different HPC environments. Conclusions: The PTC portal allows users to upload a large number of sequences to be aligned by the parallel version of TC that cannot be aligned by a single machine due to memory and execution time constraints. The web portal provides a user-friendly solution.

User-friendly parallel computations with econometric examples

This paper shows how a high level matrix programming language may be used to perform Monte Carlo simulation, bootstrapping, estimation by maximum likelihood and GMM, and kernel regression in parallel on symmetric multiprocessor computers or clusters of workstations. The implementation of parallelization is done in a way such that an investigator may use the programs without any knowledge of parallel programming. A bootable CD that allows rapid creation of a cluster for parallel computing is introduced. Examples show that parallelization can lead to important reductions in computational time. Detailed discussion of how the Monte Carlo problem was parallelized is included as an example for learning to write parallel programs for Octave.

An ordinal shapley value for economic environments (Revised version)

We propose a new solution concept to address the problem of sharing a surplus among the agents generating it. The problem is formulated in the preferences-endowments space. The solution is defined recursively, incorporating notions of consistency and fairness and relying on properties satisfied by the Shapley value for Transferable Utility (TU) games. We show a solution exists, and call it the Ordinal Shapley value (OSV). We characterize the OSV using the notion of coalitional dividends, and furthermore show it is monotone and anonymous. Finally, similarly to the weighted Shapely value for TU games, we construct a weighted OSV as well.

ParallelKnoppix - Rapid deployment of a linux cluster for MPI parallel processing using non-dedicated computers

This note describes ParallelKnoppix, a bootable CD that allows creation of a Linux cluster in very little time. An experienced user can create a cluster ready to execute MPI programs in less than 10 minutes. The computers used may be heterogeneous machines, of the IA-32 architecture. When the cluster is shut down, all machines except one are in their original state, and the last can be returned to its original state by deleting a directory. The system thus provides a means of using non-dedicated computers to create a cluster. An example session is documented.

Marx's analysis of the falling rate of profit on the first version of volume III of capital

The paper provides a description and analysis of the Hodgskin section of Theories of Surplus Value and the general law section of the first version of Volume III of Capital. It then considers Part III of Volume III, the evolution of Marx's thought and various interpretations of his theory in the light of this analysis. It is suggested that Marx thought that the rate of profit must fall and even in the 1870s hoped to be able to provide a demonstration of this. However the main conclusions are: 1. Marx's major attempt to show that the rate of profit must fall occurred in the general law section. 2. Part III does not contain a demonstration that the rate of profit must fall. 3. Marx was never able to demonstrate that the rate of profit must fall and he was aware of this.

A Descriptive and analytic look at Marx's own explanations of the falling rate of profit (second version)

This paper examines, both descriptively and analytically, Marx's arguments for the falling rate of profit from the Hodgskin section of Theories of Surplus Value, The General Law section of the recently published Volume 33 of the Collected Works and Chapter 3 of Volume III of Capital. The conclusions are as follows: First, Marx realised that his main attempt to give an intrinsic explanation of the falling rate of profit, which occurred in the General Law section, had failed; but he still hoped that he would be able to demonstrate it in the future. Second, the Hodgskin and General Law sections contain a number of subsidiary explanations, mostly related to resource scarcity, some of which are correct. Third, Part III of volume III does not contain a demonstration of the falling rate of profit, but a description of the role of the falling rate of profit in capitalist development. Forth, it also contains suppressed references to resource scarcity. And finally, in Chapter 3 of Volume III, Marx says that it is resource scarcity that causes the fall in the rate of profit described in Part III of the same volume. The key to all these conclusions in the careful analysis of the General Law section.

A foundation model for marxian breakdown theories based on a new falling rate of profit mechanism (Long version)

The paper presents a foundation model for Marxian theories of the breakdown of capitalism based on a new falling rate of profit mechanism. All of these theories are based on one or more of "the historical tendencies": a rising capital-wage bill ratio, a rising capitalist share and a falling rate of profit. The model is a foundation in the sense that it generates these tendencies in the context of a model with a constant subsistence wage. The newly discovered generating mechanism is based on neo-classical reasoning for a model with land. It is non-Ricardian in that land augmenting technical progress can be unboundedly rapid. Finally, since the model has no steady state, it is necessary to use a new technique, Chaplygin's method, to prove the result.

A descriptive and analytic look at Marxs own explanations for the falling rate of profit (Long Version)

Marxs conclusions about the falling rate of profit have been analysed exhaustively. Usually this has been done by building models which broadly conform to Marxs views and then showing that his conclusions are either correct or, more frequently, that they can not be sustained. By contrast, this paper examines, both descriptively and analytically, Marxs arguments from the Hodgskin section of Theories of Surplus Value, the General Law section of the recently published Volume 33 of the Collected Works and Chapter 3 of Volume III of Capital. It also gives a new interpretation of Part III of this last work. The main conclusions are first, that Marx had an intrinsic explanation of the falling rate of profit but was unable to give it a satisfactory demonstration and second, that he had a number of subsidiary explanations of which the most important was resource scarcity. The paper closes with an assessment of the pedigree of various currents of Marxian thought on this issue.

Payoff-dependent balancedness and cores (revised version)

We prove the non-emptiness of the core of an NTU game satisfying a condition of payoff-dependent balancedness, based on transfer rate mappings. We also define a new equilibrium condition on transfer rates and we prove the existence of core payoff vectors satisfying this condition. The additional requirement of transfer rate equilibrium refines the core concept and allows the selection of specific core payoff vectors. Lastly, the class of parametrized cooperative games is introduced. This new setting and its associated equilibrium-core solution extend the usual cooperative game framework and core solution to situations depending on an exogenous environment. A non-emptiness result for the equilibrium-core is also provided in the context of a parametrized cooperative game. Our proofs borrow mathematical tools and geometric constructions from general equilibrium theory with non convexities. Applications to extant results taken from game theory and economic theory are given.

Inequity version and team incentives

We study optimal contracts in a simple model where employees are averse to inequity as modelled by Fehr and Schmidt (1999). A "selfish" employer can profitably exploit such preferences among its employees by offering contracts which create inequity off-equilibrium and thus, they would leave employees feeling envy or guilt when they do not meet the employer's demands. Such contracts resemble team and relative performance contracts, and thus we derive conditions under which it may be beneficial to form work teams of employees with distributional concerns who were previously working individually. Similar results are obtained for status-seeking and efficiency concerns preferences.

Parallel spinors on pseudo-riemannian spin(q) manifolds

We study simply-connected irreducible non-locally symmetric pseudo-Riemannian Spin(q) manifolds admitting parallel quaternionic spinors.

Including the workload effect in the parallel program signature

Performance prediction and application behavior modeling have been the subject of exten- sive research that aim to estimate applications performance with an acceptable precision. A novel approach to predict the performance of parallel applications is based in the con- cept of Parallel Application Signatures that consists in extract an application most relevant parts (phases) and the number of times they repeat (weights). Executing these phases in a target machine and multiplying its exeuction time by its weight an estimation of the application total execution time can be made. One of the problems is that the performance of an application depends on the program workload. Every type of workload affects differently how an application performs in a given system and so affects the signature execution time. Since the workloads used in most scientific parallel applications have dimensions and data ranges well known and the behavior of these applications are mostly deterministic, a model of how the programs workload affect its performance can be obtained. We create a new methodology to model how a program’s workload affect the parallel application signature. Using regression analysis we are able to generalize each phase time execution and weight function to predict an application performance in a target system for any type of workload within predefined range. We validate our methodology using a synthetic program, benchmarks applications and well known real scientific applications.

Proposal of a parallel architecture for a motion detection algorithm

This paper proposes a parallel architecture for estimation of the motion of an underwater robot. It is well known that image processing requires a huge amount of computation, mainly at low-level processing where the algorithms are dealing with a great number of data. In a motion estimation algorithm, correspondences between two images have to be solved at the low level. In the underwater imaging, normalised correlation can be a solution in the presence of non-uniform illumination. Due to its regular processing scheme, parallel implementation of the correspondence problem can be an adequate approach to reduce the computation time. Taking into consideration the complexity of the normalised correlation criteria, a new approach using parallel organisation of every processor from the architecture is proposed

CODAPACK3D. A new version of Compositional Data Package

The statistical analysis of compositional data should be treated using logratios of parts,which are difficult to use correctly in standard statistical packages. For this reason afreeware package, named CoDaPack was created. This software implements most of thebasic statistical methods suitable for compositional data.In this paper we describe the new version of the package that now is calledCoDaPack3D. It is developed in Visual Basic for applications (associated with Excel©),Visual Basic and Open GL, and it is oriented towards users with a minimum knowledgeof computers with the aim at being simple and easy to use.This new version includes new graphical output in 2D and 3D. These outputs could bezoomed and, in 3D, rotated. Also a customization menu is included and outputs couldbe saved in jpeg format. Also this new version includes an interactive help and alldialog windows have been improved in order to facilitate its use.To use CoDaPack one has to access Excel© and introduce the data in a standardspreadsheet. These should be organized as a matrix where Excel© rows correspond tothe observations and columns to the parts. The user executes macros that returnnumerical or graphical results. There are two kinds of numerical results: new variablesand descriptive statistics, and both appear on the same sheet. Graphical output appearsin independent windows. In the present version there are 8 menus, with a total of 38submenus which, after some dialogue, directly call the corresponding macro. Thedialogues ask the user to input variables and further parameters needed, as well aswhere to put these results. The web site http://ima.udg.es/CoDaPack contains thisfreeware package and only Microsoft Excel© under Microsoft Windows© is required torun the software.Kew words: Compositional data Analysis, Software

CoDaPack. An Excel and Visual Basic based software of compositional data analysis. Current version and discussion form upcoming versions

In the eighties, John Aitchison (1986) developed a new methodological approach for the statistical analysis of compositional data. This new methodology was implemented in Basic routines grouped under the name CODA and later NEWCODA inMatlab (Aitchison, 1997). After that, several other authors have published extensions to this methodology: Marín-Fernández and others (2000), Barceló-Vidal and others (2001), Pawlowsky-Glahn and Egozcue (2001, 2002) and Egozcue and others (2003). (...)