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Performance analysis of electronic structure codes on HPC systems: a case study of SIESTA.

ABSTRACT: We report on scaling and timing tests of the SIESTA electronic structure code for ab initio molecular dynamics simulations using density-functional theory. The tests are performed on six large-scale supercomputers belonging to the PRACE Tier-0 network with four different architectures: Cray XE6, IBM BlueGene/Q, BullX, and IBM iDataPlex. We employ a systematic strategy for simultaneously testing weak and strong scaling, and propose a measure which is independent of the range of number of cores on which the tests are performed to quantify strong scaling efficiency as a function of simulation size. We find an increase in efficiency with simulation size for all machines, with a qualitatively different curve depending on the supercomputer topology, and discuss the connection of this functional form with weak scaling behaviour. We also analyze the absolute timings obtained in our tests, showing the range of system sizes and cores favourable for different machines. Our results can be employed as a guide both for running SIESTA on parallel architectures, and for executing similar scaling tests of other electronic structure codes.

SUBMITTER: Corsetti F

PROVIDER: S-EPMC3991679 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Performance analysis of electronic structure codes on HPC systems: a case study of SIESTA.

Corsetti Fabiano F

PloS one 20140418 4

We report on scaling and timing tests of the SIESTA electronic structure code for ab initio molecular dynamics simulations using density-functional theory. The tests are performed on six large-scale supercomputers belonging to the PRACE Tier-0 network with four different architectures: Cray XE6, IBM BlueGene/Q, BullX, and IBM iDataPlex. We employ a systematic strategy for simultaneously testing weak and strong scaling, and propose a measure which is independent of the range of number of cores on ...[more]

PMID: 24748385

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Project description:Background and objectives: Siesta, which is a short afternoon nap, is a habit that is commonly practiced in the Mediterranean and tropical areas. Data on the association between siesta and coronary artery disease has been conflicting. A protective effect has been demonstrated in the countries that commonly practice siesta, but a harmful effect has been observed in the countries that infrequently practice the siesta habit. Information on the association between siesta and ischemic stroke has been, however, lacking. Hence, the purpose of our study was to determine the effect of siesta on ischemic stroke. Materials and Methods: This was a case-control study, conducted on the patients with acute ischemic stroke who came for their first follow-up visit to the neurology clinic. Controls were randomly selected from the patients visiting the neurology clinic on the same day as the patients with ischemic stroke. In addition to basic demographics and the occurrence of established stroke risk factors, information about siesta practice was also collected from both groups. A multivariate logistic regression analysis was utilized to determine the relationship between siesta practice and ischemic stroke. Results: A total of 206 patients were recruited from the neurology clinic of King Khalid university hospital; of which only 194 subjects were included in the analysis (98 ischemic stroke cases and 96 controls). The mean age of the participants was 59.68 ± 13.75 years and 98 (50.52%) were male. Interestingly, 43% of the whole study cohort practiced regular siesta. However, when compared to the stroke population, the control group practiced siesta more frequently (30% vs. 56%). In a multivariate logistic regression analysis, hypertension, diabetes mellitus, excess body weight (body mass index > 25 kg/m2) and dyslipidemia were found to increase the risk of ischemic stroke (OR 2.12, 95% CI: 1.02-4.66, p = 0.005; OR 2.72, 95% CI: 1.94-4.88, p = 0.014; OR 2.94, 95% CI: 1.5164-5.7121 p = 0.0014; OR 3.27, 95% CI: 2.42-5.199, p ? 0.001, respectively). On the contrary, the practice of regular siesta lowered the risk of ischemic stroke (OR 0.58, 95% CI: 0.3551-0.9526, p = 0.031). Conclusions: Siesta was associated with a reduced risk for the occurrence of ischemic stroke. Large prospective longitudinal studies should be conducted to verify the protective effect of siesta on stroke.

Project description:Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. DFT remains the workhorse for modeling such extended macrocycles, when taking into account their size and huge conformational flexibility. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, π···π stacking, steric effects, ring strain, and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wave function methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a stronger degree of static correlation than the Hückel and twisted-Hückel structures, and as a result the relative energies of singly twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between the extrapolated MP2/CBS energies estimated from cc-pV{T,Q}Z, diffuse-augmented heavy-aug-cc-pV{T,Q}Z and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol-1 with the CCSD(T) relative energies. Regarding DFT methods, the range-separated double hybrids, such as ωB97M(2) and B2GP-PLYP, outperform other functionals with RMSDs of 0.6 and 0.8 kcal mol-1, respectively. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended π-systems, the errors drop down to 1.9 kcal mol-1 for the revised revDOD-PBEP86-NL, which eliminates the same-spin correlation energy. Minnesota meta-GGA functionals with high fractions of exact exchange (M06-2X and M08-HX) also perform reasonably well, outperforming more robust and significantly less empirically parametrized functionals like SCAN0-D3.

Project description:ObjectiveTo evaluate the phenotyping performance of three major electronic health record (EHR) components: International Classification of Disease (ICD) diagnosis codes, primary notes, and specific medications.Materials and methodsWe conducted the evaluation using de-identified Vanderbilt EHR data. We preselected ten diseases: atrial fibrillation, Alzheimer's disease, breast cancer, gout, human immunodeficiency virus infection, multiple sclerosis, Parkinson's disease, rheumatoid arthritis, and types 1 and 2 diabetes mellitus. For each disease, patients were classified into seven categories based on the presence of evidence in diagnosis codes, primary notes, and specific medications. Twenty-five patients per disease category (a total number of 175 patients for each disease, 1750 patients for all ten diseases) were randomly selected for manual chart review. Review results were used to estimate the positive predictive value (PPV), sensitivity, andF-score for each EHR component alone and in combination.ResultsThe PPVs of single components were inconsistent and inadequate for accurately phenotyping (0.06-0.71). Using two or more ICD codes improved the average PPV to 0.84. We observed a more stable and higher accuracy when using at least two components (mean ± standard deviation: 0.91 ± 0.08). Primary notes offered the best sensitivity (0.77). The sensitivity of ICD codes was 0.67. Again, two or more components provided a reasonably high and stable sensitivity (0.59 ± 0.16). Overall, the best performance (Fscore: 0.70 ± 0.12) was achieved by using two or more components. Although the overall performance of using ICD codes (0.67 ± 0.14) was only slightly lower than using two or more components, its PPV (0.71 ± 0.13) is substantially worse (0.91 ± 0.08).ConclusionMultiple EHR components provide a more consistent and higher performance than a single one for the selected phenotypes. We suggest considering multiple EHR components for future phenotyping design in order to obtain an ideal result.

Project description:The purpose of this study was to assess the measurement accuracy of the most commonly used tracking technologies in professional team sports (i.e., semi-automatic multiple-camera video technology (VID), radar-based local positioning system (LPS), and global positioning system (GPS)). The position, speed, acceleration and distance measures of each technology were compared against simultaneously recorded measures of a reference system (VICON motion capture system) and quantified by means of the root mean square error RMSE. Fourteen male soccer players (age: 17.4±0.4 years, height: 178.6±4.2 cm, body mass: 70.2±6.2 kg) playing for the U19 Bundesliga team FC Augsburg participated in the study. The test battery comprised a sport-specific course, shuttle runs, and small sided games on an outdoor soccer field. The validity of fundamental spatiotemporal tracking data differed significantly between all tested technologies. In particular, LPS showed higher validity for measuring an athlete's position (23±7 cm) than both VID (56±16 cm) and GPS (96±49 cm). Considering errors of instantaneous speed measures, GPS (0.28±0.07 m?s-1) and LPS (0.25±0.06 m?s-1) achieved significantly lower error values than VID (0.41±0.08 m?s-1). Equivalent accuracy differences were found for instant acceleration values (GPS: 0.67±0.21 m?s-2, LPS: 0.68±0.14 m?s-2, VID: 0.91±0.19 m?s-2). During small-sided games, lowest deviations from reference measures have been found in the total distance category, with errors ranging from 2.2% (GPS) to 2.7% (VID) and 4.0% (LPS). All technologies had in common that the magnitude of the error increased as the speed of the tracking object increased. Especially in performance indicators that might have a high impact on practical decisions, such as distance covered with high speed, we found >40% deviations from the reference system for each of the technologies. Overall, our results revealed significant between-system differences in the validity of tracking data, implying that any comparison of results using different tracking technologies should be done with caution.

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Performance analysis of electronic structure codes on HPC systems: a case study of SIESTA.

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Performance analysis of electronic structure codes on HPC systems: a case study of SIESTA.

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