Toward highly parallel loading of unstructured meshes

This paper presents an algorithm for highly-parallel loading and processing of unstructured mesh databases in a dis tributed memory environment of large HPC clusters without collecting data into a single process. The algorithm is proved effective, having linear speedup in the large dataset limit. Demonstrated on Ansys CDB, EnSight, VTK Legacy, and XDMF databases, we show that it is possible to efficiently reconstruct meshes with 800 million nodes and 500 million elements in several seconds on thousands of processors, even from databases that were not designed to be read in parallel. The algorithm is implemented in our MESIO library that can be used as (i) an efficient parallel loader (e.g. for numerical physical solvers) or as (ii) a high performing parallel converter between mesh databases.Web of Science166art. no. 10310

HyperQueue: overcoming limitations of HPC job managers

Available at: https://sc21.supercomputing.org/presentation/?id=rpost104&sess=sess28

Feasibility analysis of using the maui scheduler for job simulation of large-scale pbs based clusters

For large-scale High Performance Computing centers with a wide range of different projects and heterogeneous infrastructures, efficiency is an important consideration. Understanding how compute jobs are scheduled is necessary for improving the job scheduling strategies in order to optimize cluster utilization and job wait times. This increases the importance of a reliable simulation capability, which in turn requires accuracy and comparability with historic workloads from the cluster. Not all job schedulers have a simulation capability, including the Portable Batch System (PBS) resource manager. Hence, PBS based centers have no direct way to simulate changes and optimizations before they are applied to the production system. We propose and discuss how to run job simulations for large-scale PBS based clusters with the Maui Scheduler. This also includes awareness of node downtimes, scheduled and unexpected. For validation purposes, we use historic workloads collected at the IT4lnnovations supercomputing center. The viability of our approach is demonstrated by measuring the accuracy of the simulation results compared to the real workloads. In addition, we discuss how the change of the simulator's time step resolution affects the accuracy as well as simulation times. We are confident that our approach is also transferable to enable job simulations for other computing centers using PBS.Web of Science132614

Detection of embedded dynamics in the Gyorgyi-Field model

The main aim of this paper is to detect embedded dynamics of the Gyorgyi-Field model of the Belousov-Zhabotinsky chemical reaction. The corresponding three-variable model given as a set of nonlinear ordinary differential equations depends on one parameter, the flow rate. As certain values of this parameter can give rise to chaos, an analysis was performed in order to identify different dynamics regimes. Dynamical properties were qualified and quantified using classical and also new techniques; namely, phase portraits, bifurcation diagrams, the Fourier spectra analysis, the 0-1 test for chaos, approximate entropy, and the maximal Lyapunov exponent. The correlation between approximate entropy and the 0-1 test for chaos was observed and described in detail. The main discovery was that the three-stage system of nested sub-intervals of flow rates showed the same pattern in the 0-1 test for chaos and approximate entropy at every level. The investigation leads to the open problem of whether the set of flow rate parameters has Cantor-like structure.Web of Science101art. no. 2103

Pipek–Mezey localization of occupied and virtual orbitals

Recent advances in orbital localization algorithms are used to minimize the Pipek–Mezey localization function for both occupied and virtual Hartree–Fock orbitals. Virtual Pipek–Mezey orbitals for large molecular systems have previously not been considered in the literature. For this work, the Pipek–Mezey (PM) localization function is implemented for both the Mulliken and a Löwdin population analysis. The results show that the standard PM localization function (using either Mulliken or Löwdin population analyses) may yield local occupied orbitals, although for some systems the occupied orbitals are only semilocal as compared to state-of-the-art localized occupied orbitals. For the virtual orbitals, a Löwdin population analysis shows improvement in locality compared to a Mulliken population analysis, but for both Mulliken and Löwdin population analyses, the virtual orbitals are seen to be considerably less local compared to state-of-the-art localized orbitals.Web of Science34171462145

Local orbitals by minimizing powers of the orbital variance

It is demonstrated that a set of local orthonormal Hartree-Fock (HF) molecular orbitals can be obtained for both the occupied and virtual orbital spaces by minimizing powers of the orbital variance using the trust-region algorithm. For a power exponent equal to one, the Boys localization function is obtained. For increasing power exponents, the penalty for delocalized orbitals is increased and smaller maximum orbital spreads are encountered. Calculations on superbenzene, C 60 , and a fragment of the titin protein show that for a power exponent equal to one, delocalized outlier orbitals may be encountered. These disappear when the exponent is larger than one. For a small penalty, the occupied orbitals are more local than the virtual ones. When the penalty is increased, the locality of the occupied and virtual orbitals becomes similar. In fact, when increasing the cardinal number for Dunning's correlation consistent basis sets, it is seen that for larger penalties, the virtual orbitals become more local than the occupied ones. We also show that the local virtual HF orbitals are significantly more local than the redundant projected atomic orbitals, which often have been used to span the virtual orbital space in local correlated wave function calculations. Our local molecular orbitals thus appear to be a good candidate for local correlation methods