From Proposal to Production: Lessons Learned Developing the Computational Chemistry Grid Cyberinfrastructure

Dooley, Rion; Milfeld, Kent; Guiang, Chona S.; Pamidighantam, Sudhakar; Allen, Gabrielle

doi:10.1007/s10723-006-9043-7

Cited by 174 publications

(105 citation statements)

References 10 publications

Supporting

Mentioning

103

Contrasting

Order By: Relevance

“…All the computations of mentioned complex were performed using the Gaussian 09 program package [25] by means of the resources provided by GridChem Science Gateway [26].…”

Section: Fully Optimizationsmentioning

confidence: 99%

See 1 more Smart Citation

Synthesis, quantum chemical computations and x-ray crystallographic studies of a new complex based of manganese (+II)

Benyza¹,

Messai

Hamdaoui

et al. 2017

J. Fundam and Appl Sci.

View full text Add to dashboard Cite

show abstract

“…All the computations of mentioned complex were performed using the Gaussian 09 program package [25] by means of the resources provided by GridChem Science Gateway [26].…”

Section: Fully Optimizationsmentioning

confidence: 99%

“…Computational calculations were performed by using GaussView 5.0.8 [25] and Gaussian 09 AM64L-G09RevD.01 package program [26]. B3LYP functionnal was selected as computational method and LANL2DZ, 6-31G(d,p) levels where selected for the whole atoms in the molecule.…”

Section: Instrumentationmentioning

confidence: 99%

Synthesis, quantum chemical computations and x-ray crystallographic studies of a new complex based of manganese (+II)

Benyza¹,

Messai

Hamdaoui

et al. 2017

J. Fundam and Appl Sci.

View full text Add to dashboard Cite

show abstract

“…GridChem (http: www.gridchem.org) is acknowledged for computational resources and services used to perform the DFT studies. [23,24] These resources used the Extreme Science and Engineering Discovery Environment (XSEDE) which is supported by the National Science Foundation grant number OCI-1053575. The computational work was in part performed at the University of Wisconsin-Madison using Phoenix cluster supported by the National Science Foundation grant CHE-0840494.…”

Section: Acknowledgementsmentioning

confidence: 99%

Collision induced dissociations of non‐derivatized and trimethylsilyl‐derivatized estradiols: similarities in fragmentation patterns

Jeilani

Harruna

et al. 2015

J. Mass Spectrom.

View full text Add to dashboard Cite

Fragmentation mechanisms of estradiol and trimethylsilyl (TMS)-derivatized estradiol were studied by triple quadrupole tandem mass spectrometry (MSMS) and density functional theory (DFT) at B3LYP/6-311G(d,p) level. Collision induced dissociations (CID) of estradiol give product ions that are associated with the cleavage of B, C and D rings. Characteristic fragments from the cleavage of the aromatic ring A were not identified, and this was confirmed with both labeled estradiol and trimethylsilyl (TMS)-derivatized estradiol. The mechanisms are based on charge-site directed, radical-directed and charge remote fragmentations that are consistent with previous studies of steroids. CID spectra show ion pairs at m/z: 145/146, 157/158, 185/186, 211/213 and 225/226 with significant intensities, suggesting that these pairs are not from isotopic contributions. The mechanisms show similarities with some minor differences in the fragmentation patterns between the non-derivatized and the TMS-derivatized estradiol.

show abstract

“…GridChem [9,10], is a virtual organization that provides access to high performance computing resources for computational chemistry with distributed support and services, intuitive interfaces and measurable quality of service. GridChem is a Science Gateway; it allows users access to resources for their work while hiding the details of both the resources and the access mechanisms from them, allowing them to focus on the science.…”

Section: Iii4 Gridchemmentioning

confidence: 99%

Science on the TeraGrid

Katz¹,

Callaghan²,

Harkness³

et al. 2010

CMST

Self Cite

View full text Add to dashboard Cite

Abstract:The TeraGrid is an advanced, integrated, nationally-distributed, open, user-driven, US cyberinfrastructure that enables and supports leading edge scientific discovery and promotes science and technology education. It comprises supercomputing resources, storage systems, visualization resources, data collections, software, and science gateways, integrated by software systems and high bandwidth networks, coordinated through common policies and operations, and supported by technology experts. This paper discusses the TeraGrid itself, examples of the science that is occurring on the TeraGrid today, and applications that are being developed to perform science in the future. Key words: computational science applications, high performance computing, grid computing, production grid infrastructure *Steven Manos was a Research Fellow at University College London while this work was conducted CMST SI(1) 81-97 (2010 82effort to build and deploy the world's largest, fastest, most comprehensive, distributed infrastructure for general scientific research. The initial TeraGrid was homogeneous and very "griddy", with users foreseen to be running on multiple systems, both because their codes could run "anywhere", and because in some cases, multiple systems would be needed to support the large runs that were desired. The software that made up the TeraGrid was a set of identical packages on all systems. The TeraGrid has since expanded in capability and number of resource providers. This introduced heterogeneity and thus added complexity to the grid ideals of the initial DTF, as the common software no longer could be completely identical. This led to the concept of common interfaces, with potentially different software underneath the interfaces. Additionally, the users of national center supercomputers were merged into TeraGrid, which led to TeraGrid increasing its focus on supporting these users and their traditional parallel/batch usage modes. The TeraGrid is freely available for US researchers, with allocations determined by a peer-review mechanism. The TeraGrid resources are generally at least 50% dedicated to TeraGrid. Roughly similar to the TeraGrid in terms of a continental-scale set of resources with a focus on HPC users is DEISA/PRACE in Europe, which is a set of national resources with some fractions provided to a set of European users, again determined through a review process. An alternative type of infrastructure is one that is more focused on high throughput computing (HTC), initially in high-energy physics, but increasingly in other domains as well. Filling this role in the US is Open Science Grid (OSG), and in Europe, Enabling Grids for E-sciencE (EGEE), which has recently been transformed into the European Grid Infrastructure (EGI). This paper discusses the TeraGrid itself (Section II), examples of the interesting current uses of the TeraGrid cyberinfrastructure for science (Section III), and examples of applications that are being developed to perform science on the TeraGrid in the future (Section IV) 1 . ...

show abstract

From Proposal to Production: Lessons Learned Developing the Computational Chemistry Grid Cyberinfrastructure

Cited by 174 publications

References 10 publications

Synthesis, quantum chemical computations and x-ray crystallographic studies of a new complex based of manganese (+II)

Synthesis, quantum chemical computations and x-ray crystallographic studies of a new complex based of manganese (+II)

Collision induced dissociations of non‐derivatized and trimethylsilyl‐derivatized estradiols: similarities in fragmentation patterns

Science on the TeraGrid

Contact Info

Product

Resources

About