Best Practices: Application Profiling at the HPCAC High Performance Center
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Free and Open Source Software for Computational Chemistry Education
Free and Open Source Software for Computational Chemistry Education Susi Lehtola∗,y and Antti J. Karttunenz yMolecular Sciences Software Institute, Blacksburg, Virginia 24061, United States zDepartment of Chemistry and Materials Science, Aalto University, Espoo, Finland E-mail: [email protected].fi Abstract Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. We point out the existence of a variety of free and open source software (FOSS) packages for computational chemistry that offer a wide range of functionality all the way from approximate semiempirical calculations with tight- binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, both for molecular and for solid-state systems. By their very definition, FOSS packages allow usage for whatever purpose by anyone, meaning they can also be used in industrial applications without limitation. Also, FOSS software has no limitations to redistribution in source or binary form, allowing their easy distribution and installation by third parties. Many FOSS scientific software packages are available as part of popular Linux distributions, and other package managers such as pip and conda. Combined with the remarkable increase in the power of personal devices—which rival that of the fastest supercomputers in the world of the 1990s—a decentralized model for teaching computational chemistry is now possible, enabling students to perform reasonable modeling on their own computing devices, in the bring your own device 1 (BYOD) scheme. In addition to the programs’ use for various applications, open access to the programs’ source code also enables comprehensive teaching strategies, as actual algorithms’ implementations can be used in teaching. -
What Is It and How We Use It
Infiniband Overview What is it and how we use it What is Infiniband • Infiniband is a contraction of "Infinite Bandwidth" o can keep bundling links so there is no theoretical limit o Target design goal is to always be faster than the PCI bus. • Infiniband should not be the bottleneck. • Credit based flow control o data is never sent if receiver can not guarantee sufficient buffering What is Infiniband • Infiniband is a switched fabric network o low latency o high throughput o failover • Superset of VIA (Virtual Interface Architecture) o Infiniband o RoCE (RDMA over Converged Ethernet) o iWarp (Internet Wide Area RDMA Protocol) What is Infiniband • Serial traffic is split into incoming and outgoing relative to any port • Currently 5 data rates o Single Data Rate (SDR), 2.5Gbps o Double Data Rate (DDR), 5 Gbps o Quadruple Data Rate (QDR), 10 Gbps o Fourteen Data Rate (FDR), 14.0625 Gbps o Enhanced Data Rate (EDR) 25.78125 Gbps • Links can be bonded together, 1x, 4x, 8x and 12x HDR - High Data Rate NDR - Next Data Rate Infiniband Road Map (Infiniband Trade Association) What is Infiniband • SDR, DDR, and QDR use 8B/10B encoding o 10 bits carry 8 bits of data o data rate is 80% of signal rate • FDR and EDR use 64B/66B encoding o 66 bits carry 64 bits of data Signal Rate Latency SDR 200ns DDR 140ns QDR 100ns Hardware 2 Hardware vendors • Mellanox o bought Voltaire • Intel o bought Qlogic Infiniband business unit Need to standardize hardware. Mellanox and Qlogic cards work in different ways. -
Open Babel Documentation Release 2.3.1
Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options ................................................. -
In Quantum Chemistry
http://www.cca-forum.org Computational Quality of Service (CQoS) in Quantum Chemistry Joseph Kenny1, Kevin Huck2, Li Li3, Lois Curfman McInnes3, Heather Netzloff4, Boyana Norris3, Meng-Shiou Wu4, Alexander Gaenko4 , and Hirotoshi Mori5 1Sandia National Laboratories, 2University of Oregon, 3Argonne National Laboratory, 4Ames Laboratory, 5Ochanomizu University, Japan This work is a collaboration among participants in the SciDAC Center for Technology for Advanced Scientific Component Software (TASCS), Performance Engineering Research Institute (PERI), Quantum Chemistry Science Application Partnership (QCSAP), and the Tuning and Analysis Utilities (TAU) group at the University of Oregon. Quantum Chemistry and the CQoS in Quantum Chemistry: Motivation and Approach Common Component Architecture (CCA) Motivation: CQoS Approach: CCA Overview: • QCSAP Challenges: How, during runtime, can we make the best choices • Overall: Develop infrastructure for dynamic component adaptivity, i.e., • The CCA Forum provides a specification and software tools for the for reliability, accuracy, and performance of interoperable quantum composing, substituting, and reconfiguring running CCA component development of high-performance components. chemistry components based on NWChem, MPQC, and GAMESS? applications in response to changing conditions – Performance, accuracy, mathematical consistency, reliability, etc. • Components = Composition – When several QC components provide the same functionality, what • Approach: Develop CQoS tools for – A component is a unit -
Application Profiling at the HPCAC High Performance Center Pak Lui 157 Applications Best Practices Published
Best Practices: Application Profiling at the HPCAC High Performance Center Pak Lui 157 Applications Best Practices Published • Abaqus • COSMO • HPCC • Nekbone • RFD tNavigator • ABySS • CP2K • HPCG • NEMO • SNAP • AcuSolve • CPMD • HYCOM • NWChem • SPECFEM3D • Amber • Dacapo • ICON • Octopus • STAR-CCM+ • AMG • Desmond • Lattice QCD • OpenAtom • STAR-CD • AMR • DL-POLY • LAMMPS • OpenFOAM • VASP • ANSYS CFX • Eclipse • LS-DYNA • OpenMX • WRF • ANSYS Fluent • FLOW-3D • miniFE • OptiStruct • ANSYS Mechanical• GADGET-2 • MILC • PAM-CRASH / VPS • BQCD • Graph500 • MSC Nastran • PARATEC • BSMBench • GROMACS • MR Bayes • Pretty Fast Analysis • CAM-SE • Himeno • MM5 • PFLOTRAN • CCSM 4.0 • HIT3D • MPQC • Quantum ESPRESSO • CESM • HOOMD-blue • NAMD • RADIOSS For more information, visit: http://www.hpcadvisorycouncil.com/best_practices.php 2 35 Applications Installation Best Practices Published • Adaptive Mesh Refinement (AMR) • ESI PAM-CRASH / VPS 2013.1 • NEMO • Amber (for GPU/CUDA) • GADGET-2 • NWChem • Amber (for CPU) • GROMACS 5.1.2 • Octopus • ANSYS Fluent 15.0.7 • GROMACS 4.5.4 • OpenFOAM • ANSYS Fluent 17.1 • GROMACS 5.0.4 (GPU/CUDA) • OpenMX • BQCD • Himeno • PyFR • CASTEP 16.1 • HOOMD Blue • Quantum ESPRESSO 4.1.2 • CESM • LAMMPS • Quantum ESPRESSO 5.1.1 • CP2K • LAMMPS-KOKKOS • Quantum ESPRESSO 5.3.0 • CPMD • LS-DYNA • WRF 3.2.1 • DL-POLY 4 • MrBayes • WRF 3.8 • ESI PAM-CRASH 2015.1 • NAMD For more information, visit: http://www.hpcadvisorycouncil.com/subgroups_hpc_works.php 3 HPC Advisory Council HPC Center HPE Apollo 6000 HPE ProLiant -
High-Performance Algorithms and Software for Large-Scale Molecular Simulation
HIGH-PERFORMANCE ALGORITHMS AND SOFTWARE FOR LARGE-SCALE MOLECULAR SIMULATION A Thesis Presented to The Academic Faculty by Xing Liu In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the School of Computational Science and Engineering Georgia Institute of Technology May 2015 Copyright ⃝c 2015 by Xing Liu HIGH-PERFORMANCE ALGORITHMS AND SOFTWARE FOR LARGE-SCALE MOLECULAR SIMULATION Approved by: Professor Edmond Chow, Professor Richard Vuduc Committee Chair School of Computational Science and School of Computational Science and Engineering Engineering Georgia Institute of Technology Georgia Institute of Technology Professor Edmond Chow, Advisor Professor C. David Sherrill School of Computational Science and School of Chemistry and Biochemistry Engineering Georgia Institute of Technology Georgia Institute of Technology Professor David A. Bader Professor Jeffrey Skolnick School of Computational Science and Center for the Study of Systems Biology Engineering Georgia Institute of Technology Georgia Institute of Technology Date Approved: 10 December 2014 To my wife, Ying Huang the woman of my life. iii ACKNOWLEDGEMENTS I would like to first extend my deepest gratitude to my advisor, Dr. Edmond Chow, for his expertise, valuable time and unwavering support throughout my PhD study. I would also like to sincerely thank Dr. David A. Bader for recruiting me into Georgia Tech and inviting me to join in this interesting research area. My appreciation is extended to my committee members, Dr. Richard Vuduc, Dr. C. David Sherrill and Dr. Jeffrey Skolnick, for their advice and helpful discussions during my research. Similarly, I want to thank all of the faculty and staff in the School of Compu- tational Science and Engineering at Georgia Tech. -
Core Software Blocks in Quantum Chemistry: Tensors and Integrals Workshop Program
Core Software Blocks in Quantum Chemistry: Tensors and Integrals Workshop Program Start: Sunday, May 7, 2017 afternoon. Resort check-in at 4:00 pm. Finish: Wednesday, May 10, noon Lectures are in Scripps, posters are in Heather. Sunday 6:00-7:00: Dinner 7:30-9:00 Opening session 7:30–7:45 Anna Krylov (USC): “MolSSI and some lessons from previous workshop, goals of the workshop” 7:45-8:00 Theresa Windus (Iowa): “Mission of the Molecular Science Consortium” 8:00-9:00 Introduction of participants: 2 min presentation, can have one slide (send in advance) 9:00-10:30 Reception and posters Monday Breakfast: 7:30-9:00 9:00-11:45 Session I: Overview of tensors projects and current developments (moderator Daniel Smith) 9:00-9:10 Daniel Smith (MolSSI): Overview of tensor projects 9:10-9:30 Evgeny Epifanovsky (Q-Chem): Overview of Libtensor 9:30-9:50 Ed Solomonik: "An Overview of Cyclops Tensor Framework" 9:50-10:10 Ed Valeev (VT): "TiledArray: A composable massively parallel block-sparse tensor framework" 10:10-10:30 Coffee break 10:30-10:50 Devin Matthews (UT Austin): "Aquarius and TBLIS: Orthogonal Axes in Multilinear Algebra" 10:50-11:10 Karol Kowalskii (PNNL, NWChem): "NWChem, NWChemEX , and new tensor algebra systems for many-body methods" 11:10-11:30 Peng Chong (VT): "Many-body toolkit in re-designed Massively Parallel Quantum Chemistry package" 11:30-11:55 Moderated discussion: "What problems are we *still* solving?” Lunch: 12:00-1:00 Free time for unstructured discussions 5:00 Posters (coffee/tea) Dinner: 6-7:00 7:15-9:00 Session II: Computer -
IBM Flex System IB6131 Infiniband Switch User's Guide
IBM Flex System IB6131 InfiniBand Switch User’s Guide ii IBM Flex System IB6131 InfiniBand Switch User’s Guide IBM Flex System IB6131 InfiniBand Switch User’s Guide Note: Before using this information and the product it supports, read the general information in , ʺAppen‐ dix B: Noticesʺ on page 33, the Safety Information and Environmental Notices and Userʹs Guide docu‐ ments on the IBM Notices for Network Devices CD, and the Warranty Information document that comes with the product. First Edition February 2012 © Copyright IBM Corporation 2012. US Government Users Restricted Rights – Use, duplication or disclosure restricted by GSA ADP Schedule Contract with IBM Corp. Contents Safety . vii Chapter1. Introduction . 1 Related documentation. 1 Notices and statements in this document . 3 Features and specifications. 3 Specifications . 4 Major components of the switch . 5 Chapter2. Installing the switch and basic setup. 7 Installing the IBM Flex system blade . 7 CMM . 7 Serial port access (Method 1) . 7 Configuration . 9 Configuration Wizard (Method 2) . 9 Cabling the switch . 15 Chapter3. LEDs and interfaces. 17 Port LEDs . 17 Switch status lights . 17 Power LED . 18 Fault LED . 18 Unit identification switch identifier LED . 18 RS‐232 interface through mini connector. 18 RJ‐45 Ethernet connector . 19 Configuring the IBM Flex System IB6131 InfiniBand switch . 19 Rerunning the Wizard. 19 Updating the switch software . 20 Chapter4. Connecting to the switch platform . 25 Starting an SSH connection to the switch (CLI) . 25 Starting a WebUI connection to the switch . 25 Managing the IBM Flex System IB6131 InfiniBand switch . 26 Chapter5. Solving problems . 27 Running POST . -
Global MV Standards English
www.visiononline.org www.emva.org www.jiia.org www.china-vision.org www.vdma.com/vision Member-supported trade associations promote the growth of the global vision and imaging industry. Standards development is key to the success of the industry and its trade groups help fund, maintain, manage and promote standards. In 2009, three leading vision associations, AIA, EMVA and JIIA began a cooperative initiative to coordinate the development of globally adopted vision standards. In 2015 they were joined by CMVU and VDMA-MV. This publication is one product of this cooperative effort. Version: April 2016 Copyright 2013, AIA, EMVA and JIIA. All rights reserved. Data within is intended as an information resource and no warranty for its use is given. Camera Link (including PoCL and PoCL-Lite), Camera Link HS, GigE Vision and USB3 Vision are the trademarks of AIA. GenICam is the trademark of EMVA. CoaXPress and IIDC2 are the trademarks of JIIA. FireWire is the trademark of Apple Inc. IEEE 1394 is the trademark of The 1394 Trade Association. USB is the trademark of USB Implementers Forum, Inc. All other names are trademarks or trade names of their respective companies. This is a comprehensive look at the various digital hardware and software interface standards used in machine vision and imaging. In the early days of machine vision, the industry adopted existing analog television standards such as CCIR or RS-170 for the interface between cameras and frame grabbers. The defining In the 1990s, digital technology became characteristics of today’s prevalent and a multitude of proprietary hardware and software interface solutions were used. -
Infiniband Trade Association Integrators' List
InfiniBand Trade Association Integrators’ List April 2019 © InfiniBand Trade Association SPACE IBTA InfiniBand Integrators' List April 2019 Manufacturer Description Model Type Speed FW SW ConnectX®-3 Pro VPI, FDR IB (56Gb/s) and 40/56GbE MLNX_OFED_LINUX 4.4- Mellanox MCX354A-FCCT HCA FDR 2.42.5000 Dual-port QSFP, PCIe3.0 x8 2.0.7.0 ConnectX®-4 VPI, EDR IB (100Gb/s) and 100GbE MLNX_OFED_LINUX 4.5- Mellanox MCX456A-ECAT HCA EDR 12.24.1000 Dual-port QSFP28, PCIe3.0 x16 1.0.1.0 ConnectX®-5 VPI, EDR IB (100Gb/s) and 100GbE MLNX_OFED_LINUX 4.5- Mellanox MCX556A-EDAT HCA EDR 16.24.1000 Dual-port QSFP28, PCIe4.0 x16 1.0.1.0 ConnectX®-6 VPI adapter card, HDR IB (200Gb/s) and 200GbE, MLNX_OFED_LINUX 4.5- Mellanox MCX653A-HCAT HCA HDR 20.25.0330 dual-port QSFP56, Socket Direct 2x PCIe3.0 x16 1.0.1.0 SwitchX®2 InfiniBand to Ethernet gateway, 36 QSFP ports, Mellanox MSX6036G-2SFS Switch FDR 9.4.5070 3.6.8010 Managed Switch Switch-IB 2 based EDR InfiniBand 1U Switch, 36 QSFP28 ports, Mellanox MSB7800-ES2F Switch EDR 15.1910.0618 3.7.1134 x86 dual core Mellanox® Quantum(TM) HDR InfiniBand Switch, 40 QSFP56 Mellanox MQM8700-HS2F Switch HDR 27.2000.1016 3.7.1942 ports, 2 Power Supplies (AC), x86 dual core Software Versions Diagnostic Software Operating System Cent OS 7.5.1804 ibutils2 MLNX OFED 4.5-1.0.1.0 Mellanox OFED MLNX OFED 4.5-1.0.1.0 Compliance Test Suite v. 1.0.52 Open MPII Open MPI 3.1.2 Benchmark Intel MPI Benchmarks Benchmarks Performed Test Plan Software Forge IBTA MOI Suite PingPong Gather Duration 2-5 Minutes PingPing Gatherv Sendrecv Scatter Conditions for Passing Testing Exchange Scatterv Link Width Link width is @ expected width - i.e. -
A Summary of ERCAP Survey of the Users of Top Chemistry Codes
A survey of codes and algorithms used in NERSC chemical science allocations Lin-Wang Wang NERSC System Architecture Team Lawrence Berkeley National Laboratory We have analyzed the codes and their usages in the NERSC allocations in chemical science category. This is done mainly based on the ERCAP NERSC allocation data. While the MPP hours are based on actually ERCAP award for each account, the time spent on each code within an account is estimated based on the user’s estimated partition (if the user provided such estimation), or based on an equal partition among the codes within an account (if the user did not provide the partition estimation). Everything is based on 2007 allocation, before the computer time of Franklin machine is allocated. Besides the ERCAP data analysis, we have also conducted a direct user survey via email for a few most heavily used codes. We have received responses from 10 users. The user survey not only provide us with the code usage for MPP hours, more importantly, it provides us with information on how the users use their codes, e.g., on which machine, on how many processors, and how long are their simulations? We have the following observations based on our analysis. (1) There are 48 accounts under chemistry category. This is only second to the material science category. The total MPP allocation for these 48 accounts is 7.7 million hours. This is about 12% of the 66.7 MPP hours annually available for the whole NERSC facility (not accounting Franklin). The allocation is very tight. The majority of the accounts are only awarded less than half of what they requested for. -
Infiniband Technology Overview
InfiniBand Technology Overview Dror Goldenberg, Mellanox Technologies SNIA Legal Notice The material contained in this tutorial is copyrighted by the SNIA. Member companies and individuals may use this material in presentations and literature under the following conditions: Any slide or slides used must be reproduced without modification The SNIA must be acknowledged as source of any material used in the body of any document containing material from these presentations. This presentation is a project of the SNIA Education Committee. InfiniBand Technology Overview 2 © 2008 Storage Networking Industry Association. All Rights Reserved. Abstract InfiniBand Technology Overview The InfiniBand architecture brings fabric consolidation to the data center. Storage networking can concurrently run with clustering, communication and management fabrics over the same infrastructure, preserving the behavior of multiple fabrics. The tutorial provides an overview of the InfiniBand architecture including discussion of High Speed – Low Latency, Channel I/O, QoS scheduling, partitioning, high availability and protocol offload. InfiniBand based storage protocols, iSER (iSCSI RDMA Protocol), NFS over RDMA and SCSI RDMA Protocol (SRP), are introduced and compared with alternative storage protocols, such as iSCSI and FCP. The tutorial further enumerates value-add features that the InfiniBand brings to clustered storage, such as atomic operations and end to end data integrity. Learning Objectives: Understand the InfiniBand architecture and feature set. Understand the benefits of InfiniBand for networked storage. Understand the standard InfiniBand storage protocols. InfiniBand Technology Overview 3 © 2008 Storage Networking Industry Association. All Rights Reserved. Agenda Motivation and General Overview Protocol Stack Layers Storage Protocols over InfiniBand Benefits InfiniBand Technology Overview 4 © 2008 Storage Networking Industry Association.