addusers

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Adding Users to Control $ sudo useradd -m -d /home/users/ -p -s /bin/bash $ sudo nano /etc/group #Add newuser to appropriate group(s) (usually scratch, wsi) $ sudo nano /etc/ssh/sshd_config #Add newuser to AllowUsers line for ssh access $ sudo service ssh restart #If given ssh access

afterschool

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

After School Programs General resources: Make Time Eldorado Here you will find resources for Woodruff's MakeTime classes, run on Saturday mornings. Circuits 1

am

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Additive Manufacturing Our interest in 3D printing is initially for the production of plasma diagnostics at much reduced cost. However, the technology is maturing, and so the application of the techniques to a wider range of subsystems that are relevant to fusion energy development could potentially impact costs for fusion energy itself.

arpa-e2017

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Primary findings and recommendations of the 2017 ARPA-E costing

arpa-e2019

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

For 2019, we are going to be doing some things differently

aws

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

AWS for the 2016 Bootcamp Throughout this course we'll be connecting to some computers in the cloud. Here's how to connect to them and login. First, you will need to download a certificate on to your lab machine. Ask James for the key. Save this somewhere you can find it again - for example, to the Downloads directory or to the Desktop.

background

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Background

bout

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

BOUT ++

coding

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Coding Best Practices and Resources Version Control Git, SVN Functions Comments Compiling Makefiles

compilenersc

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Compiling Nimrod at NERSC Tips for getting nimrod to compile at nersc. Compile on your login node, test and run on compute nodes (see: Running Jobs at NERSC) Modules Software that Nimrod needs can easily be used by loading modules. Typically needed: acml, parmetis, superlu_dist

corsica

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

CORSICA Welcome to the CORSICA wiki. This wiki will be populated with information about the CORSICA code suite. The purpose is to bring together CORSICA resources that cannot currently be found in a central location. ---------- What CORSICA is The LLNL CORSICA code provides a comprehensive predictive capability for axisymmetric toroidal plasmas. It has been applied successfully to many tokamaks, to the SSPX spheromak, and to the reversed-field pinches MST and RFX. At the heart of CORSICA is …

dropbox

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Dropbox Troubleshooting Restoring Deleted Files Sometimes files might get accidentally deleted from a personal or shared Dropbox folder. You can restore any file for 30 days (as of November 2015). * Go to the Dropbox Website and login * Click on 'Deleted Files' on the left, or the Trashcan icon near the top

fed

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Fusion Engineering and Design

fusion_costing_code

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

During the last 10 years, WSI has developed a costing model in collaboration with Decysive Systems and most recently with Bechtel for the costing of most of the major fusion subsystems. We have worked under contract with ARPA-E to produce the cost analysis for 4 of the ALPHA program fusion concepts.

hifi_install

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

HiFi Installation Notes Prequisite Libraries Use this guide: [HiFi installation guide] Use the same mpi compilers for PETsc, HDF5, and HiFi (netCDF can use serial compilers). Libraries on Control * PETsc 3.4.4 * HDF5 1.8.12 * netCDF 4.1.1 Compiling at NERSC module swap PrgEnv-intel/5.2.82 PrgEnv-gnu module load cray-hdf5-parallel cray-netcdf-hdf5parallel cray-petsc export PHYSICS="lnxmhd4"

hifi

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

HiFi The distinguishing capabilities of the HiFi code include adaptive spectral element spatial representation with flexible 3D geometry, highly parallelizable implicit time advance, and general flux-source form of the partial differential equations and boundary conditions that can be implemented in its framework. Early algorithm development and extensive verification studies of the two-dimensional version of the code have been previously described

high_performance_computing_and_best_practices

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

High Performance Computing and Best Practices Background HPC Vs. Single Processors Serial Computing - Instructions run one at a time: Parallel Computing - Problem is split into multiple problems, each problem can be run concurrently (at the same time) on multiple processors

mcnp6

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Main links for useful things relating to MCNP: User manuals: Here's a full text: Launch with "./mcnp6 N=SAMPLE" Or "./mcnp6 IP N=SAMPLE" for plot window

mhdcodes

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

MHD Our main tools for MHD simulations are NIMROD, HiFi and BOUT++. Equilibrium Several tools are in use at WSI for exploring equilibria in magnetic fusion systems. Primarily we use CORSICA for most of the major systems under study, however sometimes it is easier to set up an initial condition for MHD simulations with NIMEQ. For the development of new magnetic configurations (say we are designing a tokamak from the ground up), then we use both FIESTA and CORSICA at the same time, in part to …

nfs

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Scratch2 Troubleshooting Sometimes scratch2 becomes inacessible. This guide should help get it up and running again. Login to control If /export/users/scratch2 is empty: Applications > System Tools > Terminal $ sudo mount --bind /home/users/scratch2 /export/users/scratch2

nimrod_2022

Anonymous (anonymous@undisclosed.example.com) — 2022-09-14T08:29:32+00:00

NIMROD 2022 The method for getting NIMROD running at NERSC has changed slightly as the default version of some modules on NERSC have changed. This wiki will give instructions to help set up the most recent version of nimdevel and include some tips to help compile older versions of NIMROD. This page will run through the steps necessary to compile the code at NERSC.

nimrod

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

NIMROD Spectral finite element discretization in two dimensions, Finite Fourier series in the third dimension, Semi-implicit and implicit temporal discretization for the range of temporal scales found in fusion experiments, Simulation particles for kinetic effects from a minority species of energetic ions, and Integro-differential methods for kinetic effects from free-streaming.

petsc

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

PETSc Documentation The Portable, Extensible Toolkit for Scientific Compu- tation (PETSc) is a suite of data structures and routines that provide the building blocks for the implemen- tation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication.

runnersc

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Running Jobs at NERSC Logging on to NERSC $ ssh simonw@cori.nersc.gov Use the home directory to store data, but don't run codes here as space is limited. See Compiling Codes at NERSC Use the scratch directory to compile and run codes, but don't use scratch as longterm storage.

scbc_daily_schedule

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Monday * Introductions * What is Scientific Computing? * Fundamentals (I still don't care for this here. Perhaps we could work it in with some relevance to the LCM machines? -K) * Parallelism * Shared memory model * Historical context

scbc_syllabus

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Syllabus - 2016 Scientific Computing Bootcamp Woodruff Scientific, Inc., 4000 Aurora Ave. N, Seattle, WA 98103 ---------- SCBC1 – Grand Challenges in Computational Plasma Physics * Computation as third pillar of science * Multi-physics and multi-scales for nuclear fusion simulations

scbc_unplaced

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

* numerical (in)stability just the first example might be perfect for SCBC2 or SCBC6: might be an interesting choice, depending on how the FORTRAN went: I see the Dendy text mentions that things should be numerically stable, p. 180 --- Just an interesting resource overall:

scbc1

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Grand Challenges in Computational Plasma Physics Energy and matter, which are the basic components of our physical world, are manifested in various ways under different physical conditions and are affected by various processes. The fusion of light nuclides forms the basis of energy release in the universe, which can potentially be harnessed and used as a clean and sustainable supply of energy. One excellent example of an international program for the development of fusion as an economic energy…

scbc2

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Some Computer Science Considerations In this session we explore what a model is, and how a simulation is different. We draw on our experience with simulating plasmas but also on the experience of general simulations. Useful references also include Oberkampf's Verification and Validation in Scientific Computing (e.g. Chapter 2).

scbc3

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Introduction to Plasma R&D Codes This session is intended as an introduction to the codes that we use on a day-to-day basis to service existing or new contracts. The aim is to show similarities and differences of the codes. We define the differences between commercial (or industry hardened) codes and those codes that are being developed by research programs to address new challenges in the science (e.g. tough physics) or to take advantages of new available resources (e.g. new faster computers)…

scbc4

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

High Performance Computing and Best Practices The terms high-performance computing and supercomputing are sometimes used interchangeably, however, high-performance computing (HPC) is the use of supercomputers and parallel processing techniques for numerical solution of scientific problems. HPC Best Practices focuses on developing best procedures for managing HPC resources so that the resources are used as efficiently as possible.

scbc5

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Post-Processing There are now a vast array of tools are available for examining data from simulations. More recently due to the development of predictive capabilities for codes, the requirements for post-processing are evolving to derive parameters that are akin to experimental measurements for direct comparison, such are called 'synthetic diagnostics'. We have developed a range of these under contract to ITER, and are described below.

scbc6

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Verification and Validation in Scientific Computing The value of any scientific model is in it's ability to predict. The accuracy of the prediction of a scientific model developed for numerical solution has until recently been of low priority in plasma physics mainly due to the maturity of the computational model (only recently have plasma physics models reached a sufficient level of development that we can have confidence that they entail the necessary physics set). Other scientific disciplin…

scbc7

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Intro to Mesh Generation and Finite Element Methods The finite element method is a technique for solving partial differential equations by first discretizing these equations in their space dimensions. The discretization is carried out locally over small regions of simple but arbitrary shape (

scbc8

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Contemporary Issues in Plasma Physics and Nuclear Fusion Components and Modeling Support for Validation Platforms for Fusion Science The FES Experimental Plasma Research program has the long term performance measure of demonstrating enhanced fundamental understanding of magnetic confinement and improving the basis for future burning plasma experiments. This can be accomplished through investigations and validations of the linkage between prediction and measurement for scientific leverage in te…

scbc9

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Future of Scientific Computing What will the future hold? Generally in plasma physics the driving force for larger and larger computations is the need to perform multiphysics simulations, coupling between many different models from the atomic scale through to full system descriptions. The methodology is evolving too - moving towards more of a validation activity than algorithm and physics description phase: the future entails more validation analysis than previously. Finally, the technology …

scbc10

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

A Beginning History of Scientific Computing The history of scientific computing arguably began in the 20th Century, when computers were designed and built specifically to solve scientific problems. The history can be traced through the development of the technology, computing algorithms, operating systems and computer languages. In terms of the technology, valve computing was replaced by transistors, and silicon chip transistor density has been following Moore's law ever since

sidebar

Anonymous (anonymous@undisclosed.example.com) — 2022-09-14T04:54:26+00:00

Main Page * Fusion costing code * Background to this costing analysis * Fusion Engineering and Design 2015 * ARPA-E 2017 Costing * ARPA-E 2019 Costing * MHD CODES * CORSICA * NIMROD * PETSc Docs * Running at NERSC * Compiling Nimrod at NERSC * NIMROD 2022 * HiFi * Installation * PETSc Docs * BOUT++ * Coding Best Practices * Adding Users to Control * Restoring Deleted Dropbox Files * Scratch2 …

slurm_tutorial

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Using SLURM What is SLURM? SLURM is an open-source resource manager designed for Linux clusters of all sizes. It provides three key functions. First it allocates exclusive and/or non-exclusive access to resources (computer nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (typically a parallel job) on a set of allocated nodes. Finally, it arbitrates contention for resources by managing a queue of pen…

start

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

WSI Wiki Here you'll find all of the codes and tutorials for our regular Scientific Computing Bootcamp. Please register for the training here, or take a look at some of our past modeling/simulation work here. Sign up to our newsletter to keep up to speed! Since 2005 we have designed, built and tested custom magnetic coils, pulsed power systems and

torque_tutorial

Anonymous (anonymous@undisclosed.example.com) — 2022-07-21T06:59:32+00:00

Overview Jobs on Hopper execute on one or more “compute” nodes dedicated to that job. These nodes are distinct from the shared “login” nodes that host interactive sessions. Typically, users write the batch script with a text editor and submit it to the system using the

WSI Code Wiki

addusers

afterschool

am

arpa-e2017

arpa-e2019

aws

background

bout

coding

compilenersc

corsica

dropbox

fed

fusion_costing_code

hifi_install

hifi

high_performance_computing_and_best_practices

mcnp6

mhdcodes

nfs

nimrod_2022

nimrod

petsc

runnersc

scbc_daily_schedule

scbc_syllabus

scbc_unplaced

scbc1

scbc2

scbc3

scbc4

scbc5

scbc6

scbc7

scbc8

scbc9

scbc10

sidebar

slurm_tutorial

start

torque_tutorial