Visualization Infrastructure and Services at the MPCDF

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Visualization Infrastructure and Services at the MPCDF

Markus Rampp & Klaus Reuter

Max Planck Computing and Data Facility (MPCDF)

([email protected])

Interdisciplinary Cluster Workshop on Visualization Garching, Nov 4, 2015

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Outline

Topics

.

overview remote visualization services

· hardware & software infrastructure

· project support

.

challenges and outlook

MPCDF Visualization Team

.

people involved (part-time, main focus is HPC)

Elena Erastova

(visualization projects)

Klaus Reuter

(software and hardware coordination, consulting, projects, training)

Markus Rampp

(consulting, projects, training)

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Visualization infrastructure for the Max-Planck-Society

MPCDF visualization services:

.

provide central software and hardware infrastructure for remote visualization

.

target: interactive data exploration & analysis, presentation

.

support for adaptation and instrumentation of simulation codes

.

guidance for selection, adoption and usage of analysis & visualization software

.

dedicated support for individual (particularly demanding) visualization projects

Main conceptual challenges:

.

broad range of disciplines in MPG: Plasmaphysics, Astrophysics, . . . , comp. Biology

y

many different scientific contexts

y

variety of simulation codes: ”home-grown”, commercial, open-source, third-party, . . .

y

non-standardized, heterogeneous data structures and formats

y

”legacy” analysis pipelines, . . .

.

massive datasets from HPC simulations:

(

massive:

amount of raw data, memory requirements, complexity)

◦

multidimensional (3D + time), multi-variate data

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Visualization infrastructure for the Max-Planck-Society

Status

.

consulting & dedicated project support since 2008

.

MPG visualization cluster operational since Sep. 2010

.

open to all MPG scientists and collaboration partners

.

many projects supported (some highlights by K. Reuter)

.

broad userbase (beyond Garching campus)

Rationale for centralized visualization in the MPG:

.

a

necessity for a HPC centre

rather than an optional service

· huge amounts of output data produced by HPC simulations

· transfer of raw data for local analysis & visualization no more possible

· even dumping the RAM is becoming prohibitive due to I/O constraints

y

in-situ

visualization (not covered here)

· visualization requires HPC-like resources (specialized hardware, housing, . . . )

· requires substantial expertise on methods, software, . . .

_y

sustainability

.

Technological prerequisites

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Central visualization infrastructure: technical prerequisites

traditional ”X over ssh” (e.g. ssh -X)

. 3D data are transfered to the client

. fails to deliver interactive frame rates

. uses X-server/graphics card of the client

y not suited for 3D applications

server-side rendering

. only (compressed) image stream is transferred

. delivers interactive frame rates with moderate WAN bandwidth

. uses X-server/graphics card(s) of the server

. generic solution (OpenGL)

. mature software solutions/products:

· VirtualGL/TurboVNC (Open Source, ex SUN)

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Remote-visualization cluster

Focus:

.

enable our (geographically dispersed) scientific users to perform complex visualization tasks

with-out special technical prerequisites (software, hardware)

y

remote

visualization

Hardware overview (HP cluster)

. 5 ”standard” visualization nodes each equipped with: · 2 Intel quadcore CPUs: 8 cores, 144 GB RAM · 2 NVidia FX 5800 graphics cards

. 1 ”high-end” visualization node:

· 4 Intel hexacore CPUs, 24 cores, 256 GB RAM · 2 NVidia FX 5800 graphics cards

. 1 login node: viz00.rzg.mpg.de

. dedicated disk system (GPFS, ' 30 TB)

. GPFS filesystem /ptmp of HPC system Hydra mounted

. 2 graphics workplaces (active stereo) in MPCDF offices

Software stack

. SLES 11 (MPCDF standard cluster setup), VizStack middleware (GPUs, X-servers, . . . )

. web-based reservation system (HP, MPCDF)

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User interface

Remote desktop (via TurboVNC)

. a standard desktop in a separate window

. application agnostic

. desktop icons for main applications

. preconfigured according to session properties (number of GPUs, CPUs)

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Software for Visualization

Software for interactive data visualization and analysis

. VisIt: main workhorse for 3D analysis

. Paraview: main workhorse for 3D analysis

. VAPOR: large-scale data (requires preprocessing)

. Voreen: volume rendering

Tools and libraries

. GNU R, IDL, MATLAB, gnuplot, . . .

. VTK, HDF5, SILO, . . .

. mencoder: scripts for x264 encoding of movies

Special-purpose software

. Splotch: a (non-interactive), parallel ray tracer for SPH data.

. VMD (Visual Molecular Dynamics): a molecular graphics software.

. POV-Ray: a freeware multi-platform ray-tracing package.

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Application support

Documentation

.

http://www.rzg.mpg.de/services/visualisation/

Training

.

courses (

http://www.rzg.mpg.de/services/visualisation/scientificdata/presentations

)

· K. Reuter: RZG-Services zur Visualisierung wissenschaftlicher Datens¨atze, DV-Treffen der Max-Planck-Institute, G¨ottingen, Sep 15, 2010

· K. Reuter: Scientific Visualisation Services at RZG, Seventh GOTiT High Level Course, Garching, Oct 19, 2010 · M. Rampp: Introduction to VisIt, LRZ course on ”Visualisation of Large Data Sets on Supercomputers”, 2010 –

2011

· M. Rampp: Introduction to VisIT, 11th Summer school on scientific visualization, CINECA Bologna/Italy, Jun 13, 2012

· M. Rampp: Visualization of HPC simulation data: overview and tutorial, ISSS-12, Prague (2015)

· overview talks at Max-Planck-Institutes: MPA, Garching (2009), FHI, Berlin (2011), MPI f. Biophysics, Frankfurt (2014), . . .

Project support

.

dedicated support for visualization projects at different levels:

· from basic ”first level” support to comprehensive visualization and analysis tasks

· requires (considerable) insight to scientific domain

· several completed and ongoing projects, in close collab. with the users/scientists:

http://www.rzg.mpg.de/services/visualisation/scientificdata/projects

.

contact:

[email protected]

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MPG/MPCDF reference applications

Projects with MPCDF support (in close collab. with research groups)

.

application domains:

· Plasmaphysics

: MHD turbulence simulations for nuclear fusion research (IPP)

· Stellar astrophysics

: Supernova simulations, NS mergers (MPA)

· Cosmology

: Structure and star formation (MPE)

· Molecular dynamics

: Materials research for plasma-wall-interaction (IPP), DFT (FHI)

· CFD

: DNS simulations of turbulent Taylor-Couette flows (MPI-DS)

.

data structures/grids:

· regular: cartesian, polar (2D, 3D), block-structured (”Yin-Yan”)

· irregular: (mapped) point clouds

.

data sizes, dimensions:

· up to

2048

3

(cartesian),

1000

×

180 ×

360 (polar),

2048

×

769 ×

1153

(cylindrical)

· up to

'

10

6

(particles in 3D),

'

10

7

(nodes in 3D unstructured mesh)

· all: multi-variable (scalar, vector), time-dependent

Challenges & outlook

Technological

.

hitting the limits of general-purpose software tools (VisIT, Paraview): interactivity, memory

demands:

O

(1000

3

)

data

y

use GPUs in HPC system, e.g. MPG Hydra with Nvidia K20x GPUs

y

enables

in-situ visualization

: a big buzz or something interesting to watch ?

◦ basic technique: implement library calls in simulation code (APIs for C, FORTRAN)

◦ mediates callbacks to visualization tool

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Challenges & outlook

Organizational

.

dedicated project support is of key importance (but not scalable)

.

beyond

scientific

data analysis and insights

· ever increasing standards and expectations for public understanding of science

· are we the right people to ”direct” professional animations (TV documentaries) ?

· do we need ”real” scientific data for this at all ?

· credits ?

_y

Max-Planck Visualization Award

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