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How to setup MateriApps LIVE!
MateriApps LIVE! Development Team
2021/05/18 [for version 3.3]
MateriApps — a Portal Site for Materials Science Simulation
• Aiming at the community formation through the promotion of application
MateriApps, 2013-2021. All rights reserved.
2
• Introducing 282 materials science
applications and tools (as of 2021.5)

• Finding applications

• search tags: features, targets,
calculation methods/algorithms

• Information of applications

• brief introduction, link to o
ffi
cial
pages, information installation,
usage, etc

• Information of hands-on sessions,
software update, etc

• Glossary of keywords, Concierge,
Reviews

• 22,000+ page views / month, 6,500+
unique visitors / month (FY2020)
since May 2013
DFT
AkaiKKR☆
OpenMX☆
xTAPP☆
ABINIT☆
...
Quantum
Chemistry
FMO☆
SMASH☆
GAMESS☆
DC☆
...
Molecular
Dynamics
MODYLAS☆
Gromacs☆
ERmod☆
MDACP...
Lattice
Models
ALPS☆
DSQSS
BLOCK
DMRG++
Continuum Simulation
ANSYS Multiphysics
Octa ...
Data Analysis
CLUPAN☆
phonopy☆
Visualization
fu☆
TAPIOCA☆
☆ included in MateriApps LIVE!
• Introducing 273 materials science applications and tools
Applications on MateriApps
MateriApps, 2013-2021. All rights reserved.
3
(80) (38) (31) (58)
(12) (59) (37)
Database (12), Integrated Environment (4)


Machine Learning (20), Quantum Computing (6)
Current status in computational materials science
• From developers’ viewpoint

• New algorithms should be implemented and used. Or, it will
be forgotten ever existed.

• It cost much to write and update documents

• Development of software itself is hardly considered as
scienti
fi
c achievements

• From users’ viewpoint

• What kind of applications? Who develop them?
Which application should I use for my problem?

• Manual and documentation are not well prepared.

• How to evaluate the accuracy of results?

• Goal of MateriApps project

• Forming of community in the
fi
eld of computational materials
science through the promotion of open source software
MateriApps, 2013-2021. All rights reserved.
4
What MateriApps will provide
• To
fi
nd and learn application software

• catalog of application/tool on MateriApps web

• To start using application software

• MateriApps LIVE!

• To active use application software

• pre-installation to Fugaku, supercomputers, etc: MateriApps Installer

• Infrastructure for easily starting materials science simulations for theoreticians,
experimentalists, researchers in companies, students, and more…
MateriApps, 2013-2021. All rights reserved.
5
Flagship system (K, post-K,...)
HPC infrastructure supercomputers in Japan
Supercomputers for shared-use in research fields
Cloud computing, on-premises PC clusters
Personal workstations, PCs
Installer
Hands-on Cloud
Fugaku
• Live Linux bootable on virtual machine

• run on Windows, Macintosh, etc

• just boot and get ready for materials science
simulations without installation

• Version 3.3 was released in May 2021

• Pre-installed applications and tools

• abinit, AkaiKKR, ALAMODE, ALPS, CONQUEST,

Feram, DCore, DSQSS, HΦ, LAMMPS, mVMC,
OCTA, OpenMX, Quantum ESPRESSO, PHYSBO,
SMASH, TeNeS, xTAPP, etc

• OVITO, ParaView, Tapioca, VESTA, VMD, XCrysDen…

• GUI installer for CASINO, GAMESS, and VMD

• Available from MateriApps LIVE! webpage

• c.a. 12,000+ copies distributed since July, 2013
MateriApps, 2013-2021. All rights reserved.
6
MateriApps LIVE! is useful for ...
• Hands-on sessions using MateriApps LIVE!

• MateriApps LIVE! Tutorials

• HΦ, xTAPP, ALPS, DCore, mVMC, ALAMODE, DDMRG, DSQSS, SALMON,
CASINO, TeNeS, etc.

• Practices in lectures

• Computational Physics

• Computer Experiments (UNIX + C, LaTeX, VCS)

• Used by experimentalists, researchers in private companies

• Used by researchers in the
fi
eld of computer science

• Easy setup (c.a. 15min) without no troubles

• Useful for operation check, trouble shooting, user support
MateriApps, 2013-2021. All rights reserved.
7
Materials Science Simulation by MateriApps LIVE!
• Introduction / Setup

• First-principles band calculation (OpenMX / Quantum ESPRESSO / xTAPP)

• Simulation of solution by molecular dynamics (LAMMPS / Gromacs)

• Lattice model simulation (ALPS / HΦ / mVMC)

• Quantum chemistry calculation (in preparation)

• Hands-on materials are available at https://github.com/cmsi/MateriAppsLive/wiki/
MaLiveTutorial (currently only in Japanese)
MateriApps, 2013-2021. All rights reserved.
8
Wanna larger-scale simulations?
• For Debian/Ubuntu Linux workstations

• Debian package for MateriApps LIVE! can be used

• https://github.com/cmsi/MateriAppsLive/wiki/UsingMateriAppsInDebian

• (Can also be installed on Google Colab)

• For PC clusters, clouds, supercomputers at ISSP and IT centers, Fugaku, etc

• MateriApps Installer https://ma.issp.u-tokyo.ac.jp/app/268

• Renewed in ISSP Project for Advancement of Software Usability in Materials
Science, FY2020
MateriApps, 2013-2021. All rights reserved.
9
Flagship system (K, post-K,...)
HPC infrastructure supercomputers in Japan
Supercomputers for shared-use in research fields
Cloud computing, on-premises PC clusters
Personal workstations, PCs
Installer
Hands-on Cloud
• MateriApps LIVE! USB

• setup.pdf, setup-en.pdf

this document

• README.html, README-en.html

(copy from https://github.com/cmsi/MateriAppsLive/wiki/MateriAppsLive-ova)

• VirtualBox Installer: VirtualBox-*-OSX.dmg, VirtualBox-*-Win.exe

(available at https://www.virtualbox.org/wiki/Downloads)

• MateriApps LIVE! VitualBox Disk Image: MateriAppsLive-*-amd64.ova

(available at http://sourceforge.net/projects/materiappslive/
fi
les/)
What are included in USB Stick?
MateriApps, 2013-2021. All rights reserved.
10
Let's get started
✓ Copy
fi
les in USB stick memory to hard disk

• copy all the
fi
les to your PC, e.g. to desktop

✓ Install VirtualBox by double-clicking the installer

• For Windows: VirutalBox-*-Win.exe

• For Macintosh: VirtualBox-*-OSX.dmg

✓ Import MateriApps LIVE!

• double-click MateriAppsLive-*.ova

• VirtualBox will start automatically and import window will open. Then press
“import” button

• VirtualBox Manager window will appear in two or three minutes

• Host (host OS): operating system (Windows, Mac OS X, etc) on which VirtualBox is
running

• Virtual machine (guest OS): operating system (= MateriApps LIVE!) running on
VirtualBox
MateriApps, 2013-2021. All rights reserved.
11
Boot in VirtualBox
1. Choose “MateriAppsLive…”

2. Press “Start” button.

3. Wait until login window will
appear.
MateriApps, 2013-2021. All rights reserved.
12
• Login by using

• User name (login): user

• Password: live

• Desktop (right) will appear

• start menu

• How to open a terminal window

start menu “System Tools” “LXTerminal”

• How to shutdown the virtual machine

start menu “Logout” “Shutdown”
Login to MateriApps LIVE!
MateriApps, 2013-2021. All rights reserved.
13
CD-ROM button
Additional settings (1/2)
✓ Using Japanese keyboard

• start menu “System Tools” “Switch to Japanese Keyboard Layout” 

• check if “@” key works correctly

✓ Changing resolution and scale of the virtual machine window

• Resolution (number of pixels): “800 x 600” by default

• Scale (pixel density): “200%” by default

• The resolution and scale can be changed from the “View” menu “Virtual
screen 1” of the host OS

• When using visualization software such as VESTA, OVITO, ParaView, set the
resolution to “1024 x 768” or higher

• If characters are small and di
ffi
cult to see, increase the scale
MateriApps, 2013-2021. All rights reserved.
14
Additional settings (2/2)
✓ File sharing between host OS and virtual machine

• shutdown the virtual machine, if it is running

• choose MateriAppsLive-* in VirtualBox Manager window, then “Settings”

• open “Shared Folders” tab and click “+” on the right

• click “v” on the right of “Folder Path”, choose “Other…”, and select the folder
to be shared

• check “Auto-mount” box and press “OK”. Then press “OK” again

• the folder speci
fi
ed above can be accessed as /media/sf_... after restarting
the virtual machine

✓ Browsing contents of ISO image
fi
le (*.iso) from the virtual machine

• click CD-ROM icon at the bottom of the virtual machine window frame, select
“Choose disk image ...", and select the ISO image
fi
le

• contents of ISO image
fi
le are accessible via /media/cdrom0
MateriApps, 2013-2021. All rights reserved.
15
Tips
✓ Copy & Paste: How to paste strings copied from a PDF
fi
le on host OS?

• right click on terminal window “Paste”

• or press “V” with “shift” and “control” keys

• right click “Copy”, or “shift + control + C” to copy a string

✓ Completion/history/sequential search of command lines and
fi
lenames

• Hit the tab key in the terminal to complete the command name or the
fi
lename

• Hit the “↑” key in the terminal to trace back the history of commands

• Execute the “history” command in the terminal to display the list of
commands executed

• Hit “Ctrl + r” in the terminal to search the commands executed so far (reverse
incremental search)
MateriApps, 2013-2021. All rights reserved.
16
MateriApps planning & production
• Administration:

• Center for Computational Materials Science, Institute for Solid State Physics, University
of Tokyo (ISSP-CCMS)

• MateriApps Development Team

• Kota Ido (ISSP), Shusuke Kasamatsu (Dept. of Phys., Yamagata Univ.),
Takeo Kato (ISSP), Naoki Kawashima (ISSP), Hikaru Kouta (ISSP),
Synge Todo (Dept. of Phys., Univ. of Tokyo/ISSP), Masahito Fukuda (ISSP),
Kanako Yoshizawa (RIST)

• (contract) Yusuke Konishi and Gotai Yamada

• Cooperation:

• Research Organization for Information Science and Technology (RIST)

• Sponsor

• Elements Strategy Initiative

• Program for Promoting Researches on the Supercomputer Fugaku: DPMSD
(Development of high-performance Permanent Magnets by large-scale Simulations and
Data-driven approaches)
MateriApps, 2013-2021. All rights reserved.
17

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How to setup MateriApps LIVE!

  • 1. How to setup MateriApps LIVE! MateriApps LIVE! Development Team 2021/05/18 [for version 3.3]
  • 2. MateriApps — a Portal Site for Materials Science Simulation • Aiming at the community formation through the promotion of application MateriApps, 2013-2021. All rights reserved. 2 • Introducing 282 materials science applications and tools (as of 2021.5) • Finding applications • search tags: features, targets, calculation methods/algorithms • Information of applications • brief introduction, link to o ffi cial pages, information installation, usage, etc • Information of hands-on sessions, software update, etc • Glossary of keywords, Concierge, Reviews • 22,000+ page views / month, 6,500+ unique visitors / month (FY2020) since May 2013
  • 3. DFT AkaiKKR☆ OpenMX☆ xTAPP☆ ABINIT☆ ... Quantum Chemistry FMO☆ SMASH☆ GAMESS☆ DC☆ ... Molecular Dynamics MODYLAS☆ Gromacs☆ ERmod☆ MDACP... Lattice Models ALPS☆ DSQSS BLOCK DMRG++ Continuum Simulation ANSYS Multiphysics Octa ... Data Analysis CLUPAN☆ phonopy☆ Visualization fu☆ TAPIOCA☆ ☆ included in MateriApps LIVE! • Introducing 273 materials science applications and tools Applications on MateriApps MateriApps, 2013-2021. All rights reserved. 3 (80) (38) (31) (58) (12) (59) (37) Database (12), Integrated Environment (4) Machine Learning (20), Quantum Computing (6)
  • 4. Current status in computational materials science • From developers’ viewpoint • New algorithms should be implemented and used. Or, it will be forgotten ever existed. • It cost much to write and update documents • Development of software itself is hardly considered as scienti fi c achievements • From users’ viewpoint • What kind of applications? Who develop them? Which application should I use for my problem? • Manual and documentation are not well prepared. • How to evaluate the accuracy of results? • Goal of MateriApps project • Forming of community in the fi eld of computational materials science through the promotion of open source software MateriApps, 2013-2021. All rights reserved. 4
  • 5. What MateriApps will provide • To fi nd and learn application software • catalog of application/tool on MateriApps web • To start using application software • MateriApps LIVE! • To active use application software • pre-installation to Fugaku, supercomputers, etc: MateriApps Installer • Infrastructure for easily starting materials science simulations for theoreticians, experimentalists, researchers in companies, students, and more… MateriApps, 2013-2021. All rights reserved. 5 Flagship system (K, post-K,...) HPC infrastructure supercomputers in Japan Supercomputers for shared-use in research fields Cloud computing, on-premises PC clusters Personal workstations, PCs Installer Hands-on Cloud
  • 6. Fugaku • Live Linux bootable on virtual machine • run on Windows, Macintosh, etc • just boot and get ready for materials science simulations without installation • Version 3.3 was released in May 2021 • Pre-installed applications and tools • abinit, AkaiKKR, ALAMODE, ALPS, CONQUEST,
 Feram, DCore, DSQSS, HΦ, LAMMPS, mVMC, OCTA, OpenMX, Quantum ESPRESSO, PHYSBO, SMASH, TeNeS, xTAPP, etc • OVITO, ParaView, Tapioca, VESTA, VMD, XCrysDen… • GUI installer for CASINO, GAMESS, and VMD • Available from MateriApps LIVE! webpage • c.a. 12,000+ copies distributed since July, 2013 MateriApps, 2013-2021. All rights reserved. 6
  • 7. MateriApps LIVE! is useful for ... • Hands-on sessions using MateriApps LIVE! • MateriApps LIVE! Tutorials • HΦ, xTAPP, ALPS, DCore, mVMC, ALAMODE, DDMRG, DSQSS, SALMON, CASINO, TeNeS, etc. • Practices in lectures • Computational Physics • Computer Experiments (UNIX + C, LaTeX, VCS) • Used by experimentalists, researchers in private companies • Used by researchers in the fi eld of computer science • Easy setup (c.a. 15min) without no troubles • Useful for operation check, trouble shooting, user support MateriApps, 2013-2021. All rights reserved. 7
  • 8. Materials Science Simulation by MateriApps LIVE! • Introduction / Setup • First-principles band calculation (OpenMX / Quantum ESPRESSO / xTAPP) • Simulation of solution by molecular dynamics (LAMMPS / Gromacs) • Lattice model simulation (ALPS / HΦ / mVMC) • Quantum chemistry calculation (in preparation) • Hands-on materials are available at https://github.com/cmsi/MateriAppsLive/wiki/ MaLiveTutorial (currently only in Japanese) MateriApps, 2013-2021. All rights reserved. 8
  • 9. Wanna larger-scale simulations? • For Debian/Ubuntu Linux workstations • Debian package for MateriApps LIVE! can be used • https://github.com/cmsi/MateriAppsLive/wiki/UsingMateriAppsInDebian • (Can also be installed on Google Colab) • For PC clusters, clouds, supercomputers at ISSP and IT centers, Fugaku, etc • MateriApps Installer https://ma.issp.u-tokyo.ac.jp/app/268 • Renewed in ISSP Project for Advancement of Software Usability in Materials Science, FY2020 MateriApps, 2013-2021. All rights reserved. 9 Flagship system (K, post-K,...) HPC infrastructure supercomputers in Japan Supercomputers for shared-use in research fields Cloud computing, on-premises PC clusters Personal workstations, PCs Installer Hands-on Cloud
  • 10. • MateriApps LIVE! USB • setup.pdf, setup-en.pdf
 this document • README.html, README-en.html
 (copy from https://github.com/cmsi/MateriAppsLive/wiki/MateriAppsLive-ova) • VirtualBox Installer: VirtualBox-*-OSX.dmg, VirtualBox-*-Win.exe
 (available at https://www.virtualbox.org/wiki/Downloads) • MateriApps LIVE! VitualBox Disk Image: MateriAppsLive-*-amd64.ova
 (available at http://sourceforge.net/projects/materiappslive/ fi les/) What are included in USB Stick? MateriApps, 2013-2021. All rights reserved. 10
  • 11. Let's get started ✓ Copy fi les in USB stick memory to hard disk • copy all the fi les to your PC, e.g. to desktop ✓ Install VirtualBox by double-clicking the installer • For Windows: VirutalBox-*-Win.exe • For Macintosh: VirtualBox-*-OSX.dmg ✓ Import MateriApps LIVE! • double-click MateriAppsLive-*.ova • VirtualBox will start automatically and import window will open. Then press “import” button • VirtualBox Manager window will appear in two or three minutes • Host (host OS): operating system (Windows, Mac OS X, etc) on which VirtualBox is running • Virtual machine (guest OS): operating system (= MateriApps LIVE!) running on VirtualBox MateriApps, 2013-2021. All rights reserved. 11
  • 12. Boot in VirtualBox 1. Choose “MateriAppsLive…” 2. Press “Start” button. 3. Wait until login window will appear. MateriApps, 2013-2021. All rights reserved. 12
  • 13. • Login by using • User name (login): user • Password: live • Desktop (right) will appear • start menu • How to open a terminal window
 start menu “System Tools” “LXTerminal” • How to shutdown the virtual machine
 start menu “Logout” “Shutdown” Login to MateriApps LIVE! MateriApps, 2013-2021. All rights reserved. 13 CD-ROM button
  • 14. Additional settings (1/2) ✓ Using Japanese keyboard • start menu “System Tools” “Switch to Japanese Keyboard Layout” • check if “@” key works correctly ✓ Changing resolution and scale of the virtual machine window • Resolution (number of pixels): “800 x 600” by default • Scale (pixel density): “200%” by default • The resolution and scale can be changed from the “View” menu “Virtual screen 1” of the host OS • When using visualization software such as VESTA, OVITO, ParaView, set the resolution to “1024 x 768” or higher • If characters are small and di ffi cult to see, increase the scale MateriApps, 2013-2021. All rights reserved. 14
  • 15. Additional settings (2/2) ✓ File sharing between host OS and virtual machine • shutdown the virtual machine, if it is running • choose MateriAppsLive-* in VirtualBox Manager window, then “Settings” • open “Shared Folders” tab and click “+” on the right • click “v” on the right of “Folder Path”, choose “Other…”, and select the folder to be shared • check “Auto-mount” box and press “OK”. Then press “OK” again • the folder speci fi ed above can be accessed as /media/sf_... after restarting the virtual machine ✓ Browsing contents of ISO image fi le (*.iso) from the virtual machine • click CD-ROM icon at the bottom of the virtual machine window frame, select “Choose disk image ...", and select the ISO image fi le • contents of ISO image fi le are accessible via /media/cdrom0 MateriApps, 2013-2021. All rights reserved. 15
  • 16. Tips ✓ Copy & Paste: How to paste strings copied from a PDF fi le on host OS? • right click on terminal window “Paste” • or press “V” with “shift” and “control” keys • right click “Copy”, or “shift + control + C” to copy a string ✓ Completion/history/sequential search of command lines and fi lenames • Hit the tab key in the terminal to complete the command name or the fi lename • Hit the “↑” key in the terminal to trace back the history of commands • Execute the “history” command in the terminal to display the list of commands executed • Hit “Ctrl + r” in the terminal to search the commands executed so far (reverse incremental search) MateriApps, 2013-2021. All rights reserved. 16
  • 17. MateriApps planning & production • Administration: • Center for Computational Materials Science, Institute for Solid State Physics, University of Tokyo (ISSP-CCMS) • MateriApps Development Team • Kota Ido (ISSP), Shusuke Kasamatsu (Dept. of Phys., Yamagata Univ.), Takeo Kato (ISSP), Naoki Kawashima (ISSP), Hikaru Kouta (ISSP), Synge Todo (Dept. of Phys., Univ. of Tokyo/ISSP), Masahito Fukuda (ISSP), Kanako Yoshizawa (RIST) • (contract) Yusuke Konishi and Gotai Yamada • Cooperation: • Research Organization for Information Science and Technology (RIST) • Sponsor • Elements Strategy Initiative • Program for Promoting Researches on the Supercomputer Fugaku: DPMSD (Development of high-performance Permanent Magnets by large-scale Simulations and Data-driven approaches) MateriApps, 2013-2021. All rights reserved. 17