BASICS OF SCIENTIFIC COMPUTING INFRASTRUCTURES: LAB 6

YOUR NAME

Please feel free to ask for any help if there are portions that are unclear. Do upload allof the scripts and source code for programs you use in this exercise in a single compressedfile. You are encouraged to use LaTeX to typeset your answers. Apart from the referencebelow https://www.sharelatex.com may help you use LaTeX without the installationpain.

1. Study material

• Beowulf Clusterhttps://en.wikipedia.org/wiki/Beowulf_cluster

• Topology Optimizationhttps://en.wikipedia.org/wiki/Topology_optimization

• LaTeXhttps://en.wikibooks.org/wiki/LaTeX

2. Questions

1) What are PETSc[19] and Trilinos[20]? Where may they be useful in scientificcomputing?ANSWERCOMMENTGRADE

2) Build a mini cluster using 4 Raspberry Pi’s. Documentation can be found athttps://courses.cs.ut.ee/t/kids/Main/Raspcluster.

a) Run the Linpack and stream benchmarks on a single core. Record your resultsbelow.ANSWERCOMMENTGRADE

b) Run the Linpack benchmark on your cluster. Estimate the power efficiencyfor the Linpack benchmark. Compare this to the efficiency of computers inthe Top500 in terms of flops per watt.ANSWERCOMMENTGRADE

3) In this exercise you will use optimal design to obtain a structure that can be 3Dprinted. You will use TopOpt to generate an optimal truss design on Juur. Yourdesign will be printed using PLX or ABS plastic on an Ultimaker 2 3D printer.

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a) Examine the TopOpt website http://www.topopt.dtu.dk/. Try the onlinedemonstrations and read some of the papers. Did you find anything interestingor fun? What is topology optimization and in what areas might it be useful?

b) Examine the script supplied in the programs to install PETSc (http://www.mcs.anl.gov/petsc/) and the large scale topology optimization code usingPETSc (http://www.topopt.dtu.dk/?q=node/898/). How might you opti-mize the speed of the resulting installed codes?

c) Using either the script in the supplied programs, or your optimized version,install PETSc (http://www.mcs.anl.gov/petsc/) and the large scale topol-ogy optimization code using PETSc (http://www.topopt.dtu.dk/?q=node/898/). Run the code with the default settings. Transfer the files to your laptopor a workstation. Install Paraview[15], and then import the files.

– Import a vtu file– Display xPhys coordinate as a surface plot– Apply thresholding filter for a values between 0.75 and 1 (feel free to

adjust this to get a better fully connected result)– Apply the Extract surface filter to extract a bounding surface– Then apply the triangulate filter so one can save an STL file– Finally save an STL file.

The Protokeskus[14] has an Ultimaker 2 which will be used to 3D print yourprogram output. Download CURA for your computer from [13] under theproducts tab (https://ultimaker.com/en/products/software). Open upthe STL format surface in Cura.In the basic CURA settings, choose

– layer height – 0.1 mm– shell thickness – 0.8 mm– fill density – 100%– bottom/top thickness – 0.8 mm– support type – Everywhere– platform adhesion type – Brim

Finally, re-size the design so that it prints in less than 60 minutes then saveyour model in GCode format for uploading to 3D printer. Repeat these steps,but change the topology optimization settings. Size your new structure sothat in under 120 minutes we can 3D print the new optimal structure that youhave designed. Include a couple pictures of your design in your writeup, forexample as in Figs. 1 and 2. For 3D printing choose your optimized structureand send links to your STL and GCode files to alo.peets@ut.ee. We will printyour design and give it to you at the exam session. In case you want to see3D printer at work call ALO PEETS 53541122 and negotiate a time for you(group).

ANSWERCOMMENTGRADE

BASICS OF SCIENTIFIC COMPUTING INFRASTRUCTURES: LAB 6 YOUR NAME 3

Figure 1. One view of a topology optimized structure

Figure 2. Another view of a topology optimized structure

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4) Examine https://prezi.com/tsqmrceierpy/the-high-performance-computing-center/?utm_campaign=share&utm_medium=copy. Do you find anything interesting? Whatfilesystem is best for using on Vedur, /gpfs/hpchome or /gpfs/rocket? What filesystem is backed up?ANSWERCOMMENTGRADE

5) What are the PGAS languages Titanium, Chapel, UPC and CAF? Where mightyou be able to download/find implementations of these languages and try themout?ANSWERCOMMENTGRADE

References

[1] http://diy3dprinting.blogspot.com

[2] Tymrak B.M., Kreiger M., Pearce, J.M. “Mechanical properties of components fabricated with open-source 3-D printers under realistic environmental conditions” Materials and Design 58:242-246 (2014)http://dx.doi.org/10.1016/j.matdes.2014.02.038

[3] Aage N., Andreassen E., Lazarov B.S., “Topology optimization using PETSC: an easy-to-use, fullyparallel, open source topology optimization framework” Structural and Multidisciplinary Optimization51(3):565-572 (2015) http://dx.doi.org/10.1007/s00158-014-1157-0

[4] http://www.top500.org/

[5] http://icl.cs.utk.edu/hpcc/

[6] Andreassen E., Lazarov B.S., Sigmund O., “Design of manufacturable 3D extremal elastic microstruc-ture” Mechanics of Materials 69:1-10 (2014) http://dx.doi.org/10.1016/j.mechmat.2013.09.018

[7] Cox S.J., Cox J.T., Boardman R.P., Johnson S.J., Scott M., O’Brien N.S., “Irdis-pi: a low-cost,compact demonstration cluster” Cluster Computing 17:349-358 (2014) http://dx.doi.org/10.1007/

s10586-013-0282-7 http://www.southampton.ac.uk/~sjc/raspberrypi/

[8] Tso F.P., White D.R., Jouet S., Singer J., Pezaros D.P., “A Scale model for cloud computinginfrastructures” Proc. 2013 IEEE 33rd International Conference on Distributed Computing Sys-tems Workshops (ICDCSW), pp 108-112 (2013) http://dx.doi.org/10.1109/ICDCSW.2013.25 https://raspberrypicloud.wordpress.com/

[9] Breuning S., “Banoffe Pi Server” http://banoffeepiserver.com/

[10] Balakrishnan N., “Building and benchmarking a low power ARM cluster” MSC thesis, Univer-sity of Edinburgh https://www.epcc.ed.ac.uk/sites/default/files/Dissertations/2011-2012/

Submission-1126390.pdf

[11] Kiepert J., “Creating a Raspberry Pi-Based Beowulf Cluster” Pre-print 2013 https://www.epcc.ed.

ac.uk/sites/default/files/Dissertations/2011-2012/Submission-1126390.pdf

[12] Andreassen E., Clausen A., Schevenels M., Lazarov B.S., Sigmund O., “Efficient topology optimizationin MATLAB using 88 lines of code” Structural and Multidisciplinary Optimization 43(1):1-16 (2011)http://dx.doi.org/10.1007/s00158-010-0594-7 http://www.topopt.dtu.dk/?q=node/751

[13] Ultimaker https://ultimaker.com/

[14] Protokeskus https://ideelab.wordpress.com/team-up/protokeskus/

[15] ParaView http://www.paraview.org/

[16] TopOpt http://www.topopt.dtu.dk/

BASICS OF SCIENTIFIC COMPUTING INFRASTRUCTURES: LAB 6 YOUR NAME 5

[17] Bendsøe M.P., Sigmund O., “Topology Optimization: Theory, Methods and Applications” 2nd ed.Springer (2004)

[18] Notes on Rasberry Pi cluster setup https://courses.cs.ut.ee/t/kids/Main/Raspcluster

[19] PETSc http://www.mcs.anl.gov/petsc/index.html

[20] Trilinos http://trilinos.org/