Monthly Archives: March 2015

High Performance Scientific Computing on the Cloud?

What is this blog about?

Scientific Computing has been dominated and owned by elite scientists and engineers from premium universities and large engineering and aeronautical companies. There was little scope for students and enthusiasts to understand and learn:

With the advent of Amazon, Rackspace, Penguin as Cloud leaders, has this changed? Let us explore in this blog. This blog targets Geeks like me who want to setup an opensource solver on the HPC cloud.

Background on what I have been doing:

From past one year, I have been working with a worlds leading aeronautical company, automating their aircraft analysis and design workflow processes. There were lot of security restrictions to access any of their Solvers or understand how their High Performance Computing Servers work. This is very near to my background in mechanical engineering and a while ago had done a project in CFD and Finite Element Analysis using Ansys, I wanted to understand what is going on. Being a geek, I was curious to understand the nuts and bolts of High Performance Scientific Computing. Below is what I understood so far.

Nuts and Bolts of High Performance Scientific Computing

Solvers:

There are lot of open source solvers, there is a good discussion on, Why isn’t open source CFD solution for everyone?. One of the leading one is Stanford University Unstructured (SU2) solver. SU2 is back bone of some of the cloudbased tools like SimScale. Interestingly the sourcecode is in Github. So let us dive into it. It will take hardly couple of hrs to set this solver on Ubuntu Linux and run a simple airfoil mesh generation and view the airfoil on an opensource plot viewer, ParaView.

For quick start, you need gc++ and make utility. Git clone SU2_EDU source code and Run the SU2_EDU first, the instructions are provided in the link itself. Before running, go to bin directory and do few tweaks to the configuration file ConfigFile_RANS.cfg as below.

# Replace OUTPUT_FORMAT= TECPLOT to PARAVIEW
OUTPUT_FORMAT= PARAVIEW

#run command ./SU2_EDU
# Select option1
# Select the file airfoil_rae2822_lednicer.dat
# it will run for 2000 iterations and creates flow.vtk and solver_flow.vtk files.

once your run is complete, open ParaView GUI and load the flow.vtk and solver_flow.vtk files and you can see the airfoil mesh and volume grids.

Cloud based HPC:

A quick googling will show there are 2 leaders in HPC on the cloud, Rackspace and Penguin Computing. Penguin has a free plan to run a 5min HPC job. You just need to register and run the job to experience how to run a Solver on HPC.

Integrating Solver with HPC:

If you want to run the solver in a Cloud based HPC server the key is to re-build su2 with OpenMPI capabilities as below,

./configure --with-MPI=mpicxx --with-Metis-lib=/usr/local/metis-4.0.3 --with-Metis-include=/usr/local/metis-4.0.3/Lib

Once you build it, you can upload the binaries on the cloud and run the solver in as many CPU’s as you can, the response time will be considerable good. one way to test the details of the job is,

qstat -w <the PBS id returned>

Final Verdict

It is absolutely possible to setup a open source decent solver on the HPC cloud and run few solutions. Hope this blog was helpful.

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