3 minute read

In the last post, I discussed my trip to Puerto Rico.  Now that my trip is over, and I am back in Lincoln, I would like to share some of the successes of the trip.  I had a great time exploring old San Juan.  I have pictures as well.

Presenting the Holland Computing Center grid

Creating a new User

But on a more relevant note, the Campus Grid in Puerto Rico gained a new user while I was there.  I always feel that computing infrastructure is best built by user's demand.  That has certainly been the case at HCC, where we run between 95%+ utilization on our HPC clusters.  I met with Steve Massey to find how the Island Grid can help him.

Steve Massey is a bio-informatician at the University of Puerto Rico -- Rio Pedres.  His work is an ideal fit for High Throughput Computing.  His processing follows the model of using the same executable against many, many protein pdb files.  We talked for a while on Tuesday, both before and after the power was cut to the UPR campus, about how we can enable this work onto the UPR campus grid, flocking to UNL, and finally to the OSG.  While I was in PR, I worked with Steve to run one of his workflows on the OSG.

I'm not going to pretend to know what is really happening with the workflow, but it takes as input a set of DNA sequences that where pre-calculated (I believe somewhat random) and a pdb file, and calculates the robustness using an external application, Scwrl4.  The output is a robustness file that lists the robustness for the protein with the DNA sequences.

I was able to run this workflow on the OSG using Nebraska's GlideinWMS interface.  I created a submit.sh script that wrote out a simple Condor submit script, and wrapper.sh, that configured the environment on the worker node.  Both of the scripts are available on github.  Together, these two components create the workflow.

There is still work to be done.  The executable that Steve wrote does not properly detect the length of the strand of the amino acid, and therefore is not able to properly calculate robustness and/or send to Scwrl4.

Also, there is another workflow that Steve would like to run.  I hope to continue to work with him to enable these workflows.

Onto the Grid!

In addition to talking to Steve about creating workflows, I also discussed how to integrate his small cluster into the Island Grid in Puerto Rico.  The primary difficulty with adding his cluster is the university's very restrictive firewall.  Therefore, we will be unable to run a central submission host on his cluster, and flocking is out.  But, I believe between Jose and myself, we have a solution.  Either he can run BOSCO and submit through SSH to Steve's SGE cluster, or install Condor worker nodes on Steve's cluster to report to the primary campus cluster, nanobio.

I also talked with a Computer Science researcher to discuss putting his Mac Mini cluster on the Grid.  He is running Linux on the Mac Mini's, therefore it would be a good fit for the grid.  The frontend node to the Mac Mini cluster is not running linux, therefore BOSCO will not work as it needs a consistent platform on the frontend node and the worker nodes.  Instead we will have to install Condor worker nodes on the nodes themselves in order to access the Mac Mini's.


I believe that Puerto Rico has a lot to benefit from creating an Island (Campus) Grid.  They also have a very energetic administrator, Jose, who can spearhead the implementation, with close collaboration with myself and the campus grids team.

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