[Simbiosnews] Job Opening for Software Engineer with Molecular Dynamics Expertise

Joy P. Ku joyku at stanford.edu
Mon Jul 2 13:14:05 PDT 2012

Dear Simbios friends:


We have an opening for a software engineer with expertise in molecular
dynamics simulations and high performance scientific computing.  Details
about the position are given below.  To learn more or to apply, please
visit  http://bit.ly/ypYq8w.  


Please forward this to others who may be interested.


Thank you,





Software Engineer, Exempt, 4P3, 2 Year Fixed Term 

Simbios, the Center for Physics-based Simulation of Biological Structures,
is one of eight national centers funded by the National Institutes of
Health to build a biomedical-computing infrastructure to speed progress in
biomedical research. 

We are looking for a software engineer with expertise in molecular
dynamics simulations and high performance scientific computing to support
and extend the functionality of our OpenMM and Folding at Home software

OpenMM (http://simtk.org/home/openmm) is an open-source molecular dynamics
prototyping and simulation software package that runs accelerated
calculations on GPUs. Folding at home (http://folding.stanford.edu) is a
distributed computing project that uses the power of hundreds of thousands
of CPUs and GPUs around the world to study protein folding. 

This position is a fixed term position that will be conterminous with our
grant funding from NIH. Our NIH grant is scheduled to end on August 31,
2014. Should our funding continue beyond this date, this position would
likely be extended. 


You will be responsible for the entire software pipeline, including but
not limited to: 

*	Develop new algorithms and improve the performance of OpenMM, 
*	Test and validate OpenMM 
*	Migrate OpenMM code into the Folding at home framework 
*	Coordinate the release of new Folding at home GPU cores 
*	Act as liaison to GPU manufacturers NVIDIA and AMD 
*	Actively participate in both the OpenMM and Folding at home support
*	Contribute to user documentation 


Minimum Requirements 

*	Experience in scientific algorithm development, high performance
computing applications, and molecular dynamics simulations 
*	Requires a minimum of five years programming experience 
*	Four year college degree or equivalent years of applicable
*	Experience and comfort with professional software development
*	Excellent communication skills, both written and oral 
*	Possess an understanding of the underlying biology 

Desired Requirements 

*	MS or PhD in physics, biochemistry, bioinformatics, computer
science, engineering, or life sciences or an equivalent combination of
education and experience 
*	Experience programming in C++, Python, and OpenCL 
*	Experience programming graphics processing units (GPUs) 
*	Experience with Windows, Unix, Linux, Mac platform
*	Has experience working in an interdisciplinary environment 

Resume & Cover Letter are mandatory for consideration. 

The final candidate will need to successfully pass a background check to
be considered for this position. 

Stanford University values diversity and is committed to equal opportunity
in employment. 


To learn more or to apply, please visit  http://bit.ly/ypYq8w






Joy P. Ku, PhD

Director, Simbios



Director of Communications & Training,

National Center for Simulation in Rehabilitation Research



(W)  650.736.8434, (F)  650.723.7461

Email:  joyku at stanford.edu


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