Sr. High-Performance Computing Application Associate

Posted: Jun. 08, 2020

Silicon Therapeutics (“SITX”) is a privately held, physics-driven integrated drug discovery company in the preclinical IND stage targeting innate immunity to start, but with the capability to move into many other franchise opportunities. The Company’s initial pipeline is focused on modulation of the innate immune system to “light the spark” within immunologically cold tumors by using its physics-enabled drug discovery engine for the design of small molecule therapeutics and the lead program is in late stage preclinical studies. SITX’s discovery efforts as well as physics-based platform are all completely in-house, with a full wet lab as well as a team of over 25 experienced R&D professionals spanning biology, biochemistry, chemistry, biophysics (NMR + X-ray) & preclinical sciences. SITX’s engine leverages quantum mechanics and molecular dynamics, which are deployed on its own internal supercomputer composed of over 400 GPU’s and FPGA’s and allows SITX to accurately simulate the physical motion and properties of biological targets at an atomistic level resolution. The platform is completely proprietary to SITX and was built from the ground up with the purpose of addressing difficult targets and using simulations to break through bottlenecks that has plagued traditional drug discovery approaches on such targets. It is currently the ONLY company which owns the entire spectrum of physics-driven drug discovery from chip-to-clinic with a team of over 50 individuals in Boston.

The Company’s initial focus in on innate immunity and its pipeline is currently composed of one project entering IND-enabling studies, another one entering hit-to-lead and two more ramping up. Its unique advantage in designing small molecules using all atom simulations has allowed it to advance a systemically available small molecule STING agonist into a preclinical development. The program is ramping up for IND enabling studies entry to the clinic in 2020. This differentiated product can be administered systemically via an IV dose and has single agent effects in early mouse efficacy studies using PD1 resistant tumor models and is a “rule-of-5” compliant small molecule. Beyond this one program, the Company is also advancing an ADAR inhibitor which can be considered an innate immune checkpoint as well as a multitude of targets that explore Innate Immunity’s role in cancer biology.

Job Summary

High-performance computing (HPC) is central to operations at Silicon Therapeutics —our HPC resources include an on-premises GPU cluster and cloud operations with multiple cloud providers ( We are currently looking for an HPC user specialist to work directly with our growing users at the intersection of applications and infrastructure.  This position will directly interface with users supporting their applications on our GPU cluster and potentially on the cloud. The ideal candidate will be able to independently diagnose user issues, profile bottlenecks and suggest and implement solutions through changes in the application and infrastructure. 

Job Responsibilities

  • Provide an effective, reliable, high performance, scalable computing environment to users through effective and independent communication.  
  • Work in collaboration with senior HPC staff to manage the hardware and software infrastructure, and application issues. 
  • Proactively suggest solutions to alleviate bottlenecks with different application workloads and/or system infrastructure. 
  • Improve system reliability and performance.  
  • Profile scientific codes for CPU, GPU, memory, I/O usage and optimize aspects of hardware and infrastructure if needed.  


  • Bachelor’s degree in Computer Science or a master’s degree in Computer Science or related field with 3+ years of High-Performance Computing experience preferred 
  • Experience with schedulers such as SLURM, distributed file systems (BeeGFS/Lustre), application workflow engines such as Airflow.  
  • Must have a background in HPC with experience in computational chemistry applications.
  • Experience dealing with and debugging aspects of HPC infrastructure such as schedulers, distributed file system, application workflow engines such as Airflow is required. 
  • Comfortable profiling workflows at all levels of execution including CPUs/GPUs, storage and memory. 
  • Programming experience with GPUs and/or multi-core CPUs as well as leveraging cloud for scientific workloads is highly desirable for the position.  
  • Skilled in Bash/Python/Jenkins/Ansible.  
  • Familiarity with GPU/CPU profiling and programming frameworks such as CUDA; CPU libraries such as MPI, OpenMP, POSIX threads is highly desirable.  
  • Must possess excellent communication skills.  

Silicon Therapeutics provides equal employment opportunities to all employees and applicants for employment and prohibits discrimination and harassment of any type without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal, state or local laws.