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HPC Technology

Overview

 

The Department of Molecular Biology at Massachusetts General Hospital is a part of both the research community of the hospital and the Division of Medical Sciences of the Harvard Graduate School of Arts and Sciences. It also has a strong connection with the Department of Genetics at Harvard Medical School, where most of its scientists hold concurrent appointments.

The Department of Molecular Biology at Massachusetts General Hospital (MGH) was founded in conjunction with the Department of Genetics at Harvard Medical School (HMS).  Thus, from its inception, the Department of Genetics has had two main units – a Quadrangle-based unit and an MGH based unit.  While separated geographically, they nonetheless function as a single department with all members involved in mentoring junior faculty and in recruiting new faculty, a tradition that continues today.

Members of Molecular Biology carry out fundamental studies in bioinformatics, genetics, molecular biology, and related disciplines, on a variety of topics at the cutting edge of science and medicine.  High Performance Computing (HPC) is an important part of the department.

Challenges

Research at MGH’s Department of Molecular Biology is highly collaborative, spanning multiple institutions. Many researchers conduct significant activities at affiliated organizations such as The Broad Institute and Harvard’s CryoEM Center. This creates the operational challenge of transferring and protecting extremely large data sets for analysis back at MGH.

A single CryoEM microscope run can produce tens of terabytes of raw data at a time. Mainstream backup vendors often focused on high pricing, using ransomware fear-mongering to justify excessive licensing quotes. With substantial data volumes and multi-institution data movement, the department needed a solution that could:

  • Efficiently capture sudden, unexpected data dumps
  • Protect critical research data without performance degradation
  • Avoid complex, error-prone configurations
  • Deliver an enterprise solution at a reasonable cost

Why Bacula Enterprise

The department had years of experience using open-source Bacula, giving the team confidence in its stability, speed, and reliability. After evaluating multiple mainstream solutions, Bacula Enterprise stood out as the only platform capable of meeting their HPC-driven requirements without sacrificing performance or driving costs unnecessarily high.

Bacula’s HPCAccelerator technology proved especially valuable, enabling the team to manage massive data migrations quickly and efficiently.

Over the years we have tried and tested many mainstream backup solutions.  As we produce more data, we couldn’t continue to pay exorbitant licensing fees that scale with our data footprint. We have historically had a small open source Bacula environment to cover non-standard systems, such as FreeBSD, that most backup vendors do not support

The recent uncertainty in future research funding prompted us to look for more cost efficient solutions.  Many backup vendors were fear-mongering the risk of ransomware to justify outrageous quotes for their licensing.  Bacula Enterprise was one of the few reasonable quotes we received.  Their support also stood out among the other vendors we interacted with.  They dedicated many hours of their time working on our POC, testing various modules and edge cases we identified, before we were even a paying customer.  By the end of our POC, it became clear that only Bacula made sense.

Our researchers utilize several affiliated HPC resources in additional to our departmental offerings.  These resources include MGH’s ERISTwo cluster, HMS’s O2 cluster, and The Broad Institute’s Terra platform.  They also take advantage of specialized microscopes at affiliated institutions.  With all of these resources at their disposal, it often seems like our researchers are generating new data faster than we can produce storage to accommodate it.

 

Bacula, with their new HPCAccelerator technology, provides a reliable and robust solution to backup these large amounts of data, without sacrificing performance or requiring a complicated configuration prone to human error, when it is introduced into our environment.

– Tim Venezia , Systems Manager, Department of Molecular Biology; MGH

Conclusion

The Department of Molecular Biology at Massachusetts General Hospital relies on Bacula Enterprise to power a flexible, high-performance, and cost-effective backup infrastructure tailored to HPC workloads. Bacula’s ability to handle massive data flows from advanced research institutions—without performance trade-offs or inflated licensing fees—makes it an ideal fit for scientific environments dealing with extreme data volumes and interdisciplinary collaboration.