Category Archives: High Throughput Parallel Computing (HTPC)
Introduction Hadoop has become a fixture where big data is concerned but it has been difficult to use in HPC and HTC cluster environments. This is becoming unfortunate as an increasing number of new algorithms assume Hadoop’s an option. I … Continue reading
Overview NAMD simulates molecular motion, especially of large molecules so it’s often used to simulate molecular docking problems. One particularly interesting class of docking problem is the interaction of protein molecules with other molecules such as the cell membrane. The … Continue reading
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Our first researcher using Amber PMEMD on the OSG reports molecular dynamics are four to eight times faster on the OSG than with the infrastructure she had access to previously. That’s for the all CPU version, i.e. without the Nvidia … Continue reading
Molecular Dynamics Proteins are important and their structure complex. And then they move. The way they move determines how organisms work … or fail. The shape of the protein determines its function so motion means its shape is in flux … Continue reading
PMEMD for OSG is live. Gratia statistics for January: All runs are 8-way parallel MPI jobs so we get eight hours of CPU time per hour of wall time.