[Dock-fans] Single processor optimization

[Francesco Pietra]

This post is mostly to users of dual-opteron and Linux with a final brief question to the developers.

While performing a continuous flex docking for a large ligand on a big protein (NUMA-type machine, opteron 875, 2.2MHz, 8GB RAM taken by the process (%MEM 29.3); 1150 min to date, as from top; no idea how much time will still be required, should hopefully no crash occur) I was reading the IBM Redpaper "High throughput computing validation for drug discovery using the dock program on a massively parallel system" recently referred to in the Dock6 manual.

Section "Single processor optimization" describes a 43% improvement in speed by using specialized math libraries. I am using the standard GNU libraries (compilation was with gcc 4.2.3) provided by Debian Linux lenny. I wonder whether anyone has found improvements for this platform.

To the developers: since most of the time with this CPU-bound code is spent on scoring (Redpaper above), is there any plan to implement a monitoring of the progress of the scoring, no matter how approximate it might be?

Thanks
francesco pietra


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