Friday, December 17, 2010

amber11 pmemd + LAM-7,1,4/torque

The default optimization flag for pmemd.MPI is -fast, which causes some trouble in our cluster since the torque library doesn't like -static at all. You might already know that -fast is equivalent to "-xHOST -O3 -ipo -no-prec-div -static". My suggestion is to use "-axSTP -O3 -ipo -no-prec-div" instead. The reason for that is compatibility, -xHost also isn't a good optimization flag either. All processors in our cluster are not exactly the same, -xHost is just adding a possibility to mess with.

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