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NAMD is installed on the IBM SP at SDSC
NAMD 2.5b1 for IBM-SP is available for
download.
NAMD 2.3 is installed as
/usr/local/apps/namd
Interactive Runs
NAMD may be run directly under POE:
/usr/local/apps/namd run.namd -nodes n -tasks_per_node m > run.log
Batch Jobs
Submit batch jobs using the LoadLeveler environment:
llsubmit scriptfile
Many options are required for good performance.
You must either carefully read the Blue Horizon documentation,
or use the automatic
batch script generator provided by SDSC.
Run NAMD in your script without any options:
/usr/local/apps/namd run.namd > run.log
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