Recheck the units for that last number …. Catch ya,
Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of Albert Sent: Friday, 6 January 2012 3:24 PM To: gromacs maillist Subject: [gmx-users] another question about performance Hello: here is my log file for mdrun: Writing final coordinates. step 100000, remaining runtime: 0 s Average load imbalance: 10.8 % Part of the total run time spent waiting due to load imbalance: 4.3 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 19 % Z 0 % Average PME mesh/force load: 0.665 Part of the total run time spent waiting due to PP/PME imbalance: 5.7 % NOTE: 5.7 % performance was lost because the PME nodes had less work to do than the PP nodes. You might want to decrease the number of PME nodes or decrease the cut-off and the grid spacing. NOTE: 9 % of the run time was spent communicating energies, you might want to use the -gcom option of mdrun Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 2435.554 2435.554 100.0 40:35 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 409.701 22.103 7.095 3.383 gcq#149: "It's Against the Rules" (Pulp Fiction) As we can see from the end of this log file, the performance is 7.1ns/day, 3.4ns/hour. I am very confused about this output. How could this happen? Is there only two hours something each day? THX
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