From: g srinivasa murthy (g_s_murthyin_at_yahoo.co.in)
Date: Sat Feb 21 2004 - 22:58:26 CST
We are using Namd on our 18 node Cluster. The
Master node has dual Xeon 2.4 GHz, with 2GB RAM and
Slaves which are dual Xeon 1GB RAM. Cluster runs RH8.0
We Compiled MPI version of NAMD2.5 from source( we
have LAM 6.5.6/MPI2).
We faced no problems running NAMD till now.
Now there seems to be problem when NAMD jobs are
launched. Cluster gets hung during NAMD runs. We are
running a SMD simulation of a protein(~3000 atoms) for
nano second(Previous runs of 100ns for small systems
(~200 atoms) ran smoothly).
The user's guide suggests that the max memory usuage
by NAMD will be around 300MB(max) for simulations of
over 100 thousand atoms.
Is hyper-threading a cause of Problem? Any one out
there faced problems with NAMD running on LAM.
Help of any sort is appreciated.
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