Running QM-MM tutorial on a cluster

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Nov 17 2018 - 13:30:02 CST

Hi all
Back to namd qm-mm for a project, after a survey of the tutorial one year
ago. At that time Example1 was run completely with mopac and up to the LINE
MINIMIZER BRACKET step 7 with orca (did not take notice of the time). All
that on a desktop with 4 core, on /dev/shm/ with orca.

Now I am trying the tutorial with orca on a cluster with namd2/12 mpi, in
order to establish how the simulations for the project can be best carried
out. On 4 nodes, 144 core (144 tasks, 1 cpu per task) along 1/2 hour the
simulation was still carrying out qm calculations:

TCL: Minimizing for 100 steps
Info: List of ranks running QM simulations: 2.

It is now running from scratch on a single node, 36 core 110GB mem, 24hr
limit. After12hr, the namd log output is as above.
Is there a way to verify the progress done by orca? Should the allowed
24hr be not enough to arrive at step 1 of the qm calculation, or a minimum
is not reached, how to restart the simulation?

Is the scalability of Example1 known? I.e. how many tasks should be best
used?

Grateful for advice.
francesco pietra

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