Running QM-MM MOPAC on a cluster

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Dec 14 2018 - 04:21:04 CST

Hi all
I resumed my attempts at finding the best settings for running namd qmmm on
a cluster. I used Example1, Polyala).

In order to use namd2/13 multicore night build, I was limited to a single
multicore node, 2*18-core Intel(R) Xeon(R) E5-2697 v4 @ 2.30GHz and 128
GB RAM (Broadwell)

Settings
qmConfigLine "PM7 XYZ T=2M 1SCF MOZYME CUTOFF=9.0 AUX LET GRAD QMMM
GEO-OK"

qmExecPath "/galileo/home/userexternal/fpietra0/mopac/MOPAC2016.exe"

of course, on the cluster the simulation can't be run on shm

execution line
/galileo/home/userexternal/fpietra0/NAMD_Git-2018-11-22_Linux-x86_64-multicore/namd2
namd-01.conf +p# > namd-01.log

where # was either 4, 10, 15, 36

With either 36 or 15 core; segmentation fault

With either 4 of 10 core, execution of the 20,000 steps of Example 1 took
nearly two hours. From the .ou file in folder /0, the execution took 0.18
seconds.

My question is what is wrong in my attempts to rationalize such
disappointing performance.

Thanks for advice

francesco pietra

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