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

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:24 CST