Re: Running QM-MM MOPAC on a cluster

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Dec 16 2018 - 01:47:41 CST

I had early taken into consideration the relative nr of threads, by
imposing them also to MOPAC.
Out of the many such trials, namd.config:

qmConfigLine "PM7 XYZ T=2M 1SCF MOZYME CUTOFF=9.0 AUX LET GRAD QMMM
GEO-OK THREADS=24"

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

corresponding SLURM:
#SBATCH --nodes=1
#SBATCH --ntasks=10
#SBATCH --cpus-per-task=1
/galileo/home/userexternal/fpietra0/NAMD_Git-2018-11-22_Linux-x86_64-multicore/namd2
namd-01.conf +p10 > namd-01.log

Thus, 24+10=34, while the number of cores on the node was 36. Again,
execution took nearly two hours, slower than on my vintage VAIO with two
cores (1hr and half).

As to the MKL_NUM_THREADS, I am lost, there is no such environment variable
in MOPAC's list. On the other hand, the namd night build I used performs as
effective as it should with classical MD simulations on one node of the
same cluster.

thanks
fp

On Fri, Dec 14, 2018 at 4:29 PM Jim Phillips <jim_at_ks.uiuc.edu> wrote:

>
> The performance of a QM/MM simulation is typically limited by the QM
> program, not the MD program. Do you know how many threads MOPAC is
> launching? Do you need to set the MKL_NUM_THREADS environment variable?
> You want the number of NAMD threads (+p#) plus the number of MOPAC threads
> to be less than the number of cores on your machine.
>
> Jim
>
>
> On Fri, 14 Dec 2018, Francesco Pietra wrote:
>
> > 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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