Re: Tuning QM-MM with namd-orca on one cluster node

From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Thu Jan 31 2019 - 13:07:53 CST

Hi Francesco,

The first line in your namd.log says
"Info: Running on 5 processors, 1 nodes, 1 physical nodes."
Which indicates NAMD is indeed using the 5 cores you requested with "+p5".
Some times "top" will show just one process, but the CPU usage of the
process will show 500%, for example, indicating 5 cores. This happens in
some cluster management systems too.

As for ORCA, your "qm config line" does not indicate you are requesting it
to use multiple cores, so it most likely is really using just one. You
should be using the keyword "PAL?", where the question mark indicates the
number of requested cores: use "PAL8", for example, to ask for 8 cores.
You should become familiarized with the commands that control how ORCA
distributes its computations in a cluster (their manual is very good), as
you may need to provide a "hostfile" indicating the name(s) of the node(s)
where ORCA will find available processors. This is something every cluster
makes available when the queuing system reserves nodes for a job, so you
should find out how to access that in your cluster.

As a final note, even in parallel, calculating 341 QM atoms (QM system +
link atoms) using DFT will be slow. Really slow. Maybe not 10 hours per
timestep, but you just went from a medium sized semi-empirical (parallel
MOPAC) calculation to large DFT one. Even in parallel, MOPAC could take a
couple of seconds per timestep (depending on CPU power). ORCA/DFT will take
much more than that.

Best,
Marcelo

---
Marcelo Cardoso dos Reis Melo, PhD
Postdoctoral Research Associate
Luthey-Schulten Group
University of Illinois at Urbana-Champaign
crdsdsr2_at_illinois.edu
+1 (217) 244-5983
On Thu, 31 Jan 2019 at 12:27, Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> Hello
> Having obtained very good performance of NAMD(nightbuild)-MOPAC on one
> cluster node on my system (large qm part, see below, including two iron
> ions) , I am now trying the same with NAMD(nightbuild)-ORCA on the same
> cluster (36 cores along two sockets). So far I was unable to have namd and
> orca running on more than one core each.
>
> namd.conf
> qmConfigLine    "! UKS BP86 RI SV def2/J enGrad SlowConv"
> qmConfigLine    "%%output Printlevel Mini Print\[ P_Mulliken \] 1
> Print\[P_AtCharges_M\] 1 end"
> (SCF already converged by omitting "enGrad")
>
> namd.job
> #SBATCH --nodes=1
> #SBATCH --ntasks=1
> #SBATCH --cpus-per-task=36
> /galileo/home/userexternal/fpietra0/NAMD_Git-2018-11-22_Linux-x86_64-multicore/namd2
> namd-01.conf +p5 +setcpuaffinity + showcpuaffinity > namd-01.log
>
> namd.log
> Info: Running on 5 processors, 1 nodes, 1 physical nodes.
> Info: Number of QM atoms (excluding Dummy atoms): 315
> Info: We found 26 QM-MM bonds.
> Info: Applying user defined multiplicity 1 to QM group ID 1
> Info: 1) Group ID: 1 ; Group size: 315 atoms ; Total PSF charge: -1
> Info: Found user defined charge 1 for QM group ID 1. Will ignore PSF
> charge.
> Info: MM-QM pair: 180:191 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 208:195 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 243:258 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 273:262 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 296:313 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 324:317 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 358:373 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 394:377 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 704:724 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 742:728 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 756:769 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 799:788 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 820:830 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 864:851 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 1461:1479 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 1511:1500 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 1532:1547 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 1566:1551 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 1933:1946 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 1991:1974 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 2011:2018 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 2050:2037 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 2072:2083 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 2098:2087 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 2139:2154 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> Info: MM-QM pair: 2174:2158 -> Value (distance or ratio): 1.09 (QM Group 0
> ID 1)
> TCL: Minimizing for 200 steps
> Info: List of ranks running QM simulations: 0.
> Nothing about affinity!! (which was clearly displayed in MOPAC case)
>
> /0/qmm_0_input.TmpOut shows SCF ITERATIONS
>
> "top" shown a single PR for both namd and orca.
> ___-
> I had already tried a different job setting
> #SBATCH --nodes=1
> #SBATCH --ntasks-per-node=4
> #SBATCH --ntasks-per-socket=2
> module load profile/archive
> module load autoload openmpi/2.1.1--gnu--6.1.0
> /galileo/home/userexternal/fpietra0/NAMD_Git-2018-11-22_Linux-x86_64-multicore/namd2
> namd-01.conf +p5 > namd-01.log
>
> Here too, "top" showed a single PR for both namd and orca, so that in
> about 20 hous, namd.log  was at "ENERGY 2", indicating that 1400 hrs were
> needed to complete the simulation.
>
> Thanks for advice
> francesco pietra
>
>
>

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