Re: Running QM-MM multinode

From: Gerard Rowe (GerardR_at_usca.edu)
Date: Tue Feb 19 2019 - 11:25:59 CST

Have you successfully run Orca across multiple nodes when it isn't being spawned by NAMD? I know that it can be tricky. I've not spent that much time trying because you hit diminishing returns in RI-DFT calculations when the number of processors exceeds 16.

-Gerard

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From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Francesco Pietra <chiendarret_at_gmail.com>
Sent: Sunday, February 17, 2019 2:41 AM
To: Bennion, Brian
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Running QM-MM multinode

With ntasks=4 most threads visible with "top" command are of "rcuob/##" character on each node. With the second, third and fourth node only, namd.mpi (the executable) appears as one thread. ORCA does not appear at all. In fact, /0/..TmpOut shows that ORCA has received a correct input from NAMD but (it seems to me) had no space where to work.
francesco

On Sat, Feb 16, 2019 at 7:03 PM Bennion, Brian <bennion1_at_llnl.gov<mailto:bennion1_at_llnl.gov>> wrote:
Maybe you already tried this but change the ntasks to 4. This may reproduce the environment of the single node and free up CPU’s in the 4 nodes for orca.

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On February 16, 2019 at 12:18:37 AM PST, Francesco Pietra <chiendarret_at_gmail.com<mailto:chiendarret_at_gmail.com>> wrote:
Hello
Although implied in a previous mail, the problem of running QM-MM multinode with NAMD is presented here in detail.
FIRST ON ONE NODE (SOLVED)
namd.conf
qmConfigLine    "! UKS BP86 RI SV def2/J enGrad SlowConv"
qmConfigLine     "%%maxcore 2500 %%pal nproc 34 end"
# qmConfigLine     "%%pal nproc 34 end"
qmConfigLine      "%%scf MaxIter 5000 end"
qmConfigLine    "%%output Printlevel Mini Print\[ P_Mulliken \] 1 Print\[P_AtCharges_M\] 1 end"
namd.job (SLURM)
#SBATCH --nodes=1
#SBATCH --ntasks=36
#SBATCH --cpus-per-task=1
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 +p1 +CmiSleepOnIdle > namd-01.log
whereby NAMD runs by occupying one cpu only, leaving the other ones to ORCA. It runs fantastically well but the number of processes proved to be insufficient for the large system at high spin.
MULTINODE
namd.conf
as above
namd.job
#SBATCH --nodes=4
#SBATCH --ntasks=144
#SBATCH --cpus-per-task=1
module load profile/archive
module load autoload namd/2.12
namd2=$(which namd.mpi)
srun $namd2 namd-01.conf +p1 +CmiSleepOnIdle > namd-01.log
whereby NAMD occpies all 144 cores, leaving scarce resources to ORCA.
My question is whether the multinode settings could be tuned so as NAMD occupies only a very small fraction of the hardware, in order to fulfill the alluring statement "For simulations of large systems that are distributed across several computer nodes" about Hybrid QM/MM NAMD <http://www.ks.uiuc.edu/Research/qmmm/>
I must add that, on multinode, I tried to simplify the molecular system by using only the charge groups facing the Tmetal ions (instead of full residues as in the above work), but it did not work. I got the error message "ORCA needs multiplicity values for all QM regions", while there is a single QM region. Probably the qm.pdb file was not correctly constructed.
Thanks for advice
francesco pietra

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