Re: Running QM-MM MOPAC on a cluster

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jan 01 2019 - 03:24:43 CST

Thanks a lot for these suggestions. There must be some restriction
hindering the suggested settings. Slurm, namd-01.conf, and error are shown
below in the given order:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=10
#SBATCH --cpus-per-task=1
#SBATCH --time=00:30:00
#SBATCH --job-name=namd-01
#SBATCH --output namd-01.out
#SBATCH --error namd-01.err
#SBATCH --partition=gll_usr_prod
#SBATCH --mem=115GB
#SBATCH --account=IscrC_QMMM-FER_1
# goto launch directory
cd $SLURM_SUBMIT_DIR
/galileo/home/userexternal/fpietra0/NAMD_Git-2018-11-22_Linux-x86_64-multicore/namd2
namd-01.conf +p10 +setcpuaffinity > namd-01.log

qmExecPath "numactl -C +10-33
/galileo/home/userexternal/fpietra0/mopac/MOPAC2016.exe"

$ cat *err
pthread_setaffinity: Invalid argument
pthread_setaffinity: Invalid argument
pthread_setaffinity: Invalid argument
------------- Processor 7 Exiting: Called CmiAbort ------------
Reason: set cpu affinity abort!

Charm++ fatal error:
set cpu affinity abort!

/var/spool/slurmd/job540826/slurm_script: line 14: 21114 Segmentation
fault
/galileo/home/userexternal/fpietra0/NAMD_Git-2018-11-22_Linux-x86_64-multicore/namd2
namd-01.conf +p10 +setcpuaffinity > namd-01.log

fp

On Mon, Dec 31, 2018 at 4:42 PM Jim Phillips <jim_at_ks.uiuc.edu> wrote:

>
> Well, that's progress at least. I have one other idea to ensure that NAMD
> and MOPAC aren't competing with each other for the same cores:
>
> 1) Add "+setcpuaffinity" to the NAMD command line before ">".
>
> 2) Add "numactl -C +10-33" to the beginning of qmExecPath in namd-01.conf
> (quote the string, e.g., "numactl -C +10-33 /path/to/MOPAC.exe")
>
> This should keep NAMD on your first ten cores and MOPAC on the next 24.
>
> What is qmBaseDir set to? Something in /dev/shm is the best choice. If
> qmBaseDir is on a network filesystem that could slow things down.
>
> Jim
>
>
> On Fri, 21 Dec 2018, Francesco Pietra wrote:
>
> > I finally learned how to ssh on a given node. The results for
> > #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
> >
> > qmConfigLine "PM7 XYZ T=2M 1SCF MOZYME CUTOFF=9.0 AUX LET GRAD QMMM
> > GEO-OK THREADS=24"
> >
> > are
> >
> > ssh node181
> > namd %cpu 720-750
> > mopac %cpu 1-30
> > 1 (per-core load):
> > %Cpu0-4: 90-100
> > %Cpu18-22: 60-100
> > %Cpu5-17: 0.0
> > %Cpu23-34: 0.0
> >
> > namd.log: 0.5/step (at 11min executed 1346 steps)
> > ______________________
> > As above, only changing
> >
> > SBATCH --nodes=1
> > #SBATCH --ntasks=1
> > #SBATCH --cpus-per-task=34
> >
> > ssh node181
> > namd %cpu 900
> > mopac %cpu 0-34
> > 1
> > %Cpu0-34: 0.3-100.0
> >
> > namd.log: 0.3/step (at 11min executed 2080 steps)
> >
> > Despite all cpus used, disappointing performance. I can't say whether
> namd
> > and mopac compete, at least in part, for the same cores.
> >
> > francesco
> >
> >
> > On Mon, Dec 17, 2018 at 4:12 PM Jim Phillips <jim_at_ks.uiuc.edu> wrote:
> >
> >>
> >> Since you are asking Slurm for 10 tasks with 1 cpu-per-task it is
> possible
> >> that all 34 threads are running on a single core. You can check this
> with
> >> top (hit "1" to see per-core load) if you can ssh to the execution host.
> >>
> >> You should probably request --ntasks=1 --cpus-per-task=34 (or 36) so
> that
> >> Slurm will allocate all of the cores you wish to use. The number of
> cores
> >> used by NAMD is controlled by +p10 and you will need THREADS=24 for
> MOPAC.
> >>
> >> It is a good idea to use top to confirm that all cores are being used.
> >>
> >> Jim
> >>
> >>
> >> On Sun, 16 Dec 2018, Francesco Pietra wrote:
> >>
> >>> 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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