Re: Running QM-MM MOPAC on a cluster

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Dec 31 2018 - 09:42:27 CST

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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