From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Sat Sep 11 2021 - 00:27:46 CDT
Hi Herald,
It looks like you are requesting a relatively expensive calculation from a
~110 atom system, and this is taking ~35minutes to calculate each SCF (52
hours is the time remaining to run ALL steps in your simulation). I don't
think this is terrible, and improving this time will depend on how much
parallelism you can achieve and what your hardware may look like.
You can test the ratio NAMD/ORCA to find the optimal spot, maybe having as
few as 2 or 3 cores for NAMD, and 37 cores for ORCA is the best balance for
you.
Do you have 40 cores or 40 threads on your system (as in 20 dual-thread
cores)? NAMD and ORCA will likely use all the CPU, and using multithreading
will decrease the performance.
Best,
Marcelo
On Thu, 9 Sept 2021 at 21:00, Herald Delis <bioinfo2021great_at_gmail.com>
wrote:
> Hello Marcelo,
>
> Thank you for reply,
>
> Q: 1. Is 75.000 the total number of atoms in your entire system, or in
> your QM regions? How large is the QM region itself?
> If you have more than a few hundred atoms in your QM region, I would
> expect ORCA to take a while to calculate it.
>
> A1: 75,000 is the total atoms, 113 atoms in QM region.
>
>
> Q: 2. In your NAMD execution line, you could ask for fewer nodes, like 5
> or 10, and leave the rest for ORCA.
> For example:
> NAMD2 -> namd2 +p10 Min.conf
> ORCA -> qmConfigLine "% PAL NPROCS 30 END" (from Min.conf)
>
> A2: This works and speeds up. But it is still showing 52 hours remaining.
>
> QMENERGY: 16 1.0000 -3517431.7765 -3517172.7403
>
> (From Step 16)
> Info: Writing QM charge output at step 16
> Info: Writing QM position output at step 16
> PRESSURE: 16 -3304.93 308.224 -262.003 312.544 -2742.12 -82.5491 -261.689
> -85.8746 -2603.54
> GPRESSURE: 16 -7758.39 303.504 -166.053 239.227 -6827.13 -132.006 -216.514
> 120.539 -6983.22
> TIMING: 16 CPU: 4.09771, 0.11225/step Wall: 40290.3, 2258.54/step,
> 52.6993 hours remaining, 532.187500 MB of memory in use.
> ENERGY: 16 8544.0808 5371.1756 4389.7518
> 47.8456 -255440.1271 20369.6414 1.7922 -3517172.7403
> 0.0000 -3733888.5801 0.0000 -3733888.5801
> -3733888.5801 0.0000 -2883.5306 -7189.5819
> 806859.3967 -2883.5306 -7189.5819
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 16
> LINE MINIMIZER BRACKET: DX 0.000456178 0.000121109 DU -1281.69 90.8142
> DUDX -5.59903e+06 2423.13 1.49124e+06
> MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
> LINE MINIMIZER REDUCING GRADIENT FROM 1.29277e+07 TO 12927.7
> WRITING COORDINATES TO DCD FILE QMMM-MinX.dcd AT STEP 16
> WRITING COORDINATES TO RESTART FILE AT STEP 16
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 16
> FINISHED WRITING RESTART VELOCITIES
>
> Q:3. If you only have one QM region in your system, you only need to ask
> for 1 QM simulations per node. This won't change your calculation.
>
> A: This works too. But please check the above answer.
>
> 4. What kind of QM calculation are you running? semi empirical? HF?
>
> A: QM Calculation:
>
> ! uks BP86 def2-TZVP def2/J EnGrad TightSCF
> %maxcore 3000
> % PAL NPROCS 30 END
> % basis
> newgto C "DEF2-SVP" end
> newgto H "DEF2-SVP" end
> end
> % scf
> MaxIter 500
> end
> %pointcharges "qmmm_exec/QMMM-Min/0/qmmm_0.input.pntchrg"
>
>
> %coords
> CTyp xyz
> Charge 3.000000
> Mult 1.000000
> Units Angs
> coords
>
>
> Additionationlly, I am using extrabonds for keeping my metal ion in place.
> Will it affect the speed or the calculation in any way?
>
> Thanks and regards,
> Herald
>
> On Fri, Sep 10, 2021 at 2:09 AM Marcelo C. R. Melo <melomcr_at_gmail.com>
> wrote:
>
>> Hi Herald,
>>
>> I may have a couple of suggestions and questions for you.
>>
>> 1. Is 75.000 the total number of atoms in your entire system, or in your
>> QM regions? How large is the QM region itself?
>> If you have more than a few hundred atoms in your QM region, I would
>> expect ORCA to take a while to calculate it.
>>
>> 2. In your NAMD execution line, you could ask for fewer nodes, like 5 or
>> 10, and leave the rest for ORCA.
>> For example:
>> NAMD2 -> namd2 +p10 Min.conf
>> ORCA -> qmConfigLine "% PAL NPROCS 30 END" (from Min.conf)
>>
>> 3. If you only have one QM region in your system, you only need to ask
>> for 1 QM simulations per node. This won't change your calculation.
>>
>> 4. What kind of QM calculation are you running? semi empirical? HF?
>>
>> Best,
>> Marcelo
>>
>> On Thu, 9 Sept 2021 at 06:53, Herald Delis <bioinfo2021great_at_gmail.com>
>> wrote:
>>
>>> [image: image.gif]Dear All,
>>>
>>> I am trying to run QMMM-MD using orca-namd2.
>>> But it happens to be too slow, I wanted to know if I am doing something
>>> wrong or is there a better way.
>>> I have a CPU node with 40 cores (and 4 unused GPU), my calculations of
>>> 75,000 atoms QMMM-Minimization takes 4 days.
>>>
>>> NAMD2 -> namd2 +p22 Min.conf
>>> ORCA -> qmConfigLine "% PAL NPROCS 20 END" (from Min.conf)
>>>
>>> # Number of simultaneous QM simulations per node
>>> QMSimsPerNode 20
>>>
>>> Thanks and regards,
>>> Herald
>>>
>>>
>>>
>>>
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