Thanks Jason. I guess I have to use sander.MPI because I have to set
itgtmd == 1. Thanks for your answer.
Best regards,
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
-----------------------------------------------------------
On Wed, 12 Jan 2011, Jason Swails wrote:
> Targeted MD can be done with or without positional restraints, and
> positional restraints can be used whether or not you turn on targeted MD.
> pmemd can't handle itgtmd != 0, but it CAN handle ntr=1. However, because
> it does not have a mask parser built in yet, you can't input your atom
> selection via restraintmask, you have to use the GROUP input instead.
>
> For instance, the first input file will work for sander only, whereas the
> second input file will do the same exact thing and will work for both sander
> and pmemd
>
> restrained MD
> &cntrl
> nstlim=50000, dt=0.002, ntc=2, ntf=2,
> tempi=0, irest=0, ntx=1, ig=-1, ntt=3,
> ntb=2, ntp=1, ioutfm=1, ntr=1,
> restraint_wt=5.0, restraintmask=':1-300.CA',
> /
>
>
> restrained MD 2
> &cntrl
> nstlim=50000, dt=0.002, ntc=2, ntf=2,
> tempi=0, irest=0, ntx=1, ig=-1, ntt=3,
> ntb=2, ntp=1, ioutfm=1, ntr=1,
> /
> Restraint atom specification
> 5.0
> FIND
> * CA * *
> SEARCH
> RES 1 300
> END
> END
>
> Hope this helps,
> Jason
>
> On Wed, Jan 12, 2011 at 1:49 PM, Ilyas Yildirim <i-yildirim.northwestern.edu
>> wrote:
>
>> Hmm, I am checking out the targetted MD part in AMBER 11 Manual (pp104),
>> and it seems that in order to use positional restraints, I need to set
>> ntr=1. This is same with AMBER 9.
>>
>> Ilyas Yildirim, Ph.D.
>> -----------------------------------------------------------
>> = Department of Chemistry - 2145 Sheridan Road =
>> = Northwestern University - Evanston, IL 60208 =
>> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
>> = http://www.pas.rochester.edu/~yildirim/<http://www.pas.rochester.edu/%7Eyildirim/> =
>> -----------------------------------------------------------
>>
>>
>> On Tue, 11 Jan 2011, Jason Swails wrote:
>>
>>> Hello,
>>>
>>> This is a comment about your last statement. pmemd can handle positional
>>> restraints (even in amber10 I think, but at least in amber11). You just
>>> need to use the GROUP input format instead of restraintmask and
>>> restraint_wt.
>>>
>>> I'll let others comment on the benchmarking as I've not invested too much
>>> time doing that.
>>>
>>> Good luck,
>>> Jason
>>>
>>> On Tue, Jan 11, 2011 at 3:58 PM, Ilyas Yildirim <
>> i-yildirim.northwestern.edu
>>>> wrote:
>>>
>>>> Hi All,
>>>>
>>>> I am benchmarking 3 systems on a linux cluster with infiniband switch
>>>> before submitted my jobs. I have compiled amber9 and pmemd using
>>>> intel/11.1-064 compilers, and mpi/openmpi-intel-1.3.3.
>>>>
>>>> There are 2 types of nodes in the system, which I am benchmarking.
>>>>
>>>> i. 8 core nodes (Intel Xeon E5520 2.27GHz - Intel Nehalem) - old
>> system
>>>> ii. 12 core nodes (Intel Xeon X5650 2.67GHz - Intel Westmere) - new
>> system
>>>>
>>>> The 3 systems have 63401, 70317, and 31365 atoms, respectively. Here are
>>>> the results:
>>>>
>>>> ###########################################################
>>>> # System # 1:
>>>> # 63401 atoms (62 residues, 540 Na+/Cl-, 60831 WAT)
>>>> #
>>>> # old Quest
>>>> # (Intel(R) Xeon(R) CPU E5520 . 2.27GHz - 8 core/node)
>>>> #
>>>> # pmemd (hrs) sander.MPI (hrs)
>>>> 8 1.32 1.78
>>>> 16 0.77 1.28
>>>> 24 0.64 1.02
>>>> 32 0.50 0.95
>>>> 40 0.44 0.88
>>>> 48 0.41 0.87
>>>> 56 0.41 0.87
>>>> 64 0.40 0.85
>>>> 72 0.39 0.85
>>>> 80 0.39 0.87
>>>> #
>>>> # new Quest
>>>> # (Intel(R) Xeon(R) CPU X5650 . 2.67GHz - 12 core/node)
>>>> #
>>>> # pmemd (hrs) sander.MPI (hrs)
>>>> 12 0.86 1.23
>>>> 24 0.55 0.94
>>>> 36 0.41 0.82
>>>> 48 0.36 0.82
>>>> 60 0.32 0.75
>>>> 72 0.32 0.77
>>>> 84 0.31 0.73
>>>> 96 0.31 0.78
>>>> #
>>>> ###########################################################
>>>>
>>>> ###########################################################
>>>> # System # 2:
>>>> # 70317 atoms (128 residues, 1328 Na+/Cl-, 64689 WAT)
>>>> #
>>>> # old Quest
>>>> # (Intel(R) Xeon(R) CPU E5520 . 2.27GHz - 8 core/node)
>>>> #
>>>> # pmemd (hrs)
>>>> 8 1.35
>>>> 16 0.81
>>>> 24 0.62
>>>> 32 0.51
>>>> 40 0.46
>>>> 48 0.43
>>>> 56 0.41
>>>> 64 0.42
>>>> 72 0.40
>>>> 80 0.39
>>>> #
>>>> # new Quest
>>>> # (Intel(R) Xeon(R) CPU X5650 . 2.67GHz - 12 core/node)
>>>> #
>>>> # pmemd (hrs)
>>>> 12 0.89
>>>> 24 0.56
>>>> 36 0.43
>>>> 48 0.37
>>>> 60 0.33
>>>> 72 0.32
>>>> 84 0.32
>>>> 96 0.31
>>>> #
>>>> ###########################################################
>>>>
>>>> ###########################################################
>>>> # System # 3:
>>>> # 31365 (28 residues, 680 Na+/Cl-, 26382 WAT, 3430 heavy atom)
>>>> #
>>>> # (hours)
>>>> # sander.MPI sander.MPI(new)
>>>> 8 0.91 0.91
>>>> 16 0.63 0.63
>>>> 24 0.55 0.54
>>>> 32 0.52 0.52
>>>> 40 0.49 0.49
>>>> 48 0.50 0.50
>>>> 56 0.50 0.50
>>>> 64 0.53 0.53
>>>> 72 0.47 0.46
>>>> 80 0.47 0.47
>>>> #
>>>> # new Quest
>>>> # (Intel(R) Xeon(R) CPU X5650 . 2.67GHz - 12 core/node)
>>>> #
>>>> # sander.MPI (hrs)
>>>> 12 0.62
>>>> 24 0.49
>>>> 36 0.46
>>>> 48 0.45
>>>> 60 0.47
>>>> 72 0.38
>>>> 84 0.39
>>>> 96 0.40
>>>> #
>>>> ###########################################################
>>>>
>>>> It seems that I am hitting the peak around 48 cpus. In the amber mailing
>>>> list, I found some threads where Ross Walker and Robert Duke discusses
>> the
>>>> efficiency and scaling of pmemd. For a system with over 70K, I am unable
>>>> to get a peak around 128 cpu, which Ross was talking in one of the
>> thread
>>>> (for a system with 90K atoms). Therefore, I have some questions and will
>>>> appreciate any comments.
>>>>
>>>> 1. How does sander.MPI and pmemd divide the system when multiple cores
>> are
>>>> used? Does it divide the system randomly or according to the number of
>>>> residues (excluding water and ions)?
>>>>
>>>> 2. Is these results compatible with anyone's experience? I heard that
>> with
>>>> LAMMPS and NAMD, people can get a good scaling up to 256 cores (for
>>>> systems with 1 millions of atoms). Just for curiosity; would pmemd scale
>>>> efficiently on a system with over 1 millions of atoms?
>>>>
>>>> 3. I am using AMBER9. Does the scaling get better on AMBER10 or AMBER11?
>>>>
>>>> 4. In system # 3, I cannot use pmemd because of the positional
>> restraints
>>>> imposed on the system. Can I use the new versions of pmemd with
>> positional
>>>> restraints?
>>>>
>>>> Thanks in advance. Best regards,
>>>>
>>>> Ilyas Yildirim, Ph.D.
>>>> -----------------------------------------------------------
>>>> = Department of Chemistry - 2145 Sheridan Road =
>>>> = Northwestern University - Evanston, IL 60208 =
>>>> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
>>>> = http://www.pas.rochester.edu/~yildirim/<http://www.pas.rochester.edu/%7Eyildirim/>
>> <http://www.pas.rochester.edu/%7Eyildirim/> =
>>>> -----------------------------------------------------------
>>>>
>>>>
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Graduate Student
>>> 352-392-4032
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 12 2011 - 13:30:02 PST
