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/ =
-----------------------------------------------------------
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/> =
>> -----------------------------------------------------------
>>
>>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Wed Jan 12 2011 - 11:00:04 PST
