[gmx-users] Slow Runs
Denny Frost
dsfrost at cableone.net
Fri Jan 28 20:21:24 CET 2011
I just realized that that was a very old mdp file. Here is an mdp file from
my most recent run as well as what I think are the domain decomposition
statistics.
mdp file:
title = BMIM+PF6
cpp = /lib/cpp
constraints = hbonds
integrator = md
dt = 0.002 ; ps !
nsteps = 4000000 ; total 8ns.
nstcomm = 1
nstxout = 50000
nstvout = 50000
nstfout = 0
nstlog = 5000
nstenergy = 5000
nstxtcout = 25000
nstlist = 10
ns_type = grid
pbc = xyz
coulombtype = PME
vdwtype = Cut-off
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc_grps = BMI PF6
tau_t = 0.2 0.2
ref_t = 300 300
nsttcouple = 1
; Energy monitoring
energygrps = BMI PF6
; Isotropic pressure coupling is now on
Pcoupl = berendsen
pcoupltype = isotropic
;pc-grps = BMI PFF
tau_p = 1.0
ref_p = 1.0
compressibility = 4.5e-5
; Generate velocites is off at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 100000
domain decomposition
There are: 12800 Atoms
Max number of connections per atom is 63
Total number of connections is 286400
Max number of graph edges per atom is 6
Total number of graph edges is 24800
On Thu, Jan 27, 2011 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Denny Frost wrote:
>
>> about 12000 atoms, 8 nodes, CentOS 5.3/Linux, infiniband. Below is a copy
>> of my mdp file.
>>
>> title = BMIM+PF6
>> cpp = /lib/cpp
>> constraints = all_bonds
>> integrator = md
>> dt = 0.004 ; ps !
>> nsteps = 20000000 ; total 4ns.
>> nstcomm = 1
>> nstxout = 50000
>> nstvout = 50000
>> nstfout = 0
>> nstlog = 5000
>> nstenergy = 5000
>> nstxtcout = 25000
>> nstlist = 10
>> ns_type = grid
>> pbc = xyz
>> coulombtype = PME
>> vdwtype = Shift
>> rlist = 1.0
>> rcoulomb = 1.0
>> rvdw = 1.0
>> fourierspacing = 0.6
>>
>
> This fourierspacing is 5-6 times larger than what is normally accepted as
> sufficiently accurate. A sparse grid will make the PME algorithm faster,
> actually, but at the expense of accuracy.
>
> Can you post the domain decomposition statistics from the .log file? They
> appear just above the energies from time 0. What did grompp tell you about
> the relative PME:PP load?
>
> -Justin
>
> ;pme_order = 4
>> ewald_rtol = 1e-5
>> ; Berendsen temperature coupling is on in two groups
>> Tcoupl = berendsen
>> tc_grps = BMI PF6 tau_t = 0.1 0.1
>> ref_t = 300 300
>> nsttcouple = 1
>> ; Energy monitoring
>> energygrps = BMI PF6
>> ; Isotropic pressure coupling is now on
>> Pcoupl = berendsen
>> pcoupltype = isotropic
>> ;pc-grps = BMI PFF
>> tau_p = 1.0
>> ref_p = 1.0
>> compressibility = 4.5e-5
>>
>> ; Generate velocites is off at 300 K.
>> gen_vel = yes
>> gen_temp = 300.0
>> gen_seed = 100000
>>
>>
>> On Thu, Jan 27, 2011 at 4:12 PM, Dallas Warren <Dallas.Warren at monash.edu<mailto:
>> Dallas.Warren at monash.edu>> wrote:
>>
>> You will need to provide more details on the system. How many
>> atoms, what sort of computer system is it being run on, how many
>> nodes, copy of the mdp file etc.
>>
>>
>> Catch ya,
>>
>> Dr. Dallas Warren
>>
>> Medicinal Chemistry and Drug Action
>>
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3010
>> dallas.warren at monash.edu <mailto:dallas.warren at monash.edu>
>>
>>
>> +61 3 9903 9304
>> ---------------------------------
>> When the only tool you own is a hammer, every problem begins to
>> resemble a nail.
>>
>>
>> *From:* gmx-users-bounces at gromacs.org
>> <mailto:gmx-users-bounces at gromacs.org>
>> [mailto:gmx-users-bounces at gromacs.org
>> <mailto:gmx-users-bounces at gromacs.org>] *On Behalf Of *Denny Frost
>> *Sent:* Friday, 28 January 2011 9:34 AM
>> *To:* Discussion list for GROMACS users
>> *Subject:* [gmx-users] Slow Runs
>>
>>
>> I am taking over a project for a graduate student who did MD using
>> Gromacs 3.3.3. I now run similar simulations with Gromacs 4.5.1 and
>> find that they run only about 1/2 to 1/3 as fast as the previous
>> runs done in Gromacs 3.3.3. The runs have about the same number of
>> atoms and both use opls force fields. The mdp files is virtually
>> the same (I copied them). The only major difference is that my runs
>> have difference species and thus have different (although smaller)
>> itp files. The runs are stable and give reasonable thermodynamic
>> properties - they're just slow. Has anyone had any experience with
>> something like this?
>>
>>
>> --
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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