[gmx-users] strange lincs warning with version 4.6
Mark Abraham
mark.j.abraham at gmail.com
Tue Dec 4 18:16:18 CET 2012
I can't know why you observe things working, in part because you haven't
said what's in this system :-) Pure inflexible water would be fine because
the constraints setting doesn't matter to water.
Moreover, whether integration issues cause things to crash can depend on
non-reproducible numerical effects, and the phase of the moon when you
compiled can determine that. You may well have a real problem with GROMACS
on GPUs that might be a GROMACS bug, but at the moment we can't be sure of
that because of this other issue.
You claim your settings are "rather typical." They are, except that
constraints = hbonds and a 2fs time step are inconsistent because of the
typical time scale of the vibration of the bonds between heavy atoms. This
has been a frequent topic of conversation on this list, despite being
knowledge at least a decade old - e.g. ref 118 of GROMACS manual, Feenstra
et al.
Mark
On Tue, Dec 4, 2012 at 5:30 PM, sebastian <
sebastian.waltz at physik.uni-freiburg.de> wrote:
> On 12/04/2012 05:09 PM, Mark Abraham wrote:
>
>> 2fs is normally considered too large a time step for stable integration
>> with only bonds to hydrogen constrained, so your observation of
>> non-reproducible LINCS warnings is not indicative of some other problem.
>>
>>
>
> Sorry, but why is this whole setup running on my local desktop with GPUs?
> As far as I know this is a rather typical set of parameters.
> The only difference what I can think of is that gromacs was compiled with
> intel and mkl libs on the cluster there as it was compiled with gcc and
> fftw3 libs on the local desktop.
>
> Sebastian
>
> Also, if you ran your CPU-only calculations with nstlist=25 then AFAIK
>> this
>> works fine, but is inefficient.
>>
>> Mark
>>
>> On Tue, Dec 4, 2012 at 3:41 PM, sebastian<
>> sebastian.waltz at physik.uni-**freiburg.de<sebastian.waltz at physik.uni-freiburg.de>>
>> wrote:
>>
>>
>>
>>> On 11/23/2012 08:29 PM, Szilárd Páll wrote:
>>>
>>>
>>>
>>>> Hi,
>>>>
>>>> On Fri, Nov 23, 2012 at 9:40 AM, sebastian<
>>>> sebastian.waltz at physik.uni-**f**reiburg.de <http://freiburg.de><
>>>> sebastian.waltz@**physik.uni-freiburg.de<sebastian.waltz at physik.uni-freiburg.de>
>>>> >>
>>>>
>>>> wrote:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> Dear GROMCS user,
>>>>>
>>>>> I installed the git gromacs VERSION 4.6-dev-20121117-7a330e6-dirty on
>>>>> my
>>>>> local desktop
>>>>>
>>>>>
>>>>>
>>>>>
>>>> Watch out, the dirty version suffix means you have changed something in
>>>> the
>>>> source.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> (2*GTX 670 + i7) and everything works as smooth as possible. The
>>>>> outcomes
>>>>> are very reasonable and match the outcome of the 4.5.5 version without
>>>>> GPU
>>>>> acceleration. On our
>>>>>
>>>>>
>>>>>
>>>>>
>>>> What does "outcome" mean? If that means performance, than something is
>>>> wrong, you should see a considerable performance increase (PME,
>>>> non-bonded,
>>>> bondeds have all gotten a lot faster).
>>>>
>>>>
>>>>
>>>>
>>>>
>>> With outcome I mean the trajectory not the performance.
>>>
>>>
>>>
>>>
>>>
>>>>
>>>>
>>>>> cluster (M2090+2*Xeon X5650) I installed the VERSION
>>>>> 4.6-dev-20121120-0290409. Using the same .tpr file used for runs with
>>>>> my
>>>>> desktop I get lincs warnings that the watermolecules can't be settled.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>> The group kernels have not "stabilized" yet and there have been some
>>>> fixes
>>>> lately. Could you please the latest version and check again.
>>>>
>>>>
>>>>
>>>>
>>> I installed the beta1 release and still the water can not be settled.
>>>
>>> Additionally, you could try running our regression tests suite (
>>>
>>>
>>>> git.gromacs.org/****regressiontests<http://git.gromacs.org/**regressiontests>
>>>> <http://git.**gromacs.org/regressiontests<http://git.gromacs.org/regressiontests>
>>>> >)
>>>>
>>>> to see if at least the tests pass with the
>>>> binaries you compiled
>>>> Cheers,
>>>> --
>>>> Szilárd
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>> Cheers,
>>>
>>> Sebastian
>>>
>>>
>>> My .mdp file looks like:
>>>
>>>
>>>> ;
>>>>> title = ttt
>>>>> cpp = /lib/cpp
>>>>> include = -I../top
>>>>> constraints = hbonds
>>>>> integrator = md
>>>>> cutoff-scheme = verlet
>>>>>
>>>>> ;define = -DPOSRES ; for possition restraints
>>>>>
>>>>> dt = 0.002 ; ps !
>>>>> nsteps = 100000000 \
>>>>> nstcomm = 25 ; frequency for center of mass
>>>>> motion
>>>>> removal
>>>>> nstcalcenergy = 25
>>>>> nstxout = 100000 ; frequency for writting the
>>>>> trajectory
>>>>> nstvout = 100000 ; frequency for writting the
>>>>> velocity
>>>>> nstfout = 100000 ; frequency to write forces to
>>>>> output trajectory
>>>>> nstlog = 10000 ; frequency to write the log
>>>>> file
>>>>> nstenergy = 10000 ; frequency to write energies
>>>>> to
>>>>> energy file
>>>>> nstxtcout = 10000
>>>>>
>>>>> xtc_grps = System
>>>>>
>>>>> nstlist = 25 ; Frequency to update the neighbor
>>>>> list
>>>>> ns_type = grid ; Make a grid in the box and
>>>>> only
>>>>> check atoms in neighboring grid cells when constructing a new neighbor
>>>>> rlist = 1.4 ; cut-off distance for the
>>>>> short-range neighbor list
>>>>>
>>>>> coulombtype = PME ; Fast Particle-Mesh Ewald
>>>>> electrostatics
>>>>> rcoulomb = 1.4 ; cut-off distance for the
>>>>> coulomb
>>>>> field
>>>>> vdwtype = cut-off
>>>>> rvdw = 1.4 ; cut-off distance for the vdw
>>>>> field
>>>>> fourierspacing = 0.12 ; The maximum grid spacing for
>>>>> the
>>>>> FFT grid
>>>>> pme_order = 6 ; Interpolation order for PME
>>>>> optimize_fft = yes
>>>>> pbc = xyz
>>>>> Tcoupl = v-rescale
>>>>> tc-grps = System
>>>>> tau_t = 0.1
>>>>> ref_t = 300
>>>>>
>>>>> energygrps = Protein Non-Protein
>>>>>
>>>>> Pcoupl = no;berendsen
>>>>> tau_p = 0.1
>>>>> compressibility = 4.5e-5
>>>>> ref_p = 1.0
>>>>> nstpcouple = 5
>>>>> refcoord_scaling = all
>>>>> Pcoupltype = isotropic
>>>>> gen_vel = no;yes
>>>>> gen_temp = 300
>>>>> gen_seed = -1
>>>>>
>>>>>
>>>>> Thanks a lot
>>>>>
>>>>> Sebastian
>>>>> --
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>>>>>
>>>>>>
>>>>>>
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