[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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