[gmx-users] strange lincs warning with version 4.6

sebastian sebastian.waltz at physik.uni-freiburg.de
Wed Dec 5 10:14:01 CET 2012


On 12/04/2012 07:56 PM, Szilárd Páll wrote:
> On Tue, Dec 4, 2012 at 5:09 PM, Mark Abraham<mark.j.abraham at gmail.com>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.
>>
>> Also, if you ran your CPU-only calculations with nstlist=25 then AFAIK this
>> works fine, but is inefficient.
>>
>>      
> With the verlet scheme when running on GPUs and/or at high parallelization
> nstlist = 25, even up to 50 can give higher performance (and this is safe
> to do because the buffer is automatically adjusted).
>
> --
> Szilárd
>
>
>    
>> Mark
>>
>> On Tue, Dec 4, 2012 at 3:41 PM, sebastian<
>> 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-**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>)
>>      
>>>> to see if at least the tests pass with the
>>>> binaries you compiled
>>>> Cheers,
>>>>          

The test of the nbnxn_pme setup breaks as well after 50 steps (I 
extended the run using tpbconv) with the same lincs warning. (log attached)


>>>> --
>>>> 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
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<
>>>>>            
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>      
>>>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<
>>>>>            
>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>      
>>>>>>              
>>>>> * Please search the archive at http://www.gromacs.org/**
>>>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
>>>>> Mailing_Lists/Search<
>>>>>            
>> http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>>      
>>>>> posting!
>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>> * Can't post? Read http://www.gromacs.org/****Support/Mailing_Lists<
>>>>>            
>> http://www.gromacs.org/**Support/Mailing_Lists>
>>      
>>>>> <http://**www.gromacs.org/Support/**Mailing_Lists<
>>>>>            
>> http://www.gromacs.org/Support/Mailing_Lists>
>>      
>>>>>>              
>>>>>
>>>>>
>>>>>            
>>>>          
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>>>        
>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>      
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<
>>>        
>> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>      
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
>>>        
>> http://www.gromacs.org/Support/Mailing_Lists>
>>      
>>>        
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>      



More information about the gromacs.org_gmx-users mailing list