[gmx-users] GPU crashes

Thu Jun 7 09:57:38 CEST 2012

Did you play with the time step?  Just currious, but I woundered what happened with 0.0008, 0.0005, 0.0002.  I found if I had a good behaving protein, as soon as I added a small (non-protein) molecule which rotated wildly while attached to the protein, it would crash unless I reduced the time step to the above when constraints were removed after EQ ... always it seemed to me it didnt like the rotation or bond angles, seeing them as a violation but acted like it was an amino acid? (the same bond type but with wider rotation as one end wasnt fixed to a chain)  If your loop moves via backbone, the calculated angles, bonds or whatever might appear to the computer to be violating the parameter settings for problems, errors, etc as it cant track them fast enough over the time step. Ie atom 1-2-3 and then delta 1-2-3 with xyz parameters, but then the particular set has additional rotation, etc and may include the chain atoms which bend wildly (n-Ca-Cb-Cg maybe a dihedral) but probab
 ly not this. 

Just a thought but probably not the right answere as well, it might be the way it is broken down (above) over GPUs, which convert everything to matricies (non-standard just for basic math operations not real matricies per say) for exicution and then some library problem which would not account for long range rapid (0.0005) movements at the chain (Ca,N,O to something else) and then tries to apply these to Cb-Cg-O-H, etc using the initial points while looking at the parameters for say a single amino acid...Maybe the constraints would cause this, which would make it a pain to EQ, but this allowed me to increase the time step, but would ruin the experiment I had worked on as I needed it unconstrained to show it didnt float away when proteins were pulled, etc...I was using a different integrator though...just normal MD.  

ANd your cutoffs for vdw, etc...Why are they 0?  I dont know if this means a defautl set is then used...but if not ?  Wouldnt they try integrating using both types of formula, or would it be just using coulumb or vice versa? (dont know what that would do to the code but assume it means no vdw, and all coulumb but then zeros are alwyas a problem for computers).  

Thats my thoughts on that.  Probably something else though.

Good luck,

Stephan

-------- Original-Nachricht --------
> Datum: Wed, 06 Jun 2012 18:42:45 -0400
> Von: "Justin A. Lemkul" <jalemkul at vt.edu>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: [gmx-users] GPU crashes

> 
> Hi All,
> 
> I'm wondering if anyone has experienced what I'm seeing with Gromacs 4.5.5
> on 
> GPU.  It seems that certain systems fail inexplicably.  The system I am
> working 
> with is a heterodimeric protein complex bound to DNA.  After about 1 ns of
> simulation time using mdrun-gpu, all the energies become NaN.  The
> simulations 
> don't stop, they just carry on merrily producing nonsense.  I would love
> to see 
> some action regarding http://redmine.gromacs.org/issues/941 for this
> reason ;)
> 
> I ran simulations of each of the components of the system individually -
> each 
> protein alone, and DNA - to try to track down what might be causing this 
> problem.  The DNA simulation is perfectly stable out to 10 ns, but each
> protein 
> fails within 2 ns.  Each protein has two domains with a flexible linker,
> and it 
> seems that as soon as the linker flexes a bit, the simulations go poof. 
> Well-behaved proteins like lysozyme and DHFR (from the benchmark set) seem
> fine, 
> but anything that twitches even a small amount fails.  This is very
> unfortunate 
> for us, as we are hoping to see domain motions on a feasible time scale
> using 
> implicit solvent on GPU hardware.
> 
> Has anyone seen anything like this?  Our Gromacs implementation is being
> run on 
> an x86_64 Linux system with Tesla S2050 GPU cards.  The CUDA version is
> 3.1 and 
> Gromacs is linked against OpenMM-2.0.  An .mdp file is appended below.  I
> have 
> also tested finite values for cutoffs, but the results were worse
> (failures 
> occurred more quickly).
> 
> I have not been able to use the latest git version of Gromacs to test
> whether 
> anything has been fixed, but will post separately to gmx-developers
> regarding 
> the reasons for that soon.
> 
> -Justin
> 
> === md.mdp ===
> 
> title           = Implicit solvent test
> ; Run parameters
> integrator      = sd
> dt                  = 0.002
> nsteps          = 5000000   ; 10000 ps (10 ns)
> nstcomm         = 1
> comm_mode   = angular       ; non-periodic system
> ; Output parameters
> nstxout         = 0
> nstvout         = 0
> nstfout         = 0
> nstxtcout   = 1000          ; every 2 ps
> nstlog      = 5000          ; every 10 ps
> nstenergy   = 1000          ; every 2 ps
> ; Bond parameters
> constraint_algorithm    = lincs
> constraints             = all-bonds
> continuation    = no            ; starting up
> ; required cutoffs for implicit
> nstlist         = 0
> ns_type         = grid
> rlist           = 0
> rcoulomb        = 0
> rvdw            = 0
> ; cutoffs required for qq and vdw
> coulombtype     = cut-off
> vdwtype     = cut-off
> ; temperature coupling
> tc_grps         = System
> tau_t           = 1.0   ; inverse friction coefficient for Langevin
> (ps^-1)
> ref_t           = 310
> ; Pressure coupling is off
> Pcoupl          = no
> ; Generate velocities is on
> gen_vel         = yes
> gen_temp        = 310
> gen_seed        = 173529
> ; Periodic boundary conditions are off for implicit
> pbc                 = no
> ; Free energy must be off to use all-vs-all kernels
> free_energy = no    ; default, but just for the sake of being pedantic
> ; Implicit
> implicit_solvent    = GBSA
> gb_algorithm        = OBC
> rgbradii            = 0
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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