[gmx-users] Re: gromacs 4.6 GB/SA problem and poor performance

[Mark Abraham]

Hi,

Thanks for your reports so far, but it is difficult to follow whether you
are reporting a performance or correctness issue when the topic of the
email and the test system keeps changing.

We know GB on CPU is slow in 4.6 - we plan to fix this in the coming week
or two

We will be much more interested in investigating reports of problems with
4.5.5 or 4.5.6, not 4.5.3. Our resources are limited, and they're not well
spent investigating whether code that is several years old has problems
that have been fixed since then.

We will be much more interested in investigating reports of problems with
recent compilers (e.g. icc 12 or newer, as recommended here
http://www.gromacs.org/Documentation/Installation_Instructions). You need
the latest compilers to do a good job compiling GROMACS 4.6. We suspect icc
11 on at least some hardware does not compile 4.6 correctly, and 4.6.1 will
warn about this.

We need a .tpr file in order to reproduce a crash so we can see whether
something is wrong, and if so, where. Please file an issue at
http://redmine.gromacs.org/ and attach at least a .tpr and as much
information as you can about your machine, compiler and simulation system.

Thanks!

Mark

On Tue, Jan 22, 2013 at 4:26 AM, Changwon Yang <sht_ycw79 at hotmail.com>wrote:

> Input files: conf.gro and mdp files
>
>
> http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM
>
> cpu-imp-RF-inf.mdp
>
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  0
> nstlist             =  0
> ns_type             =  grid
> rlist               =  0
> coulombtype         =  cut-off
> vdwtype             =  cut-off
> rcoulomb            =  0
> rvdw                =  0
> pbc                 =  no
> epsilon_rf          =  0
> rgbradii            =  0
> comm_mode           =  angular
>
> implicit_solvent    = GBSA
> gb_algorithm        = OBC
> gb_epsilon_solvent  = 78.3
> sa_surface_tension  = 2.25936
>
> nstxout             = 0
> nstfout             = 0
> nstvout             = 0
> nstxtcout           = 50
> nstlog              = 0
> nstcalcenergy       = -1
> nstenergy           = 50
>
> tcoupl              = berendsen
> tc-grps             = system
> tau-t               = 0.1
> ref-t               = 300
>
>
> gromacs 4.6 (icc 11.0, centos 5.8, fftw 3.2.2)
>
> Statistics over 101 steps [ 0.0000 through 0.2000 ps ], 10 data sets
> All statistics are over 11 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>
> -------------------------------------------------------------------------------
> Angle                       4189.86         --    1094.25    2527.08
> (kJ/mol)
> Proper Dih.                 6600.66         --    234.905    471.156
> (kJ/mol)
> Improper Dih.               121.598         --    32.7574     64.572
> (kJ/mol)
> GB Polarization            -32708.8         --    1979.66   -6416.79
> (kJ/mol)
> Nonpolar Sol.               158.323         --    13.0032     42.232
> (kJ/mol)
> LJ-14                       2346.66         --    180.767    289.567
> (kJ/mol)
> Coulomb-14                  26555.4         --    1091.98   -3000.88
> (kJ/mol)
> LJ (SR)                           0         --          0          0
> (kJ/mol)
> Coulomb (SR)                      0         --          0          0
> (kJ/mol)
> Potential                   7263.71         --    1835.42   -6023.06
> (kJ/mol)
>
> gromacs 4.5.3
>
> Statistics over 101 steps [ 0.0000 through 0.2000 ps ], 10 data sets
> All statistics are over 11 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>
> -------------------------------------------------------------------------------
> Angle                       1840.12         --    178.343    561.256
> (kJ/mol)
> Proper Dih.                    6207         --    101.135    210.593
> (kJ/mol)
> Improper Dih.               68.4513         --    11.6214    29.5806
> (kJ/mol)
> GB Polarization            -13534.1         --    34.3666    95.8711
> (kJ/mol)
> Nonpolar Sol.               143.048         --    1.55868    5.13589
> (kJ/mol)
> LJ-14                       2380.44         --    26.9563    24.6177
> (kJ/mol)
> Coulomb-14                  29155.5         --    64.9054   -176.267
> (kJ/mol)
> LJ (SR)                    -5274.28         --    214.048    650.865
> (kJ/mol)
> Coulomb (SR)               -38297.8         --    143.656   -398.004
> (kJ/mol)
> Potential                  -17311.7         --    451.581    1003.65
> (kJ/mol)
>
>
> In gromacs 4.5.3 GB/SA problem
>
> Starting from fully linear peptide and using inf cut-off, I always get the
> segmentation fault error.
> Using finite cut-off, It works fine.
>
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/gromacs-4-6-GB-SA-problem-and-poor-performance-tp5004729p5004778.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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