Re: [AMBER] Segmentation fault

From: Jagdeesh C <jagc666.gmail.com>
Date: Sun, 27 Jun 2010 11:31:18 +0530

I am getting the same error with ntb=1. (Segmentation fault)

When I set ntmin=1 or 2 the job terminates normally. (Output attached)


On Sun, Jun 27, 2010 at 4:23 AM, case <case.biomaps.rutgers.edu> wrote:

> On Sat, Jun 26, 2010, Jagdeesh C wrote:
> > Dear Amber Users,
> >
> > I have provided the following input for minimization. I am getting a
> > segmentation fault error. Can someone please help explain me what might
> be
> > the reason?
> >
> >
> > Many thanks,
> > Jagdeesh
> > *
> > INPUT*
> > minimize_polak
> > &cntrl
> > imin=1, ntmin=3,
> > irest=0, ntx=1,
> > maxcyc=1000,
> > cut=8.0,ntb=2,
> > ntpr=1,
> > ntp =1,
> > /
> > &lmod
> > xmin_method = "PRCG",
> > /
>
> Setting ntb=2, ntp=1 doesn't make any sense with minimization; see if
> setting
> ntb=1 helps. Let us know what happens--if this is indeed the problem, it's
> a bug we should fix.
>
> Otherwise: what happens if you set ntmin to 1 or 2?
>
> ....dac
>
> > *
> > OUTPUT*
> >
> > Segmentation fault
> > *
> > OUTPUT FILE*
> >
> > File Assignments:
> > | MDIN: minx_02.in
> >
> > | MDOUT:
> > minx2_143d.out
> > |INPCRD:
> > min_143dx.rst
> > | PARM:
> > 143d_sol.prmtop
> > |RESTRT:
> > min_143dx2.rst
> > | REFC:
> > min_143dx.rst
> > | MDVEL:
> > mdvel
> > | MDEN:
> > mden
> > | MDCRD:
> > mdcrd
> > |MDINFO:
> > mdinfo
> > |INPDIP:
> > inpdip
> > |RSTDIP:
> > rstdip
> >
> > |INPTRA:
> > inptraj
> > |
> >
> > Here is the input file:
> >
> > polak
> >
> > &cntrl
> >
> > imin=1,
> > ntmin=3,
> > irest=0,
> > ntx=1,
> > maxcyc=1000,
> >
> > cut=8.0,ntb=2,
> >
> > ntpr=1,
> >
> > ntp
> > =1,
> > /
> >
> > &lmod
> >
> > xmin_method =
> > "PRCG",
> > /
> >
> >
> >
> --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> >
> --------------------------------------------------------------------------------
> >
> > |
> > Flags:
> >
> > getting new box info from bottom of inpcrd
> > | INFO: Old style inpcrd file read
> >
> > | peek_ewald_inpcrd: Box info found
> > |Largest sphere to fit in unit cell has radius = 23.842
> > | New format PARM file being parsed.
> > | Version = 1.000 Date = 06/01/10 Time = 11:08:47
> > NATOM = 12646 NTYPES = 17 NBONH = 12160 MBONA = 524
> > NTHETH = 592 MTHETA = 812 NPHIH = 1260 MPHIA = 1431
> > NHPARM = 0 NPARM = 0 NNB = 19884 NRES = 4013
> > NBONA = 524 NTHETA = 812 NPHIA = 1431 NUMBND = 36
> > NUMANG = 68 NPTRA = 41 NATYP = 27 NPHB = 1
> > IFBOX = 2 NMXRS = 34 IFCAP = 0 NEXTRA = 0
> > NCOPY = 0
> >
> >
> > | Memory Use Allocated
> > | Real 843928
> > | Hollerith 79891
> > | Integer 347428
> > | Max Pairs 4215333
> > | nblistReal 151752
> > | nblist Int 543090
> > | Total 28035 kbytes
> > | Duplicated 0 dihedrals
> > | Duplicated 0 dihedrals
> >
> > BOX TYPE: TRUNCATED OCTAHEDRON
> >
> >
> --------------------------------------------------------------------------------
> > 2. CONTROL DATA FOR THE RUN
> >
> --------------------------------------------------------------------------------
> >
> >
> >
> >
> > General flags:
> > imin = 1, nmropt = 0
> >
> > Nature and format of input:
> > ntx = 1, irest = 0, ntrx = 1
> >
> > Nature and format of output:
> > ntxo = 1, ntpr = 1, ntrx = 1, ntwr =
> > 500
> > iwrap = 0, ntwx = 0, ntwv = 0, ntwe
> > = 0
> > ioutfm = 0, ntwprt = 0, idecomp = 0,
> > rbornstat= 0
> >
> > Potential function:
> > ntf = 1, ntb = 2, igb = 0, nsnb =
> > 25
> > ipol = 0, gbsa = 0, iesp = 0
> > dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
> > scnb = 2.00000, scee = 1.20000
> >
> > Frozen or restrained atoms:
> > ibelly = 0, ntr = 0
> >
> > Energy minimization:
> > maxcyc = 1000, ncyc = 10, ntmin = 3
> > dx0 = 0.01000, drms = 0.00010
> >
> > LMOD:
> > xmin_method = PRCG
> > matrix_vector_product_method = forward finite difference
> > xmin_verbosity = 0
> >
> > Ewald parameters:
> > verbose = 0, ew_type = 0, nbflag = 1, use_pme
> > = 1
> > vdwmeth = 1, eedmeth = 1, netfrc = 0
> > Box X = 58.401 Box Y = 58.401 Box Z = 58.401
> > Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> > NFFT1 = 60 NFFT2 = 60 NFFT3 = 60
> > Cutoff= 8.000 Tol =0.100E-04
> > Ewald Coefficient = 0.34864
> > Interpolation order = 4
> >
> >
> --------------------------------------------------------------------------------
> > 3. ATOMIC COORDINATES AND VELOCITIES
> >
> --------------------------------------------------------------------------------
> >
> >
> >
> > begin time read from input coords = 0.000 ps
> >
> > Number of triangulated 3-point waters found: 3970
> >
> > Sum of charges from parm topology file = 0.00000006
> > Forcing neutrality...
> >
> >
> --------------------------------------------------------------------------------
> > 4. RESULTS
> >
> --------------------------------------------------------------------------------
> >
> > LMOD XMIN Minimization.
> > ---------------------------------------------------
> > APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> > using 5000.0 points per unit in tabled values
> > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> > | CHECK switch(x): max rel err = 0.3140E-14 at 2.473100
> > | CHECK d/dx switch(x): max rel err = 0.8129E-11 at 2.782960
> > ---------------------------------------------------
> > | Local SIZE OF NONBOND LIST = 2193879
> > | TOTAL SIZE OF NONBOND LIST = 2193879
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 -3.8657E+04 0.0000E+00 3.9990E+01 O 4625
> >
> > BOND = 32.6084 ANGLE = 194.8141 DIHED =
> > 419.5199
> > VDWAALS = 1860.6096 EEL = -39348.9396 HBOND =
> > 0.0000
> > 1-4 VDW = 174.0771 1-4 EEL = -1989.1934 RESTRAINT =
> > 0.0000
> > (END)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
>
> ================================================================
> David A. Case | email:
> BioMaPS Institute and Dept. of | case.biomaps.rutgers.edu
> Chemistry & Chemical Biology | fax: +1-732-445-5958
> Rutgers University | phone: +1-732-445-5885
> 610 Taylor Rd. |
> Piscataway, NJ 08854-8087 USA | http://casegroup.rutgers.edu
> ================================================================
>
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Received on Sat Jun 26 2010 - 23:30:03 PDT
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