AMBER Archive (2009)

Subject: Re: [AMBER] hpux sander.serial failure info

From: Yiannis Georgiadis (giannis_at_cc.uoa.gr)
Date: Wed Apr 15 2009 - 16:41:06 CDT


Well, I send you the cytosine output test to close this thread
A simple debugging with gdb is not informative,
an indication on $$move_byte+0x40 call is referred at time of BUS error

I am getting the prize... but as your configure_amber script has a
hpf90 option .. it is not entirely mine ... :-)

Yiannis

David A. Case wrote:
> On Fri, Apr 10, 2009, Yiannis Georgiadis wrote:
>
>
>> I send you from Univ of Athens more detailed info
>> on resolving sander building failure - bus error in many situations-
>>
>
> I must say that you win the prize for the oddest mixture of PASSED and
> FAILED test results seen so far :-)
>
> You need to go into the directories where a bus error occurred, (say the
> first one, cytosine) and see if there are any clues in the output files.
>
> [One clue I see: it looks like tests that run MD give a bus error; those
> that just do minimization seem OK.]
>
> A debugging compile and run is probably going to be needed here.
>
> ...dac
>
>
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          -------------------------------------------------------
          Amber 10 SANDER 2008
          -------------------------------------------------------

| Run on 04/10/2009 at 14:26:29
  [-O]verwriting output

File Assignments:
| MDIN: in.md
| MDOUT: cytosine.out
|INPCRD: crd.md.23
| PARM: prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 Here is the input file:

 cytosine in chloroform
 &cntrl
  irest = 1, ntx = 7,
  ntb = 2, ntp = 2, taup=0.2,
  ntt = 1, tautp=0.2,
  nstlim = 10,
  dt = 0.002, nrespa=1,
  ntpr = 1, ntave=1000,
  temp0 = 300.,
  scee = 1.2,
  ntf = 2, ntc = 2, tol=0.000005,
  vlimit=15.0
 /
 &ewald
  nfft1 = 30, nfft2 = 32, nfft3 = 36,
 /

--------------------------------------------------------------------------------
   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 = 14.997
| INFO: Old style PARM file read

 NATOM = 1271 NTYPES = 11 NBONH = 258 MBONA = 762
 NTHETH = 766 MTHETA = 765 NPHIH = 20 MPHIA = 15
 NHPARM = 0 NPARM = 0 NNB = 2830 NRES = 252
 NBONA = 762 NTHETA = 765 NPHIA = 15 NUMBND = 26
 NUMANG = 52 NPTRA = 28 NATYP = 15 NPHB = 0
 IFBOX = 1 NMXRS = 16 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 144725
| Hollerith 7880
| Integer 59386
| Max Pairs 423666
| nblistReal 15252
| nblist Int 93368
| Total 3532 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

1-methyl cytosine.

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 7, irest = 1, 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 = 2, 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

Molecular dynamics:
     nstlim = 10, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00200, vlimit = 15.00000

Berendsen (weak-coupling) temperature regulation:
     temp0 = 300.00000, tempi = 0.00000, tautp = 0.20000

Pressure regulation:
     ntp = 2
     pres0 = 1.00000, comp = 44.60000, taup = 0.20000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 29.995 Box Y = 32.790 Box Z = 33.184
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 30 NFFT2 = 32 NFFT3 = 36
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

1-methyl cytosine.
 begin time read from input coords = 5420.000 ps

 Number of triangulated 3-point waters found: 0


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