AMBER: segmentation fault of minimization

From: scopio <scopio.163.com>
Date: Tue, 30 Mar 2004 10:57:39 +0800

Dear Amber Users:

I'm using amber6 to carry out a simple minimization of Plastocyanin in
water following the tutorial at
http://amber.scripps.edu/tutorial/plastocyanin/pcy-tutorial-sh-3.html.

  From the output, it seems MAX_RSTACK should be increased. So I modified
the size.h with the follwing parameters:
-----------
#ifndef MEM_ALLOC
        parameter (MAXREA=20000000)
        parameter (MAXINT=20000000)
        parameter (MAXHOL=1000000)
        parameter (MAXPR=30000000)
#endif
        parameter (MAXDUP=1000)
        integer MAX_RSTACK,MAX_ISTACK,MAX_STACK_PTRS,MAX_HEAP_PTRS
        parameter (MAX_RSTACK=10000000)
        parameter (MAX_ISTACK=10000000)
        parameter (MAX_STACK_PTRS=100)
        parameter (MAX_HEAP_PTRS=100)
-------------
and recompiled it with g77. But I still always get segmentation fault
when I run this minimization. I think the memory should be ok, right?

Attached is the output file and any suggestions will be very appreciated!


Regards!
Liu






          -------------------------------------------------------
          Amber 6 SANDER Scripps/UCSF 1999
          -------------------------------------------------------

| Tue Mar 30 10:45:21 2004

  [-O]verwriting output

File Assignments:
|MDIN : min2.in
|MDOUT: plc.min2.out
|INPCR: plc.wat.crd
|PARM : plc.wat.top
|RESTR: plc.rst
|REFC : refc
|MDVEL: mdvel
|MDEN : mden
|MDCRD: mdcrd
|MDINF: mdinfo


 Here is the input file:

  minimization
 &cntrl
    imin=1,
    ntb=1, ntc=1,
    maxcyc=500, ntpr=25,
 &end
-------------------------------------------------------------------------------

  minimization



   1. RESOURCE USE:

 getting box info from bottom of parm
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found

   EWALD SPECIFIC INPUT:

 -------------------------------------------------
 NO EWALD INPUT FOUND: USING DEFAULTS
 -------------------------------------------------
     Largest sphere to fit in unit cell has radius = 27.984
     Calculating ew_coeff from dsum_tol,cutoff
     Box X = 58.230 Box Y = 63.857 Box Z = 55.969
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 60 NFFT2 = 64 NFFT3 = 60
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4

 NATOM = 16255 NTYPES = 19 NBONH = 15502 MBONA = 763
 NTHETH = 1628 MTHETA = 1040 NPHIH = 2933 MPHIA = 1866
 NHPARM = 0 NPARM = 0 NNB = 27809 NRES = 5039
 NBONA = 763 NTHETA = 1040 NPHIA = 1866 NUMBND = 37
 NUMANG = 74 NPTRA = 27 NATYP = 29 NPHB = 1
 IFBOX = 1 NMXRS = 22 IFCAP = 0


   EWALD MEMORY USE:

| Total heap storage needed = 997
| Adjacent nonbond minimum mask = 27809
| Max number of pointers = 25
| List build maxmask = 55618
| Maximage = 23785

   EWALD LOCMEM POINTER OFFSETS
| Real memory needed by PME = 997
| Size of EEDTABLE = 20918
| Real memory needed by EEDTABLE = 83672
| Integer memory needed by ADJ = 55618
| Integer memory used by local nonb= 875361
| Real memory used by local nonb = 266415

| MAX NONBOND PAIRS = 30000000

| Memory Use Allocated Used
| Real 20000000 1229435
| Hollerith 1000000 102571
| Integer 20000000 1225253

| Max Nonbonded Pairs:30000000

     BOX TYPE: RECTILINEAR


   2. CONTROL DATA FOR THE RUN

                                                                                

     TIMLIM= 999999. IREST = 0 IBELLY= 0
     IMIN = 1
     IPOL = 0

     NTX = 1 NTXO = 1
     IG = 71277 TEMPI = 0.00 HEAT = 0.000

     NTB = 1 BOXX = 58.230
     BOXY = 63.857 BOXZ = 55.969

     NTT = 0 TEMP0 = 300.000
     DTEMP = 0.000 TAUTP = 1.000
     VLIMIT= 0.000

     NTP = 0 PRES0 = 1.000 COMP = 44.600
     TAUP = 0.200 NPSCAL= 0

     NTCM = 0 NSCM = 9999999

     NSTLIM= 1 NTU = 1
     T = 0.000 DT = 0.00100

     NTC = 1 TOL = 0.00001 JFASTW = 0

     NTF = 1 NSNB = 25

     CUT = 8.000 SCNB = 2.000
     SCEE = 1.200 DIELC = 1.000

     NTPR = 25 NTWR = 50 NTWX = 0
     NTWV = 0 NTWE = 0 IOUTFM= 0
     NTWPRT= 0 NTWPR0= 0 NTAVE= 0

     NTR = 0 NTRX = 1
     TAUR = 0.00000 NMROPT= 0 PENCUT= 0.10000

     IVCAP = 0 MATCAP= 0 FCAP = 1.500

   OTHER DATA:

     IFCAP = 0 NATCAP= 0 CUTCAP= 0.000
     XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000

     VRAND= 0

     NATOM = 16255 NRES = 5039

     MAXCYC= 500 NCYC = 10 NTMIN = 1 DX0 = 0.010000
     DXM = 0.50000 DRMS = 0.00010

     Water definition for fast triangulated model:
     Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2

   3. ATOMIC COORDINATES AND VELOCITIES

                                                                                
 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 4931

     Sum of charges from parm topology file = -0.00000005
     Forcing neutrality...
 ---------------------------------------------------
 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 = 0.3242E-14 at 2.436720
| CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960
 ---------------------------------------------------
     Total number of mask terms = 22792
     Total number of mask terms = 45584
| Total Ewald setup time = 0.08000004
 ------------------------------------------------------------------------------



   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 3.1454E+20 4.1536E+20 5.5746E+22 N 1239

 BOND = 7024.1947 ANGLE = 954.1097 DIHED = 560.6102
 VDWAALS = ************* EEL = -54320.3184 HBOND = 0.0000
 1-4 VDW = ************* 1-4 EEL = 6912.4118 CONSTRAINT = 0.0000
MAX_RSTACK in sizes.h and recompile



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Received on Tue Mar 30 2004 - 04:53:01 PST
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