AMBER Archive (2009)

Subject: [AMBER] parallel problem of QM/MM calculation for AMBER 9

From: liu junjun (ljjlp03_at_gmail.com)
Date: Tue Apr 28 2009 - 16:53:06 CDT

Hello Everyone,
I'm trying to run semi-empirical QM/MM calculation with Sander9. To make
sure I created correct input file, I submitted the QM/MM calculation by
assigning 1 CPU. Then in the output file, the energies were printed out
every 5 steps as I defined. So I think the amber input file should be fine.
However, when I submitted the same QM/MM calculation with 2 CPU. Sander
program aborted just before "Link Atom Information" was printed out. Sounds
like a parallel problem of my Sander9 program. Anyone has an idea?

===== sander output of 2 CPU calculation ===
          -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------

| Run on 04/28/2009 at 15:58:44
  [-O]verwriting output

File Assignments:
| MDIN: min3.in

| MDOUT: min3.out

|INPCRD: min2.rst

| PARM: ap.top

|RESTRT: min3.rst

| REFC: refc

| MDVEL: mdvel

| MDEN: mden

| MDCRD: mdcrd

|MDINFO: mdinfo

|INPDIP: inpdip

|RSTDIP: rstdip

 Here is the input file:

# minimize all hydrogen

 &cntrl

 ntpr = 5,

 cut = 10.0,

 ntb = 1,

 drms=0.1

 maxcyc = 500,

 ncyc = 50,

 ntr = 0,

 ntf=1,ntc=1,

 imin = 1, ibelly=0,

 ifqnt=1

 &end

 &qmmm

 qmmask=":899-902"

 qmcharge=6

 qmtheory=1,

 qmshake=1

 qm_ewald=1

 qm_pme=1

 &end

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags: MPI

 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 = 46.261
| New format PARM file being parsed.
| Version = 1.000 Date = 03/26/09 Time = 15:51:11
 NATOM = 86948 NTYPES = 20 NBONH = 80292 MBONA = 6750
 NTHETH = 14838 MTHETA = 9172 NPHIH = 27516 MPHIA = 17998
 NHPARM = 0 NPARM = 0 NNB = 170836 NRES = 25514
 NBONA = 6750 NTHETA = 9172 NPHIA = 17998 NUMBND = 54
 NUMANG = 107 NPTRA = 47 NATYP = 38 NPHB = 1
 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 5562778
| Hollerith 547204
| Integer 2823936
| Max Pairs 25041024
| nblistReal 1043376
| nblist Int 3229991
| Total 175212 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

LOADING THE QUANTUM ATOMS AS GROUPS
     Mask :899-902; matches 21 atoms

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   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 = 5, 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 = 1, igb = 0, nsnb =
 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Energy minimization:
     maxcyc = 500, ncyc = 50, ntmin = 1
     dx0 = 0.01000, drms = 0.10000

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme =
  1
     vdwmeth = 1, eedmeth = 1, netfrc = 0
     Box X = 104.009 Box Y = 107.959 Box Z = 92.522
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 108 NFFT2 = 108 NFFT3 = 96
     Cutoff= 10.000 Tol =0.100E-04
     Ewald Coefficient = 0.27511
     Interpolation order = 4

QMMM options:
             ifqnt = True nquant = 21
              qmgb = 0 qmcharge = 6 adjust_q = 2
              spin = 1 qmcut = 10.0000 qmshake = 1
     lnk_atomic_no = 1 lnk_dis = 1.0900
          qmtheory = PM3 verbosity = 0
      tight_p_conv = False (converge density to 0.05xSqrt[SCFCRT])
           scfconv = 0.100E-07 itrmax = 1000
      printcharges = False peptide_corr = False
    qmqmrij_incore = True qmmmrij_incore = True
  qmqm_erep_incore = True
       pseudo_diag = True pseudo_diag_criteria = 0.0500
          qm_ewald = 1 qm_pme = True
            kmaxqx = 5 kmaxqy = 5 kmaxqz = 5 ksqmaxq = 27

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

 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 24594
| Atom division among processors:
| 0 43475 86948

|QMMM: Running QMMM calculation in parallel mode on 2 threads.
|QMMM: All atom division among threads:
|QMMM: Start End Count
|QMMM: Thread( 0): 1-> 43474 ( 43474)
|QMMM: Thread( 1): 43475-> 86948 ( 43474)

|QMMM: Quantum atom + link atom division among threads:
|QMMM: Start End Count
|QMMM: Thread( 0): 1-> 11 ( 11)
|QMMM: Thread( 1): 12-> 21 ( 10)

     Sum of charges from parm topology file = 0.00001955
     Forcing neutrality...
| Running AMBER/MPI version on 2 nodes

QMMM: ADJUSTING CHARGES
QMMM: ----------------------------------------------------------------------
QMMM: adjust_q = 2
QMMM: Uniformally adjusting the charge of MM atoms to conserve total charge.
QMMM: qm_charge = 6
QMMM: QM atom RESP charge sum (inc MM link) = 4.000
QMMM: Adjusting each MM atom resp charge by = 0.000
QMMM: Sum of MM + QM region is now = -6.000
QMMM: ----------------------------------------------------------------------
 ---------------------------------------------------
 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 = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 13002699
| TOTAL SIZE OF NONBOND LIST = 27119902

|QMMM: KVector division among threads:
|QMMM: Start End Count
|QMMM: Thread( 0): 1-> 155 ( 155)
|QMMM: Thread( 1): 156-> 309 ( 154)

[bcxlogin1:03913] *** Process received signal ***
[bcxlogin1:03913] Signal: Segmentation fault (11)
[bcxlogin1:03913] Signal code: Address not mapped (1)
[bcxlogin1:03913] Failing at address: 0x7effffffe0
forrtl: error (78): process killed (SIGTERM)
mpiexec noticed that job rank 0 with PID 3913 on node bcxlogin1 exited on
signal 11 (Segmentation fault).
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber