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).
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Received on Wed May 20 2009 - 13:17:18 PDT
