AMBER Archive (2009)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Apr 28 2009 - 17:24:12 CDT

Hi Liu,

Just to check have you applied all of the bugfixes? In particular bugfix 46?

Description: Some missing initialization statements can cause allocation
             failures on some machines when running QMMM.

If you can confirm that you have could then please send me some more details
about your machine. OS, Compiler version, MPI version etc as well as the
prmtop, inpcrd and mdin files and I'll see if I can reproduce the problem.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of liu junjun
> Sent: Tuesday, April 28, 2009 2:53 PM
> To: AMBER Mailing List
> Subject: [AMBER] parallel problem of QM/MM calculation for AMBER 9
>
> 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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