AMBER Archive (2009)

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

From: liu junjun (ljjlp03_at_gmail.com)
Date: Tue Apr 28 2009 - 21:18:31 CDT

Dear Dr. Walker,
I will ask our HPC administrator to apply the bugfixes. Thank you very much!

All the best!

Liu

On Tue, Apr 28, 2009 at 6:24 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> 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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> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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