AMBER Archive (2008)

Subject: RE: AMBER: AMBER10: QMMM parallel test error

From: Yang, Ping (Ping.Yang_at_pnl.gov)
Date: Wed Nov 05 2008 - 21:57:29 CST

Hi Ross,

thank you very much for your kind help. I answer your questions one by one as follows. Please let me know if any clarification is needed.

-Ping

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of Ross Walker
Sent: Wed 11/5/2008 5:41 PM
To: amber_at_scripps.edu
Subject: RE: AMBER: AMBER10: QMMM parallel test error
 
Hi Yang,

Can you give me some more info here please. What version of mvapich are you
using? What compilers and which versions? What options did you pass to
configure_amber?
mvapich: mvapich2/1.0.3-1
Compiler: intel/10.1.015
options: mostly use the default generated by configure_amber. I did modify the LOADLIB to make sure the library can be found:
                 LOADLIB=-L/hptc_cluster/apps/libraries/intel/mkl/10.0.011/lib/em64t -lmkl_solver_lp64
                 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_cdft_core -lmkl_vml_def -lguide
                  -lpthread -lm -L/usr/lib64 -libverbs.so

Also are you using MKL? If so then which version (exactly) is it?
Yes. mkl/10.0.011

Could you also please go into the test/qmmm2/1NLN_test_diagonalizers
directory and send me the output file / partial output file produced by the
Run.1NLN_dsyevr script.

I copied the whole output file here. There is nothing in "4. RESULTS".

          -------------------------------------------------------
          Amber 10 SANDER 2008
          -------------------------------------------------------

| Run on 11/05/2008 at 15:33:43
  [-O]verwriting output

File Assignments:
| MDIN: mdin
| MDOUT: mdout.1NLN_dsyevr
|INPCRD: 1NLN_15A_solv_min.rst
| PARM: 1NLN_15A_solv.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

|INPTRA: inptraj
|
 
 Here is the input file:
 
MD of 1NLN const volume - QM atoms + 3 link atoms periodic
 &cntrl
  imin=0, irest=0, ntx=1,
  nstlim=4,dt=0.002,
  temp0=300.0,tempi=300.0,
  ntc=2, ntf=2,
  ntb=1,
  cut=8.0,
  ntt=1,
  ntpr=1,
  ifqnt=1
 /
 &ewald use_pme=1 /
 &qmmm
        iqmatoms=1585,1586,1587,1588,1589,1590,
        1591,1592,1593,1594,1595,1596,1597,1598,1599,1600,1601,1602,
        1603,1604,1605,1606,1607,1608,1609,1610,1611,1612,1613,1614,
        1615,1616,1617,1618,
        3348,3349,3350,3351,3352,3353,3354,3355,
        3356,3357,3358,3359,3360,3361,3362,3363,3364,3365,3366,3367,
        3368,3369,3370,3371,3372,3373,3374,3375,3376,
        qm_theory='AM1', qmcharge=0,
        verbosity=0, qmshake=1,
        qmcut=8.0, qm_ewald=1, qm_pme=1,
        verbosity=0,writepdb=0,adjust_q=2, diag_routine=7,
 /

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

| Flags: MPI USE_MPI_IN_PLACE
 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 = 37.070
| New format PARM file being parsed.
| Version = 1.000 Date = 08/11/05 Time = 13:05:27
 NATOM = 41778 NTYPES = 17 NBONH = 40054 MBONA = 1754
 NTHETH = 3777 MTHETA = 2371 NPHIH = 7196 MPHIA = 4409
 NHPARM = 0 NPARM = 0 NNB = 69799 NRES = 13026
 NBONA = 1754 NTHETA = 2371 NPHIA = 4409 NUMBND = 42
 NUMANG = 89 NPTRA = 39 NATYP = 30 NPHB = 1
 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 2216252
| Hollerith 263696
| Integer 1160650
| Max Pairs 3481500
| nblistReal 501336
| nblist Int 1871590
| Total 47705 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500
     iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

Potential function:
     ntf = 2, ntb = 1, igb = 0, nsnb = 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

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

Molecular dynamics:
     nstlim = 4, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00200, vlimit = 20.00000

Berendsen (weak-coupling) temperature regulation:
     temp0 = 300.00000, tempi = 300.00000, tautp = 1.00000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 74.141 Box Y = 77.969 Box Z = 88.178
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 80 NFFT2 = 80 NFFT3 = 90
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4

QMMM options:
             ifqnt = True nquant = 63
              qmgb = 0 qmcharge = 0 adjust_q = 2
              spin = 1 qmcut = 8.0000 qmshake = 1
     lnk_atomic_no = 1 lnk_dis = 1.0900 qmmm_int = 1
          qm_theory = AM1 verbosity = 0
            qmqmdx = Analytical
      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
      diag_routine = 7
          qm_ewald = 1 qm_pme = True
            kmaxqx = 5 kmaxqy = 5 kmaxqz = 5 ksqmaxq = 27

| MPI Timing options:
| profile_mpi = 0

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

                                                                                
 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 12795
| Atom division among processors:
| 0 10446 20889 31332 41778

|QMMM: Running QMMM calculation in parallel mode on 4 threads.
|QMMM: All atom division among threads:
|QMMM: Start End Count
|QMMM: Thread( 0): 1-> 10445 ( 10445)
|QMMM: Thread( 1): 10446-> 20890 ( 10445)
|QMMM: Thread( 2): 20891-> 31335 ( 10445)
|QMMM: Thread( 3): 31336-> 41778 ( 10443)

|QMMM: Quantum atom + link atom division among threads:
|QMMM: Start End Count
|QMMM: Thread( 0): 1-> 16 ( 16)
|QMMM: Thread( 1): 17-> 32 ( 16)
|QMMM: Thread( 2): 33-> 48 ( 16)
|QMMM: Thread( 3): 49-> 66 ( 18)

     Sum of charges from parm topology file = -0.00000011
     Forcing neutrality...
| Running AMBER/MPI version on 4 nodes

QMMM: ADJUSTING CHARGES
QMMM: ----------------------------------------------------------------------
QMMM: adjust_q = 2
QMMM: Uniformally adjusting the charge of MM atoms to conserve total charge.
QMMM: qm_charge = 0
QMMM: QM atom RESP charge sum (inc MM link) = -0.750
QMMM: Adjusting each MM atom resp charge by = 0.000
QMMM: Sum of MM + QM region is now = 0.000
QMMM: ----------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 85280.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 85277. NUM_NOSHAKE = 0 CORRECTED RNDFP = 85277.
| TOTAL # of degrees of freedom (RNDF) = 85277.
 ---------------------------------------------------
 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 = 0.8332E-11 at 2.782960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1932382
| TOTAL SIZE OF NONBOND LIST = 7346286

|QMMM: KVector division among threads:
|QMMM: Start End Count
|QMMM: Thread( 0): 1-> 78 ( 78)
|QMMM: Thread( 1): 79-> 156 ( 78)
|QMMM: Thread( 2): 157-> 234 ( 78)
|QMMM: Thread( 3): 235-> 309 ( 75)

QMMM: Link Atom Information
QMMM: ------------------------------------------------------------------------
QMMM: nlink = 3 Link Coords Resp Charges
QMMM: MM(typ) - QM(typ) X Y Z MM QM
QMMM: 1583 N 1585 CT 0.111 2.087 -2.877 -0.348 -0.264
QMMM: 1619 CT 1617 N 0.523 4.461 3.808 -0.060 -0.416
QMMM: 3346 N 3348 CT 1.878 -1.357 3.594 -0.416 0.043
QMMM: ------------------------------------------------------------------------

--------------------------------------------------------------------------------
  3.1 QM CALCULATION INFO
--------------------------------------------------------------------------------

QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 94

| QMMM: Parameter sets in use:
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990)
 
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is disabled.
| QMMM: Using dsyevr routine (diag_routine=7).

| QMMM: Estimated QM Dynamic Memory Usage (per thread)
| QMMM: ---------------------------------------------------
| QMMM: QM Atom Type Info : 1216 bytes
| QMMM: QM RESP Charge Storage : 504 bytes
| QMMM: QM Atom Number List : 264 bytes
| QMMM: Link Atom Pairs : 120 bytes
| QMMM: QM Atomic Number List : 264 bytes
| QMMM: QM-MM Pair List : 166864 bytes
| QMMM: QM Atom Mask : 83556 bytes
| QMMM: QM Coordinate Arrays : 1338480 bytes
| QMMM: Scaled MM Charge Array : 334224 bytes
| QMMM: SCF Mulliken Charge Storage : 528 bytes
| QMMM: QM Ewald Arrays : 252528 bytes
| QMMM: QM Force Arrays : 1004256 bytes
| QMMM: Density Matrix : 113568 bytes
| QMMM: Density Matrix Copies : 114912 bytes
| QMMM: Fock2 Density Matrix Workspace : 8448 bytes
| QMMM: Fock Matrix : 113568 bytes
| QMMM: Eigen Vector Storage : 225792 bytes
| QMMM: QM-QM Elec Repulsion Integrals : 94512 bytes
| QMMM: QM 2-Elec Repulsion Integrals : 539808 bytes
| QMMM: 1-Electron Matrix : 113568 bytes
| QMMM: _REAL_ parameter storage : 108744 bytes
| QMMM: integer parameter storage : 2136 bytes
| QMMM: QM-QM RIJ Eqns storage : 30072 bytes
| QMMM: QM-MM RIJ Eqns storage : 929016 bytes
| QMMM: _REAL_ Scratch arrays : 1897632 bytes
| QMMM: Integer Scratch arrays : 565576 bytes
| QMMM: ---------------------------------------------------
| QMMM: Total Dynamic Memory Usage: 7.668 Mb

  QMMM: QM Region Cartesian Coordinates (*=link atom)
  QMMM: QM_NO. MM_NO. ATOM X Y Z
  QMMM: 1 1585 C -0.4720 1.4342 -2.2276
  QMMM: 2 1586 H -1.4629 1.8810 -2.1467
  QMMM: 3 1587 C -0.6276 0.0568 -2.8060
  QMMM: 4 1588 H 0.3408 -0.4424 -2.8394
  QMMM: 5 1589 H -1.2406 -0.5222 -2.1152
  QMMM: 6 1590 C -1.2833 -0.0146 -4.1516
  QMMM: 7 1591 H -2.3377 0.2568 -4.0994
  QMMM: 8 1592 H -0.8088 0.6881 -4.8365
  QMMM: 9 1593 C -1.1493 -1.3839 -4.7876
  QMMM: 10 1594 H -1.5525 -1.3386 -5.7993
  QMMM: 11 1595 H -0.0837 -1.5699 -4.9219
  QMMM: 12 1596 N -1.6677 -2.4993 -4.0582
  QMMM: 13 1597 H -1.1086 -2.7427 -3.2530
  QMMM: 14 1598 C -2.7942 -3.2234 -4.3521
  QMMM: 15 1599 N -3.5952 -2.9371 -5.4417
  QMMM: 16 1600 H -3.3724 -2.1734 -6.0640
  QMMM: 17 1601 H -4.4054 -3.5136 -5.6188
  QMMM: 18 1602 N -3.1072 -4.2976 -3.5389
  QMMM: 19 1603 H -2.5004 -4.4856 -2.7537
  QMMM: 20 1604 H -3.9324 -4.8610 -3.6859
  QMMM: 21 1605 C 0.0344 1.4060 -0.7793
  QMMM: 22 1606 O -0.2727 0.4854 0.0257
  QMMM: 23 1607 N 0.7707 2.5003 -0.3442
  QMMM: 24 1608 H 1.0601 3.2134 -0.9983
  QMMM: 25 1609 C 1.3612 2.5218 0.9566
  QMMM: 26 1610 H 1.0008 1.6566 1.5131
  QMMM: 27 1611 C 2.8871 2.3990 1.0078
  QMMM: 28 1612 H 3.2241 3.2554 0.4237
  QMMM: 29 1613 H 3.2196 2.6007 2.0260
  QMMM: 30 1614 S 3.7860 0.9564 0.5209
  QMMM: 31 1615 C 0.8791 3.7849 1.7760
  QMMM: 32 1616 O 0.5148 4.8610 1.2308
  QMMM: 33 1617 N 0.8384 3.6449 3.1583
  QMMM: 34 1618 H 1.1236 2.7731 3.5811
  QMMM: 35 3348 C 1.9600 -1.5251 2.5202
  QMMM: 36 3349 H 1.6905 -0.6169 1.9811
  QMMM: 37 3350 C 3.3755 -1.7855 2.0988
  QMMM: 38 3351 H 3.6908 -2.7119 2.5788
  QMMM: 39 3352 H 3.4261 -2.0334 1.0386
  QMMM: 40 3353 S 4.4054 -0.3488 2.2044
  QMMM: 41 3354 C 1.0046 -2.6213 2.1015
  QMMM: 42 3355 O 0.8619 -3.6432 2.8251
  QMMM: 43 3356 N 0.2941 -2.4008 0.9536
  QMMM: 44 3357 H 0.4108 -1.5787 0.3786
  QMMM: 45 3358 C -0.8151 -3.2410 0.5907
  QMMM: 46 3359 H -0.7582 -4.1800 1.1413
  QMMM: 47 3360 C -2.1686 -2.6105 0.9081
  QMMM: 48 3361 H -2.2550 -1.6942 0.3241
  QMMM: 49 3362 H -2.9354 -3.2939 0.5434
  QMMM: 50 3363 C -2.3860 -2.3325 2.3406
  QMMM: 51 3364 C -2.1265 -1.0616 2.8484
  QMMM: 52 3365 H -1.7242 -0.3091 2.1864
  QMMM: 53 3366 C -2.3774 -0.7639 4.1778
  QMMM: 54 3367 H -2.1947 0.2342 4.5478
  QMMM: 55 3368 C -2.8760 -1.7411 5.0265
  QMMM: 56 3369 H -3.0722 -1.5144 6.0640
  QMMM: 57 3370 C -3.1262 -3.0118 4.5326
  QMMM: 58 3371 H -3.5078 -3.7765 5.1929
  QMMM: 59 3372 C -2.8894 -3.3059 3.1988
  QMMM: 60 3373 H -3.0875 -4.2991 2.8236
  QMMM: 61 3374 C -0.7685 -3.7054 -0.9225
  QMMM: 62 3375 O -1.4237 -4.7625 -1.1889
  QMMM: 63 3376 O -0.0486 -3.0664 -1.7853
  QMMM: 64 *H 0.1111 2.0868 -2.8773
  QMMM: 65 *H 0.5232 4.4614 3.8079
  QMMM: 66 *H 1.8784 -1.3568 3.5940

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Yang, Ping
> Sent: Wednesday, November 05, 2008 3:44 PM
> To: amber_at_scripps.edu
> Subject: AMBER: AMBER10: QMMM parallel test error
>
> Greetings,
>
> I compiled the serial version and parallel version of Amber using mvapich
> and intel compiler for Barcelona processors with no error.
> The test for serial version passed smoothly along with the
> "test.parallel". However, the "test.parallel.QMMM" quited with the
> following error message:
>
>
> ==============================================================
> cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyevd
> diffing mdout.1NLN_dsyevd.save with mdout.1NLN_dsyevd
> PASSED
> ==============================================================
> cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyevr
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> libpthread.so.0 000000353C70C4F0 Unknown Unknown
> Unknown
> libmkl_lapack.so 0000002A9B4C631F Unknown Unknown
> Unknown
> rank 0 in job 150 cu0login1_55120 caused collective abort of all ranks
> exit status of rank 0: killed by signal 9
> ./Run.1NLN_dsyevr: Program error
> make[1]: *** [test.sander.QMMM] Error 1
> make[1]: Leaving directory `/home/amber/amber10/amber10/test'
> make: *** [test.sander.QMMM.MPI] Error 2
>
>
> I'd appreciate any help to solve this problem and please let me know if
> further information is needed for diagnosis.
>
> Thank you,
>
> -Ping
>
> -----------------------------------------------------------------------
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