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.scripps.edu on behalf of Ross Walker
Sent: Wed 11/5/2008 5:41 PM
To: amber.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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of Yang, Ping
> Sent: Wednesday, November 05, 2008 3:44 PM
> To: amber.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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Received on Fri Dec 05 2008 - 10:58:08 PST
